diff -pruN 5.3.3-1/allFiles.txt 5.4.0-1/allFiles.txt --- 5.3.3-1/allFiles.txt 1970-01-01 00:00:00.000000000 +0000 +++ 5.4.0-1/allFiles.txt 2018-09-11 19:21:00.000000000 +0000 @@ -0,0 +1,166 @@ +./libmassgui/AboutDlg.cpp +./libmassgui/AboutDlg.hpp +./libmassgui/About_history.hpp +./libmass/AtomCount.cpp +./libmass/MassSpectrumJsPrototype.cpp +./libmass/IsotopicPatternCalculator.hpp +./libmass/MassSpectrumJsPropertyIterator.cpp +./libmass/TraceJsPropertyIterator.cpp +./libmass/TraceJsPropertyIterator.hpp +./libmass/PeakShape.cpp +./libmass/UserSpec.cpp +./libmass/TraceJs.hpp +./libmass/AtomCount.hpp +./libmass/Atom.cpp +./libmass/MassList.cpp +./libmass/TraceJsPrototype.hpp +./libmass/MassSpectrumJs.cpp +./libmass/DataPointJsPrototype.hpp +./libmass/TraceJsPrototype.cpp +./libmass/Atom.hpp +./libmass/MsMultiHash.hpp +./libmass/Isotope.cpp +./libmass/DataPointJs.hpp +./libmass/MassList.hpp +./libmass/MsMultiHash.cpp +./libmass/PeakShapeConfig.cpp +./libmass/IonizeRule.hpp +./libmass/PeakCentroid.hpp +./libmass/Formula.hpp +./libmass/DataPointJs.cpp +./libmass/IonizeRule.cpp +./libmass/MassSpectrumJsPropertyIterator.hpp +./libmass/PeakShapeConfig.hpp +./libmass/Isotope.hpp +./libmass/Formula.cpp +./libmass/PeakCentroid.cpp +./libmass/DataPointJsPrototype.cpp +./libmass/Ponderable.hpp +./libmass/UserSpec.hpp +./libmass/TraceJs.cpp +./libmass/MassSpectrumJsPrototype.hpp +./libmass/PeakShape.hpp +./libmass/Ponderable.cpp +./libmass/IsotopicPatternCalculator.cpp +./libmass/MassSpectrumJs.hpp +./tests/src/libmass/test-MassSpectrum.cpp +./tests/src/libmass/test-Trace.cpp +./tests/src/libmass/test-MsMultiHash.cpp +./tests/src/libmass/test-DataPoint.cpp +./libmassgui/AboutDlg.cpp +./libmassgui/AboutDlg.hpp +./libmassgui/About_history.hpp +./minexpert/nongui/globals.cpp +./minexpert/nongui/globals.hpp +./massxpert/nongui/globals.cpp +./massxpert/nongui/globals.hpp +./globals/About_gpl_v30.hpp +./globals/globals.cpp +./globals/globals.hpp +./minexpert/main.cpp +./minexpert/nongui/SqlTableSpecifs.cpp +./minexpert/nongui/MassSpecDataFileLoaderSqlite3.hpp +./minexpert/nongui/MassSpecDataFileLoaderXy.hpp +./minexpert/nongui/MzIntegrationParams.hpp +./minexpert/nongui/SavGolFilterJs.cpp +./minexpert/nongui/FileFormatConverter.cpp +./minexpert/nongui/MassSpecDataFileLoaderMs1.hpp +./minexpert/nongui/MassSpecSqlite3Handler.hpp +./minexpert/nongui/SqlTableSpecifs.hpp +./minexpert/nongui/SqlMassDataSlicer.cpp +./minexpert/nongui/MassSpecDataFileLoaderBrukerXy.hpp +./minexpert/nongui/MassSpecDataFileLoaderPwiz.hpp +./minexpert/nongui/MassDataIntegrator.cpp +./minexpert/nongui/SavGolFilter.cpp +./minexpert/nongui/MassSpecDataFileLoaderMs1.cpp +./minexpert/nongui/MassSpecDataFileFormatAnalyzer.cpp +./minexpert/nongui/History.cpp +./minexpert/nongui/MassSpecFileMetaData.cpp +./minexpert/nongui/MassSpecDataFileFormatAnalyzer.hpp +./minexpert/nongui/SavGolParamsJSDoc.cpp +./minexpert/nongui/MzIntegrationParamsJs.hpp +./minexpert/nongui/History.hpp +./minexpert/nongui/MassSpecDataFileLoaderSqlite3.cpp +./minexpert/nongui/SqlMassDataSlicer.hpp +./minexpert/nongui/SqlTableFieldSpecifs.cpp +./minexpert/nongui/AnalysisPreferences.hpp +./minexpert/nongui/MassDataIntegrator.hpp +./minexpert/nongui/MassSpecDataStats.cpp +./minexpert/nongui/MassSpecDataSet.hpp +./minexpert/nongui/FileFormatConverter.hpp +./minexpert/nongui/MassSpecSqlite3Handler.cpp +./minexpert/nongui/globals.cpp +./minexpert/nongui/MzIntegrationParams.cpp +./minexpert/nongui/AnalysisPreferences.cpp +./minexpert/nongui/SavGolFilterJsPrototype.hpp +./minexpert/nongui/MassSpecDataFileLoaderDx.cpp +./minexpert/nongui/MassSpecDataSet.cpp +./minexpert/nongui/MzIntegrationParamsJsPrototype.cpp +./minexpert/nongui/HistoryItem.cpp +./minexpert/nongui/MassSpecDataFileLoaderDx.hpp +./minexpert/nongui/MzIntegrationParamsJsPrototype.hpp +./minexpert/nongui/SavGolFilterJsPrototype.cpp +./minexpert/nongui/MassSpecDataFileLoader.cpp +./minexpert/nongui/MzIntegrationParamsJs.cpp +./minexpert/nongui/MassSpecDataFileLoader.hpp +./minexpert/nongui/HistoryItem.hpp +./minexpert/nongui/MassSpecDataFileLoaderBrukerXy.cpp +./minexpert/nongui/MassSpecDataStats.hpp +./minexpert/nongui/MassSpecFileMetaData.hpp +./minexpert/nongui/MassSpecDataFileLoaderXy.cpp +./minexpert/nongui/SavGolFilter.hpp +./minexpert/nongui/SqlTableFieldSpecifs.hpp +./minexpert/nongui/CommandLineRunner.cpp +./minexpert/nongui/globals.hpp +./minexpert/nongui/MassSpecDataFileLoaderPwiz.cpp +./minexpert/nongui/CommandLineRunner.hpp +./minexpert/nongui/SavGolFilterJs.hpp +./minexpert/gui/XicExtractionWnd.cpp +./minexpert/gui/TicChromWnd.cpp +./minexpert/gui/MzIntegrationParamsWnd.cpp +./minexpert/gui/DriftSpecPlotWidget.hpp +./minexpert/gui/MainWindow.hpp +./minexpert/gui/DriftSpecWnd.cpp +./minexpert/gui/ScriptingObjectTreeWidgetItem.hpp +./minexpert/gui/DriftSpecPlotWidget.cpp +./minexpert/gui/ColorMapWnd.cpp +./minexpert/gui/ColorMapPlotWidget.cpp +./minexpert/gui/ScriptingHistoryListWidget.hpp +./minexpert/gui/ScriptingHistoryListWidget.cpp +./minexpert/gui/ScriptingObjectTreeWidgetItem.cpp +./minexpert/gui/MassSpecPlotWidget.hpp +./minexpert/gui/AbstractPlotWidget.cpp +./minexpert/gui/MassSpecWnd.cpp +./minexpert/gui/AboutMineXpertDlg.cpp +./minexpert/gui/SqlMassDataSlicerWnd.cpp +./minexpert/gui/TicChromPlotWidget.cpp +./minexpert/gui/ConsoleWnd.cpp +./minexpert/gui/AbstractPlotWidget.hpp +./minexpert/gui/AboutMineXpertDlg.hpp +./minexpert/gui/SqlMassDataSlicerWnd.hpp +./minexpert/gui/AbstractMultiPlotWnd.cpp +./minexpert/gui/OpenSpectraDlg.cpp +./minexpert/gui/TicChromWnd.hpp +./minexpert/gui/MassSpecPlotWidget.cpp +./minexpert/gui/ColorMapWnd.hpp +./minexpert/gui/TicChromPlotWidget.hpp +./minexpert/gui/AnalysisPreferencesDlg.cpp +./minexpert/gui/MzIntegrationParamsWnd.hpp +./minexpert/gui/DataPlotWidgetRelation.hpp +./minexpert/gui/DriftSpecWnd.hpp +./minexpert/gui/SaveToGraphicsFileDlg.hpp +./minexpert/gui/XicExtractionWnd.hpp +./minexpert/gui/Application.cpp +./minexpert/gui/AnalysisPreferencesDlg.hpp +./minexpert/gui/SaveToGraphicsFileDlg.cpp +./minexpert/gui/MassSpecWnd.hpp +./minexpert/gui/ScriptingWnd.hpp +./minexpert/gui/DataPlotWidgetRelation.cpp +./minexpert/gui/Application.hpp +./minexpert/gui/MainWindow.cpp +./minexpert/gui/ColorMapPlotWidget.hpp +./minexpert/gui/ScriptingWnd.cpp +./minexpert/gui/OpenSpectraDlg.hpp +./minexpert/gui/AbstractMultiPlotWnd.hpp +./minexpert/gui/ConsoleWnd.hpp +./tests/src/minexpert/test-MassSpecDataSet.cpp diff -pruN 5.3.3-1/_clang-format 5.4.0-1/_clang-format --- 5.3.3-1/_clang-format 1970-01-01 00:00:00.000000000 +0000 +++ 5.4.0-1/_clang-format 2018-09-11 19:21:00.000000000 +0000 @@ -0,0 +1,96 @@ +--- +Language: Cpp +# BasedOnStyle: LLVM +AccessModifierOffset: 0 +AlignAfterOpenBracket: Align +AlignConsecutiveAssignments: true +AlignConsecutiveDeclarations: false +AlignEscapedNewlinesLeft: true +AlignOperands: true +AlignTrailingComments: true +AllowAllParametersOfDeclarationOnNextLine: true +AllowShortBlocksOnASingleLine: false +AllowShortCaseLabelsOnASingleLine: false +AllowShortFunctionsOnASingleLine: None +AllowShortIfStatementsOnASingleLine: false +AllowShortLoopsOnASingleLine: false +# Deprecated AlwaysBreakAfterDefinitionReturnType: All +AlwaysBreakAfterReturnType: AllDefinitions +AlwaysBreakBeforeMultilineStrings: true +AlwaysBreakTemplateDeclarations: true +BinPackArguments: false +BinPackParameters: false +BraceWrapping: + AfterClass: false + AfterControlStatement: false + AfterEnum: false + AfterFunction: false + AfterNamespace: false + AfterObjCDeclaration: false + AfterStruct: false + AfterUnion: false + BeforeCatch: false + BeforeElse: false + IndentBraces: false +BreakAfterJavaFieldAnnotations: false +BreakBeforeBinaryOperators: None +BreakBeforeBraces: GNU +BreakBeforeTernaryOperators: true +BreakConstructorInitializersBeforeComma: false +BreakStringLiterals: true +ColumnLimit: 80 +CommentPragmas: '^ IWYU pragma:' +ConstructorInitializerAllOnOneLineOrOnePerLine: true +ConstructorInitializerIndentWidth: 2 +ContinuationIndentWidth: 2 +Cpp11BracedListStyle: true +DerivePointerAlignment: false +DisableFormat: false +ExperimentalAutoDetectBinPacking: false +ForEachMacros: [ foreach, Q_FOREACH, BOOST_FOREACH ] +IncludeCategories: + - Regex: '^"(llvm|llvm-c|clang|clang-c)/' + Priority: 2 + - Regex: '^(<|"(gtest|isl|json)/)' + Priority: 3 + - Regex: '.*' + Priority: 1 +IncludeIsMainRegex: '$' +IndentCaseLabels: true +IndentWidth: 2 +IndentWrappedFunctionNames: false +JavaScriptQuotes: Leave +KeepEmptyLinesAtTheStartOfBlocks: true +# Language: Cpp +MacroBlockBegin: '' +MacroBlockEnd: '' +MaxEmptyLinesToKeep: 2 +NamespaceIndentation: Inner +ObjCBlockIndentWidth: 2 +ObjCSpaceAfterProperty: false +ObjCSpaceBeforeProtocolList: true +PenaltyBreakBeforeFirstCallParameter: 19 +PenaltyBreakComment: 300 +PenaltyBreakFirstLessLess: 120 +PenaltyBreakString: 1000 +PenaltyExcessCharacter: 1000000 +PenaltyReturnTypeOnItsOwnLine: 60 +PointerAlignment: Right +ReflowComments: true +SortIncludes: false +SpaceAfterCStyleCast: false +# SpaceAfterTemplateKeyword: false +SpaceBeforeAssignmentOperators: true +SpaceBeforeParens: Never +SpaceInEmptyParentheses: false +SpacesBeforeTrailingComments: 1 +SpacesInAngles: false +SpacesInCStyleCastParentheses: false +SpacesInContainerLiterals: false +SpacesInParentheses: false +SpacesInSquareBrackets: false +Standard: Cpp11 +TabWidth: 2 +UseTab: Never +... + diff -pruN 5.3.3-1/.clang-format 5.4.0-1/.clang-format --- 5.3.3-1/.clang-format 2018-06-20 15:46:39.000000000 +0000 +++ 5.4.0-1/.clang-format 1970-01-01 00:00:00.000000000 +0000 @@ -1,95 +0,0 @@ ---- -Language: Cpp -# BasedOnStyle: LLVM -AccessModifierOffset: 0 -AlignAfterOpenBracket: Align -AlignConsecutiveAssignments: true -AlignConsecutiveDeclarations: true -AlignEscapedNewlinesLeft: false -AlignOperands: true -AlignTrailingComments: true -AllowAllParametersOfDeclarationOnNextLine: true -AllowShortBlocksOnASingleLine: false -AllowShortCaseLabelsOnASingleLine: false -AllowShortFunctionsOnASingleLine: None -AllowShortIfStatementsOnASingleLine: false -AllowShortLoopsOnASingleLine: false -AlwaysBreakAfterDefinitionReturnType: All -AlwaysBreakAfterReturnType: AllDefinitions -AlwaysBreakBeforeMultilineStrings: false -AlwaysBreakTemplateDeclarations: false -BinPackArguments: true -BinPackParameters: true -BraceWrapping: - AfterClass: false - AfterControlStatement: false - AfterEnum: false - AfterFunction: false - AfterNamespace: false - AfterObjCDeclaration: false - AfterStruct: false - AfterUnion: false - BeforeCatch: false - BeforeElse: false - IndentBraces: false -BreakBeforeBinaryOperators: None -BreakBeforeBraces: GNU -BreakBeforeTernaryOperators: true -BreakConstructorInitializersBeforeComma: true -BreakAfterJavaFieldAnnotations: false -BreakStringLiterals: true -ColumnLimit: 80 -CommentPragmas: '^ IWYU pragma:' -ConstructorInitializerAllOnOneLineOrOnePerLine: true -ConstructorInitializerIndentWidth: 2 -ContinuationIndentWidth: 2 -Cpp11BracedListStyle: true -DerivePointerAlignment: false -DisableFormat: false -ExperimentalAutoDetectBinPacking: false -ForEachMacros: [ foreach, Q_FOREACH, BOOST_FOREACH ] -IncludeCategories: - - Regex: '^"(llvm|llvm-c|clang|clang-c)/' - Priority: 2 - - Regex: '^(<|"(gtest|isl|json)/)' - Priority: 3 - - Regex: '.*' - Priority: 1 -IncludeIsMainRegex: '$' -IndentCaseLabels: true -IndentWidth: 2 -IndentWrappedFunctionNames: false -JavaScriptQuotes: Leave -JavaScriptWrapImports: true -KeepEmptyLinesAtTheStartOfBlocks: true -MacroBlockBegin: '' -MacroBlockEnd: '' -MaxEmptyLinesToKeep: 2 -NamespaceIndentation: All -ObjCBlockIndentWidth: 2 -ObjCSpaceAfterProperty: false -ObjCSpaceBeforeProtocolList: true -PenaltyBreakBeforeFirstCallParameter: 19 -PenaltyBreakComment: 300 -PenaltyBreakFirstLessLess: 120 -PenaltyBreakString: 1000 -PenaltyExcessCharacter: 1000000 -PenaltyReturnTypeOnItsOwnLine: 60 -PointerAlignment: Right -ReflowComments: true -SortIncludes: false -SpaceAfterCStyleCast: false -SpaceBeforeAssignmentOperators: true -SpaceBeforeParens: Never -SpaceInEmptyParentheses: false -SpacesBeforeTrailingComments: 1 -SpacesInAngles: false -SpacesInContainerLiterals: false -SpacesInCStyleCastParentheses: false -SpacesInParentheses: false -SpacesInSquareBrackets: false -Standard: Cpp11 -TabWidth: 2 -UseTab: Never -... - diff -pruN 5.3.3-1/CMakeLists.txt 5.4.0-1/CMakeLists.txt --- 5.3.3-1/CMakeLists.txt 2018-06-20 15:46:39.000000000 +0000 +++ 5.4.0-1/CMakeLists.txt 2018-09-11 19:21:00.000000000 +0000 @@ -34,7 +34,7 @@ include(systemUname) # Basic information about project project(msXpertSuite) -set(VERSION 5.3.3) +set(VERSION 5.4.0) # Set additional project information diff -pruN 5.3.3-1/compile_commands.json 5.4.0-1/compile_commands.json --- 5.3.3-1/compile_commands.json 2018-06-20 15:46:39.000000000 +0000 +++ 5.4.0-1/compile_commands.json 2018-09-11 19:21:00.000000000 +0000 @@ -1,1027 +1,1027 @@ [ { 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/home/rusconi/devel/msxpertsuite/build-area/minexpert/minexpert_autogen/mocs_compilation.cpp", "file": "/home/rusconi/devel/msxpertsuite/build-area/minexpert/minexpert_autogen/mocs_compilation.cpp" } ] \ No newline at end of file diff -pruN 5.3.3-1/debian/changelog 5.4.0-1/debian/changelog --- 5.3.3-1/debian/changelog 2018-06-20 15:42:48.000000000 +0000 +++ 5.4.0-1/debian/changelog 2018-09-11 17:31:02.000000000 +0000 @@ -1,3 +1,19 @@ +msxpertsuite (5.4.0-1) experimental; urgency=low + + * Port to the libqcustomplot 2.0.1 version. Mostly changes in the data + format of the plot data in the QCustomPlot class. + + * Fix bug that made the program crash when converting data from mzML to + SQLite3-based db format when Synapt ion mobility data contained NaN + values. + + * Fix reporting in the console window of TIC intensity value calculations + (no error on the result, only the reporting of that result). + + Bump-up standards version to 4.2.0, no changes required. + + -- Filippo Rusconi Tue, 11 Sep 2018 19:31:02 +0200 + msxpertsuite (5.3.3-1) unstable; urgency=low * New upstream release. diff -pruN 5.3.3-1/debian/control 5.4.0-1/debian/control --- 5.3.3-1/debian/control 2018-06-10 10:36:31.000000000 +0000 +++ 5.4.0-1/debian/control 2018-09-11 14:28:19.000000000 +0000 @@ -18,7 +18,7 @@ Build-Depends: debhelper (>=9.20130630), texlive-fonts-recommended, texlive-lang-french, texlive-lang-cyrillic, - libqcustomplot-dev(>= 1.3.2), + libqcustomplot-dev(>= 2.0.1), libpwiz-dev(>=3.0.10827), libboost-dev (>= 1.56.0), docbook-to-man, @@ -28,7 +28,7 @@ Build-Depends: debhelper (>=9.20130630), graphviz, qttools5-dev-tools, qtchooser -Standards-Version: 4.1.3 +Standards-Version: 4.2.0 Homepage: https://www.msxpertsuite.org/ Vcs-Browser: https://salsa.debian.org/debichem-team/msxpertsuite.git Vcs-Git: https://salsa.debian.org/debichem-team/msxpertsuite.git diff -pruN 5.3.3-1/debian/msxpertsuite.install 5.4.0-1/debian/msxpertsuite.install --- 5.3.3-1/debian/msxpertsuite.install 2018-01-12 08:49:07.000000000 +0000 +++ 5.4.0-1/debian/msxpertsuite.install 2018-09-11 14:28:19.000000000 +0000 @@ -1,7 +1,16 @@ debian/tmp-arch/usr/bin/* usr/bin -debian/tmp-arch/usr/share/pixmaps/msxpertsuite-icon-32.xpm usr/share/pixmaps -massxpert/massxpert.desktop usr/share/applications -minexpert/minexpert.desktop usr/share/applications + +massxpert/org.msxpertsuite.massxpert.desktop usr/share/applications +massxpert/massxpert.appstream usr/share/metainfo/org.msxpertsuite.massxpert.appdata.xml +images/msxpertsuite-icon-16.png usr/share/icons/hicolor/16x16/apps/massxpert.png +images/msxpertsuite-icon-32.png usr/share/icons/hicolor/32x32/apps/massxpert.png +images/msxpertsuite-icon-64.png usr/share/icons/hicolor/64x64/apps/massxpert.png + +minexpert/org.msxpertsuite.minexpert.desktop usr/share/applications +minexpert/minexpert.appstream usr/share/metainfo/org.msxpertsuite.minexpert.appdata.xml +images/msxpertsuite-icon-16.png usr/share/icons/hicolor/16x16/apps/minexpert.png +images/msxpertsuite-icon-32.png usr/share/icons/hicolor/32x32/apps/minexpert.png +images/msxpertsuite-icon-64.png usr/share/icons/hicolor/64x64/apps/minexpert.png doc/history.html /usr/share/doc/msxpertsuite diff -pruN 5.3.3-1/debian/msxpertsuite.menu 5.4.0-1/debian/msxpertsuite.menu --- 5.3.3-1/debian/msxpertsuite.menu 2018-01-12 08:49:07.000000000 +0000 +++ 5.4.0-1/debian/msxpertsuite.menu 1970-01-01 00:00:00.000000000 +0000 @@ -1,5 +0,0 @@ -?package(massxpert):needs="X11" section="Applications/Science/Chemistry" \ - title="massXpert" \ - longtitle="Simulation/analysis of (bio-)polymer mass spectrometric data" \ - icon="/usr/share/pixmaps/massxpert-icon-32.xpm" \ - command="/usr/bin/massxpert" Binary files 5.3.3-1/images/msxpertsuite-icon-16.png and 5.4.0-1/images/msxpertsuite-icon-16.png differ Binary files 5.3.3-1/images/splashscreen.png and 5.4.0-1/images/splashscreen.png differ diff -pruN 5.3.3-1/images/splashscreen.svg 5.4.0-1/images/splashscreen.svg --- 5.3.3-1/images/splashscreen.svg 2018-06-20 15:46:39.000000000 +0000 +++ 5.4.0-1/images/splashscreen.svg 2018-09-11 19:21:00.000000000 +0000 @@ -150,6 +150,6 @@ id="tspan4496" x="404.5647" y="963.23505" - style="stroke-width:0.33261424px">Suite version 5.3.3 + style="stroke-width:0.33261424px">Suite version 5.4.0 diff -pruN 5.3.3-1/massxpert/massxpert.appstream 5.4.0-1/massxpert/massxpert.appstream --- 5.3.3-1/massxpert/massxpert.appstream 1970-01-01 00:00:00.000000000 +0000 +++ 5.4.0-1/massxpert/massxpert.appstream 2018-09-11 19:21:00.000000000 +0000 @@ -0,0 +1,67 @@ + + + + org.msxpertsuite.massxpert + GPL-3.0+ + GPL-3.0+ + Mass spectrometry software + Model and simulate mass spec data + + Filippo Rusconi + + + +

+ + massxpert is a program used to model polymer chemistries (like proteins or + saccharides, for example) and use the models to simulat chemical reactions and + mass spectral data obtained on the reaction products. + +

+ +

The process can be summarized thusly:

+
    + +
  • Define a brand new polymer chemistry (for example, protein, shipped with the + package);
    • + +
  • Edit a polymer sequence (in this example, a protein sequence);
    • + +
  • Start performing chemical simulations, like protein digestion and + gather all the mass data related to the obtained peptides;
    • + +
  • Then select a peptide and perform a gas phase fragmentation; collect the + mass data corresponding to all the fragments theoretically expected.
    • + +
+ + + + org.msxpertsuite.massxpert.desktop + + + + + The polymer sequence editor and main mass data viewer window + http://msxpertsuite.org/screenshots/massxpert/gnulinux-sequence-editor-window-kunitz-inhibitor-multi-region-selection.png + + + + Polymer sequence cleavage and peptides + http://msxpertsuite.org/screenshots/massxpert/mswindows-polymer-sequence-cleavage-window.png + + + + Arbitrary mass search window + http://msxpertsuite.org/screenshots/massxpert/mswindows-mass-search-window.png + + + + + http://www.msxpertsuite.org + + + massxpert + + + diff -pruN 5.3.3-1/massxpert/massxpert.desktop 5.4.0-1/massxpert/massxpert.desktop --- 5.3.3-1/massxpert/massxpert.desktop 2018-06-20 15:46:39.000000000 +0000 +++ 5.4.0-1/massxpert/massxpert.desktop 1970-01-01 00:00:00.000000000 +0000 @@ -1,14 +0,0 @@ -[Desktop Entry] -Version=1.0 -Name=massXpert -Comment=Bio-polymer mass spectrometry software -GenericName=Mass spectrometry -GenericName[fr]=Spectrométrie de masse -GenericName[it]=Spettrometria di massa -TryExec=massxpert -Exec=massxpert -Terminal=true -Icon=msxpertsuite-icon-32 -Type=Application -Categories=Education;Science;Chemistry;Biology;Qt -Keywords=Mass spectrometry;Biochemistry;Modelling;Polymer chemistry diff -pruN 5.3.3-1/massxpert/org.msxpertsuite.massxpert.desktop 5.4.0-1/massxpert/org.msxpertsuite.massxpert.desktop --- 5.3.3-1/massxpert/org.msxpertsuite.massxpert.desktop 1970-01-01 00:00:00.000000000 +0000 +++ 5.4.0-1/massxpert/org.msxpertsuite.massxpert.desktop 2018-09-11 19:21:00.000000000 +0000 @@ -0,0 +1,21 @@ +[Desktop Entry] +Encoding=UTF-8 +Version=1.1 + +Type=Application +Name=massXpert + +GenericName=Mass spectrometry +GenericName[fr]=Spectrométrie de masse +GenericName[it]=Spettrometria di massa +Comment=Bio-polymer mass spectrometry modelling and simulation software +Comment[fr]=Modélisation et simulation de données de spectrométrie de masse +Comment[it]=Modellizzazione e simulazione di dati di spettrometria di massa + +Exec=massxpert + +Terminal=true +Icon=msxpertsuite-icon-32 + +Categories=Science;Chemistry;Biology;Qt +Keywords=Mass spectrometry;Biological chemistry;Modelling;Polymer chemistry Binary files 5.3.3-1/massxpert/user-manual/figures/splashscreen.png and 5.4.0-1/massxpert/user-manual/figures/splashscreen.png differ diff -pruN 5.3.3-1/massxpert/user-manual/msxpertsuite-macros.tex 5.4.0-1/massxpert/user-manual/msxpertsuite-macros.tex --- 5.3.3-1/massxpert/user-manual/msxpertsuite-macros.tex 2018-06-20 15:46:39.000000000 +0000 +++ 5.4.0-1/massxpert/user-manual/msxpertsuite-macros.tex 2018-09-11 19:21:00.000000000 +0000 @@ -2,7 +2,7 @@ \newcommand{\msxpshrefbase}[2]{\href{http://www.msxpertsuite.org/#1}{#2}} %%% Version of the software suite -\newcommand{\ver}{5.3.3} +\newcommand{\ver}{5.4.0} \newcommand{\msXpsver}{\emph{msXpertSuite} version \ver} %%% msXpertSuite diff -pruN 5.3.3-1/minexpert/gui/AbstractPlotWidget.cpp 5.4.0-1/minexpert/gui/AbstractPlotWidget.cpp --- 5.3.3-1/minexpert/gui/AbstractPlotWidget.cpp 2018-06-20 15:46:39.000000000 +0000 +++ 5.4.0-1/minexpert/gui/AbstractPlotWidget.cpp 2018-09-11 19:21:00.000000000 +0000 @@ -31,8 +31,6 @@ */ - - ///////////////////////////// Qt include @@ -47,75 +45,78 @@ #include - namespace msXpSmineXpert { - /*/js/ Class: AbstractPlotWidget - * - * This class is not exported to the JavaScript environment, but it - * serves as the base class for all the plot widget subclasses. Its methods - * are thus available to all the objects of the various subclasses, like - * MassSpecPlotWidget, DriftSpecPlotWidget, ColorMapPlotWidget and - * TicChromPlotWidget, collectively referred to as below. - * - * When using objects of the various classes above, the object name will thus - * be, for example, ticChromPlotWidget0 or driftSpecPlotWidget1. These objects - * are made available to the scripting environment in the tree view on the - * left part of the scripting window. See the user manual for - * details. - */ - - - //! Construct a AbstractPlotWidget instance. - /*! - - The instance is initialized using the set of parameters: - - \param parent pointer to the parent widget. - - \param parentWnd pointer to the parent window. - - \param name name of the plot widget. - - \param desc description of the plot widget. - - \param massSpecDataSet pointer to the MassSpecDataSet instance in which the - mass data are stored. - - \param fileName name of the file from which the data were loaded. - - \param isMultiGraph tells if \c this plot widget is deemed to receive more - than one graph. - -*/ - AbstractPlotWidget::AbstractPlotWidget(QWidget *parent, - const QString &name, const QString &desc, - const MassSpecDataSet *massSpecDataSet, const QString &fileName, - bool isMultiGraph) - : - QCustomPlot{parent}, - mp_parentWnd{parent}, - m_name{name}, - m_desc{desc}, - mp_massSpecDataSet{massSpecDataSet}, - m_fileName{fileName}, - m_isMultiGraph{isMultiGraph} - { - //qDebug() << __FILE__ << __LINE__ << __FUNCTION__ << "()" - //<< "Creating new plot widget:" << this - //<< "with parent window:" << parent; - - if(parent == Q_NULLPTR) - qFatal("Fatal error at %s@%d -- %s(). " - "Not possible that parent pointer is nullptr." - "Program aborted.", - __FILE__, __LINE__, __FUNCTION__); +/*/js/ Class: AbstractPlotWidget + * + * This class is not exported to the JavaScript environment, but it + * serves as the base class for all the plot widget subclasses. Its methods + * are thus available to all the objects of the various subclasses, like + * MassSpecPlotWidget, DriftSpecPlotWidget, ColorMapPlotWidget and + * TicChromPlotWidget, collectively referred to as below. + * + * When using objects of the various classes above, the object name will thus + * be, for example, ticChromPlotWidget0 or driftSpecPlotWidget1. These objects + * are made available to the scripting environment in the tree view on the + * left part of the scripting window. See the user manual for + * details. + */ + + +//! Construct a AbstractPlotWidget instance. +/*! + + The instance is initialized using the set of parameters: + + \param parent pointer to the parent widget. + + \param parentWnd pointer to the parent window. + + \param name name of the plot widget. + + \param desc description of the plot widget. + + \param massSpecDataSet pointer to the MassSpecDataSet instance in which the + mass data are stored. + + \param fileName name of the file from which the data were loaded. + + \param isMultiGraph tells if \c this plot widget is deemed to receive more + than one graph. + +*/ +AbstractPlotWidget::AbstractPlotWidget(QWidget *parent, + const QString &name, + const QString &desc, + const MassSpecDataSet *massSpecDataSet, + const QString &fileName, + bool isMultiGraph) + : QCustomPlot{parent}, + mp_parentWnd{parent}, + m_name{name}, + m_desc{desc}, + mp_massSpecDataSet{massSpecDataSet}, + m_fileName{fileName}, + m_isMultiGraph{isMultiGraph} +{ + // qDebug() << __FILE__ << __LINE__ << __FUNCTION__ << "()" + //<< "Creating new plot widget:" << this + //<< "with parent window:" << parent; + + if(parent == Q_NULLPTR) + qFatal( + "Fatal error at %s@%d -- %s(). " + "Not possible that parent pointer is nullptr." + "Program aborted.", + __FILE__, + __LINE__, + __FUNCTION__); - if(!setupWidget()) - qFatal("Fatal error at %s@%d. Program aborted.", __FILE__, __LINE__); + if(!setupWidget()) + qFatal("Fatal error at %s@%d. Program aborted.", __FILE__, __LINE__); - setObjectName("plotWidget"); + setObjectName("plotWidget"); #if 0 if(fileName.isEmpty()) @@ -142,2685 +143,2749 @@ namespace msXpSmineXpert } #endif - show(); - } + show(); +} - //! Destruct \c this AbstractPlotWidget instance. - /*! +//! Destruct \c this AbstractPlotWidget instance. +/*! - The destruction involves clearing the history, deleting all the axis range - history items for x and y axes. + The destruction involves clearing the history, deleting all the axis range + history items for x and y axes. */ - AbstractPlotWidget::~AbstractPlotWidget() - { - clearHistory(); +AbstractPlotWidget::~AbstractPlotWidget() +{ + clearHistory(); - // Clear all the element of the axis range histories: - for(int iter = 0; iter < m_xAxisRangeHistory.size(); ++iter) - delete m_xAxisRangeHistory.at(iter); + // Clear all the element of the axis range histories: + for(int iter = 0; iter < m_xAxisRangeHistory.size(); ++iter) + delete m_xAxisRangeHistory.at(iter); - for(int iter = 0; iter < m_yAxisRangeHistory.size(); ++iter) - delete m_yAxisRangeHistory.at(iter); + for(int iter = 0; iter < m_yAxisRangeHistory.size(); ++iter) + delete m_yAxisRangeHistory.at(iter); - // Inform the parent window that this is no longer be the last focused widget: + // Inform the parent window that this is no longer be the last focused widget: - AbstractMultiPlotWnd *parentWnd = static_cast(mp_parentWnd); + AbstractMultiPlotWnd *parentWnd = + static_cast(mp_parentWnd); - if(parentWnd == Q_NULLPTR) - qFatal("Fatal error at %s@%d -- %s(). " - "Not possible that parent pointer is nullptr." - "Program aborted.", - __FILE__, __LINE__, __FUNCTION__); + if(parentWnd == Q_NULLPTR) + qFatal( + "Fatal error at %s@%d -- %s(). " + "Not possible that parent pointer is nullptr." + "Program aborted.", + __FILE__, + __LINE__, + __FUNCTION__); - if(parentWnd->mp_lastFocusedPlotWidget == this) - parentWnd->mp_lastFocusedPlotWidget = Q_NULLPTR; - } + if(parentWnd->mp_lastFocusedPlotWidget == this) + parentWnd->mp_lastFocusedPlotWidget = Q_NULLPTR; +} - QWidget * - AbstractPlotWidget::parentWnd() - { - return mp_parentWnd; - } +QWidget * +AbstractPlotWidget::parentWnd() +{ + return mp_parentWnd; +} - //! Set the name of the plot widget. - void - AbstractPlotWidget::setName(QString name) - { - m_name = name; - } +//! Set the name of the plot widget. +void +AbstractPlotWidget::setName(QString name) +{ + m_name = name; +} - //! Get the name of the plot widget. - QString - AbstractPlotWidget::name() const - { - return m_name; - } +//! Get the name of the plot widget. +QString +AbstractPlotWidget::name() const +{ + return m_name; +} - //! Set the description of the plot widget. - void - AbstractPlotWidget::setDesc(QString desc) - { - m_desc = desc; - } +//! Set the description of the plot widget. +void +AbstractPlotWidget::setDesc(QString desc) +{ + m_desc = desc; +} - //! Get the description of the plot widget. - QString - AbstractPlotWidget::desc() const - { - return m_desc; - } +//! Get the description of the plot widget. +QString +AbstractPlotWidget::desc() const +{ + return m_desc; +} - //! Set up the widget. - /*! +//! Set up the widget. +/*! - Setting up the widget involves: + Setting up the widget involves: - - setting the focus policy - - the interactions working with the QCustomPlot - - create the context menu - - add a graph and configure it - - perform the signal/slot connections + - setting the focus policy + - the interactions working with the QCustomPlot + - create the context menu + - add a graph and configure it + - perform the signal/slot connections */ - bool - AbstractPlotWidget::setupWidget() - { - // This is required so that we get the keyboard events. - setFocusPolicy(Qt::StrongFocus); - setInteractions(QCP::iRangeZoom | QCP::iSelectPlottables | - QCP::iMultiSelect); - - addGraph(); - - m_pen.setStyle(Qt::SolidLine); - m_pen.setBrush(Qt::black); - m_pen.setWidth(1); - - graph()->setPen(m_pen); - - // Create a text item to describe the plot. - m_descText = new QCPItemText(this); - addItem(dynamic_cast(m_descText)); - m_descText->setPositionAlignment(Qt::AlignTop | Qt::AlignRight); - m_descText->position->setType(QCPItemPosition::ptAxisRectRatio); - m_descText->position->setCoords( - 1, 0); // place position at center/top of axis rect - m_descText->setText(m_desc); - m_descText->setFont(QFont(font().family(), 7)); - - // Create the lines that will act as tracers. - // The Starting tracer is the one that works without clicks and is a cross - // tracer (so we need two lines) - m_hStartTracer = new QCPItemLine(this); - m_hStartTracer->setPen(m_pen); - m_hStartTracer->start->setType(QCPItemPosition::ptPlotCoords); - m_hStartTracer->end->setType(QCPItemPosition::ptPlotCoords); - addItem(m_hStartTracer); - m_hStartTracer->start->setCoords(0, 0); - m_hStartTracer->end->setCoords(0, 0); - - // Make a copy of the pen to just change its color and set that color to - // the tracer line. - QPen pen(m_pen); - pen.setColor(QColor("green")); - - m_vStartTracer = new QCPItemLine(this); - m_vStartTracer->setPen(pen); - m_vStartTracer->start->setType(QCPItemPosition::ptPlotCoords); - m_vStartTracer->end->setType(QCPItemPosition::ptPlotCoords); - addItem(m_vStartTracer); - m_vStartTracer->start->setCoords(0, 0); - m_vStartTracer->end->setCoords(0, 0); - - // The other tracer is the tracer that is draw when a clickdrag operation is - // performed, it is only vertical. - pen.setColor(QColor("red")); - m_endTracer = new QCPItemLine(this); - - m_endTracer->setPen(pen); - m_endTracer->start->setType(QCPItemPosition::ptPlotCoords); - m_endTracer->end->setType(QCPItemPosition::ptPlotCoords); - addItem(m_endTracer); - m_endTracer->start->setCoords(0, 0); - m_endTracer->end->setCoords(0, 0); - - m_zoomRect = new QCPItemRect(this); - addItem(m_zoomRect); - m_zoomRect->setPen(m_pen); - m_zoomRect->topLeft->setType(QCPItemPosition::ptPlotCoords); - m_zoomRect->bottomRight->setType(QCPItemPosition::ptPlotCoords); - m_zoomRect->setVisible(false); - - m_selectLine = new QCPItemLine(this); - addItem(m_selectLine); - m_selectLine->setPen(m_pen); - m_selectLine->start->setType(QCPItemPosition::ptPlotCoords); - m_selectLine->end->setType(QCPItemPosition::ptPlotCoords); - m_selectLine->setVisible(false); - - m_xDeltaText = new QCPItemText(this); - addItem(m_xDeltaText); - m_xDeltaText->setPositionAlignment(Qt::AlignBottom | Qt::AlignCenter); - m_xDeltaText->position->setType(QCPItemPosition::ptPlotCoords); - m_xDeltaText->setVisible(false); - - connect(this, &AbstractPlotWidget::mouseMove, this, - &AbstractPlotWidget::mouseMoveHandler); - - connect(this, &AbstractPlotWidget::selectionChangedByUser, this, - &AbstractPlotWidget::selectionChangedHandler); - - connect(this, &AbstractPlotWidget::mousePress, this, - &AbstractPlotWidget::mousePressHandler); - - connect(this, &AbstractPlotWidget::mouseRelease, this, - &AbstractPlotWidget::mouseReleaseHandler); +bool +AbstractPlotWidget::setupWidget() +{ + // This is required so that we get the keyboard events. + setFocusPolicy(Qt::StrongFocus); + setInteractions(QCP::iRangeZoom | QCP::iSelectPlottables | QCP::iMultiSelect); + + addGraph(); + + m_pen.setStyle(Qt::SolidLine); + m_pen.setBrush(Qt::black); + m_pen.setWidth(1); + + graph()->setPen(m_pen); + + // Create a text item to describe the plot. + m_descText = new QCPItemText(this); + + // No more needed, as the new item is automatically added to *this. + // addItem(dynamic_cast(m_descText)); + // Same for all other occurrences below. + + m_descText->setPositionAlignment(Qt::AlignTop | Qt::AlignRight); + m_descText->position->setType(QCPItemPosition::ptAxisRectRatio); + m_descText->position->setCoords( + 1, 0); // place position at center/top of axis rect + m_descText->setText(m_desc); + m_descText->setFont(QFont(font().family(), 7)); + + // Create the lines that will act as tracers. + // The Starting tracer is the one that works without clicks and is a cross + // tracer (so we need two lines) + m_hStartTracer = new QCPItemLine(this); + m_hStartTracer->setPen(m_pen); + m_hStartTracer->start->setType(QCPItemPosition::ptPlotCoords); + m_hStartTracer->end->setType(QCPItemPosition::ptPlotCoords); + m_hStartTracer->start->setCoords(0, 0); + m_hStartTracer->end->setCoords(0, 0); + + // Make a copy of the pen to just change its color and set that color to + // the tracer line. + QPen pen(m_pen); + pen.setColor(QColor("green")); + + m_vStartTracer = new QCPItemLine(this); + m_vStartTracer->setPen(pen); + m_vStartTracer->start->setType(QCPItemPosition::ptPlotCoords); + m_vStartTracer->end->setType(QCPItemPosition::ptPlotCoords); + m_vStartTracer->start->setCoords(0, 0); + m_vStartTracer->end->setCoords(0, 0); + + // The other tracer is the tracer that is draw when a clickdrag operation is + // performed, it is only vertical. + pen.setColor(QColor("red")); + m_endTracer = new QCPItemLine(this); + + m_endTracer->setPen(pen); + m_endTracer->start->setType(QCPItemPosition::ptPlotCoords); + m_endTracer->end->setType(QCPItemPosition::ptPlotCoords); + m_endTracer->start->setCoords(0, 0); + m_endTracer->end->setCoords(0, 0); + + m_zoomRect = new QCPItemRect(this); + m_zoomRect->setPen(m_pen); + m_zoomRect->topLeft->setType(QCPItemPosition::ptPlotCoords); + m_zoomRect->bottomRight->setType(QCPItemPosition::ptPlotCoords); + m_zoomRect->setVisible(false); + + m_selectLine = new QCPItemLine(this); + m_selectLine->setPen(m_pen); + m_selectLine->start->setType(QCPItemPosition::ptPlotCoords); + m_selectLine->end->setType(QCPItemPosition::ptPlotCoords); + m_selectLine->setVisible(false); + + m_xDeltaText = new QCPItemText(this); + m_xDeltaText->setPositionAlignment(Qt::AlignBottom | Qt::AlignCenter); + m_xDeltaText->position->setType(QCPItemPosition::ptPlotCoords); + m_xDeltaText->setVisible(false); + + connect(this, + &AbstractPlotWidget::mouseMove, + this, + &AbstractPlotWidget::mouseMoveHandler); + + connect(this, + &AbstractPlotWidget::selectionChangedByUser, + this, + &AbstractPlotWidget::selectionChangedHandler); + + connect(this, + &AbstractPlotWidget::mousePress, + this, + &AbstractPlotWidget::mousePressHandler); + + connect(this, + &AbstractPlotWidget::mouseRelease, + this, + &AbstractPlotWidget::mouseReleaseHandler); + + connect(this, + &AbstractPlotWidget::axisDoubleClick, + this, + &AbstractPlotWidget::axisDoubleClickHandler); + + return true; +} + + +//! Create the contextual menu. +QMenu * +AbstractPlotWidget::createContextMenu() +{ + if(mpa_contextMenu != Q_NULLPTR) + delete mpa_contextMenu; - connect(this, &AbstractPlotWidget::axisDoubleClick, this, - &AbstractPlotWidget::axisDoubleClickHandler); + mpa_contextMenu = new QMenu(this); - return true; - } + if(mp_colorMap == Q_NULLPTR) + { + QMenu *exportMenu = mpa_contextMenu->addMenu("Export"); + + mpa_exportDataAction = exportMenu->addAction("&Data"); + connect(mpa_exportDataAction, + &QAction::triggered, + this, + &AbstractPlotWidget::exportData); + + mpa_plotXyFileAction = exportMenu->addAction("&Plot as xy file"); + connect(mpa_plotXyFileAction, + &QAction::triggered, + this, + &AbstractPlotWidget::exportPlot); + + mpa_contextMenu->addSeparator(); + } + + mpa_savePlotGraphics = + mpa_contextMenu->addAction("&Save plot to graphics file"); + connect(mpa_savePlotGraphics, + &QAction::triggered, + this, + &AbstractPlotWidget::savePlotToGraphicsFile); + + return mpa_contextMenu; +} + + +//! Clear the history. +void +AbstractPlotWidget::clearHistory() +{ + m_history.freeList(); + // qDebug() << __FILE__ << __LINE__ + // << "Cleared history of window:" << m_name << "--" << m_desc; +} - //! Create the contextual menu. - QMenu * - AbstractPlotWidget::createContextMenu() - { - if(mpa_contextMenu != Q_NULLPTR) - delete mpa_contextMenu; - mpa_contextMenu = new QMenu(this); +//! Add (append) the \p item HistoryItem instance to the member \c m_history. +void +AbstractPlotWidget::addHistoryItem(HistoryItem *item) +{ + m_history.appendHistoryItem(item); +} - if(mp_colorMap == Q_NULLPTR) - { - QMenu *exportMenu = mpa_contextMenu->addMenu("Export"); - mpa_exportDataAction = exportMenu->addAction("&Data"); - connect(mpa_exportDataAction, &QAction::triggered, this, &AbstractPlotWidget::exportData); +/*/js/ + * .showHistory() + * + * Shows a tooltip with the History of this plot widget. + */ +//! Craft a tooltip and display it with text describing the History of \c this +//! AbstractPlotWidget instance. +/*! - mpa_plotXyFileAction = exportMenu->addAction("&Plot as xy file"); - connect(mpa_plotXyFileAction, &QAction::triggered, this, &AbstractPlotWidget::exportPlot); + \sa historyAsText(). - mpa_contextMenu->addSeparator(); - } +*/ +void +AbstractPlotWidget::showHistory() +{ + // We want to craft a tooltip widget with the brief history of *this + // widget. - mpa_savePlotGraphics = mpa_contextMenu->addAction("&Save plot to graphics file"); - connect(mpa_savePlotGraphics, &QAction::triggered, this, &AbstractPlotWidget::savePlotToGraphicsFile); + QString text = m_history.asText(QString(), QString(), true /* brief */); + text += m_history.innermostRangesAsText(); - return mpa_contextMenu; - } + QSize widgetSize = size(); + QPoint windowPos = mp_parentWnd->pos(); + QPoint toolTipPos = windowPos + QPoint(widgetSize.width() / 5, 0); + // Let's position the tooltip at the left upper corner. + QToolTip::showText(toolTipPos, text, this, QRect(), 10000); +} - //! Clear the history. - void - AbstractPlotWidget::clearHistory() - { - m_history.freeList(); - // qDebug() << __FILE__ << __LINE__ - // << "Cleared history of window:" << m_name << "--" << m_desc; - } +/*/js/ + * .historyAsText() + * + * Return a textual representation of the history of this plot widget. + */ +//! Craft a textual representation of \c this AbstractPlotWidget History. +/*! + \return A string with a textual representation of the innermost ranges of + the \c m_history History. - //! Add (append) the \p item HistoryItem instance to the member \c m_history. - void - AbstractPlotWidget::addHistoryItem(HistoryItem *item) - { - m_history.appendHistoryItem(item); - } + \sa showHistory(). +*/ +QString +AbstractPlotWidget::historyAsText() +{ + QString text = m_history.asText(QString(), QString(), true /* brief */); + text += m_history.innermostRangesAsText(); - /*/js/ - * .showHistory() - * - * Shows a tooltip with the History of this plot widget. - */ - //! Craft a tooltip and display it with text describing the History of \c this AbstractPlotWidget instance. - /*! + return text; +} - \sa historyAsText(). -*/ - void - AbstractPlotWidget::showHistory() - { - // We want to craft a tooltip widget with the brief history of *this - // widget. +//! Find a minimal integration range starting at an existing data point +/*! - QString text = m_history.asText(QString(), QString(), true /* brief */); - text += m_history.innermostRangesAsText(); + If the user clicks onto a plot at a location that is not a true data point, + get a data range that begins at the preceding data point and that ends at + the clicked location point. - QSize widgetSize = size(); - QPoint windowPos = mp_parentWnd->pos(); +*/ +bool +AbstractPlotWidget::findIntegrationLowerRangeForKey(double key, + QCPRange *p_range) +{ + if(p_range == Q_NULLPTR) + qFatal( + "Fatal error at %s@%d -- %s(). " + "Pointer cannot be nullptr." + "Program aborted.", + __FILE__, + __LINE__, + __FUNCTION__); + + // Given a key double value, we want to know what is the range that will + // frame correctly the key double value if that key value is not exactly + // the one of a point of the trace. + + // First of all get the keys of the graph. + + QCPGraph *theGraph = graph(); + + if(theGraph == Q_NULLPTR) + qFatal( + "Fatal error at %s@%d -- %s(). " + "Programming error." + "Program aborted.", + __FILE__, + __LINE__, + __FUNCTION__); + + + QSharedPointer p_graphDataContainer = theGraph->data(); + // QCPGraphDataContainer is a typedef QCPDataContainer and + // QCPDataContainer< DataType > is a Class Template. So in this context, + // DataType is QCPGraphData. + // QCPGraphData is the data point, that is the (key,value) pair. + + QCPDataRange dataRange = p_graphDataContainer->dataRange(); + + if(!dataRange.isValid()) + return false; + + if(!dataRange.size()) + return false; + + if(dataRange.size() > 1) + { + double firstKey = p_graphDataContainer->at(dataRange.begin())->key; + double lastKey = p_graphDataContainer->at(dataRange.end())->key; + + // There is one check to be done: the user might erroneously set the mouse + // cursor beyond the last point of the graph. If that is the case, then + // upper key needs to be that very point. All we need to do is return the + // lower key, that is the pre-last key of the keys list. No need to + // iterate in the keys list. + + if(key > lastKey) + { + // No need to search for the key in the keys, just get the lower key + // immediately, that is, the key that is one slot left the last key. + p_range->lower = p_graphDataContainer->at(dataRange.end() - 2)->key; + p_range->upper = p_graphDataContainer->at(dataRange.end() - 1)->key; + + return true; + } + + // Likewise, if the cursor is set left of the first plot point, then that + // will be the lower range point. All we need is to provide the upper + // range point as the second point of the plot. + + if(key < firstKey) + { + p_range->lower = firstKey; + p_range->upper = p_graphDataContainer->at(dataRange.begin() + 1)->key; + + return true; + } + + // Finally the generic case where the user point to any point *in* the + // graph. + + p_range->lower = + p_graphDataContainer->findBegin(key, /*expandedRange*/ true)->key; + p_range->upper = + std::prev(p_graphDataContainer->findEnd(key, /*expandedRange*/ true)) + ->key; + + return true; + } + + return false; +} + + +//! Clear the history of the axis ranges. +/*! + + Each time a view on a plot is modified by zooming/unzooming panning via the + axes, the new view ranges are stored. It is thus possible to rewind the axis + range history (using the backspace key). This function clears that history. - QPoint toolTipPos = windowPos + QPoint(widgetSize.width() / 5, 0); +*/ +void +AbstractPlotWidget::clearAxisRangeHistory() +{ + while(!m_xAxisRangeHistory.isEmpty()) + delete m_xAxisRangeHistory.takeFirst(); - // Let's position the tooltip at the left upper corner. - QToolTip::showText(toolTipPos, text, this, QRect(), 10000); - } + while(!m_yAxisRangeHistory.isEmpty()) + delete m_yAxisRangeHistory.takeFirst(); + m_lastAxisRangeHistoryIndex = -1; +} - /*/js/ - * .historyAsText() - * - * Return a textual representation of the history of this plot widget. - */ - //! Craft a textual representation of \c this AbstractPlotWidget History. - /*! - \return A string with a textual representation of the innermost ranges of - the \c m_history History. +//! Create new axis range history items and append them to the history. +/*! - \sa showHistory(). + The plot widget is queried to get the current x/y-axis ranges and the + current ranges are appended to the history for x-axis and for y-axis. */ - QString - AbstractPlotWidget::historyAsText() - { - QString text = m_history.asText(QString(), QString(), true /* brief */); - text += m_history.innermostRangesAsText(); +void +AbstractPlotWidget::updateAxisRangeHistory() +{ + m_xAxisRangeHistory.append(new QCPRange(xAxis->range())); + m_yAxisRangeHistory.append(new QCPRange(yAxis->range())); - return text; - } + // Set the indices to the current position -1; + m_lastAxisRangeHistoryIndex = m_xAxisRangeHistory.size() - 1; + // qDebug() << __FILE__ << __LINE__ + // << "AbstractPlotWidget::updateAxisRangeHistory"; +} - //! Find a minimal integration range starting at an existing data point - /*! - If the user clicks onto a plot at a location that is not a true data point, - get a data range that begins at the preceding data point and that ends at - the clicked location point. +//! Go up one history element in the axis history. +/*! + + If possible, back up one history item in the axis histories and update the + plot's x/y-axis ranges to match that history item. */ - bool - AbstractPlotWidget::findIntegrationLowerRangeForKey(double key, QCPRange *p_range) - { - if(p_range == Q_NULLPTR) - qFatal("Fatal error at %s@%d -- %s(). " - "Pointer cannot be nullptr." - "Program aborted.", - __FILE__, __LINE__, __FUNCTION__); +void +AbstractPlotWidget::backOneAxisHistoryStep() +{ + if(m_lastAxisRangeHistoryIndex <= 0) + return; - // Given a key double value, we want to know what is the range that will - // frame correctly the key double value if that key value is not exactly - // the one of a point of the trace. + setAxisRangesWithHistoryIndex(--m_lastAxisRangeHistoryIndex); +} - // First of all get the keys of the graph. - QCPGraph *theGraph = graph(); +//! Get the axis histories at index \p index and update the plot ranges. +/*! - if(theGraph == Q_NULLPTR) - qFatal("Fatal error at %s@%d -- %s(). " - "Programming error." - "Program aborted.", - __FILE__, __LINE__, __FUNCTION__); + \param index index at which to select the axis history item. + \sa updateAxisRangeHistory(). - QCPDataMap *mapData = theGraph->data(); +*/ +void +AbstractPlotWidget::setAxisRangesWithHistoryIndex(int index) +{ + if(index >= m_xAxisRangeHistory.size()) + return; - QList keys = mapData->keys(); + xAxis->setRange(*(m_xAxisRangeHistory.at(index))); + yAxis->setRange(*(m_yAxisRangeHistory.at(index))); - // There is one check to be done: the user might erroneously set the mouse - // cursor beyond the last point of the graph. If that is the case, then - // upper key needs to be that very point. All we need to do is return the - // lower key, that is the pre-last key of the keys list. No need to - // iterate in the keys list. + replot(); +} - if(key > keys.last() && keys.size() > 1) - { - // No need to search for the key in the keys, just get the lower key - // immediately. - p_range->lower = keys.at(keys.size() - 2); - p_range->upper = keys.at(keys.size() - 1); - return true; - } +//! Clear the plot. +/*! - // Likewise, if the cursor is set left of the first plot point, then that - // will be the lower range point. All we need is to provide the upper - // range point as the second point of the plot. + The graph is asked to clear its data, the axes are reset and the graph is + replot to update it as an empty plot. - if(key < keys.first()) - { - if(keys.size() < 1) - return false; +*/ +void +AbstractPlotWidget::clearPlot() +{ + graph()->data().clear(); - p_range->lower = keys.at(0); - p_range->upper = keys.at(1); + // Set axes ranges, so we see all data: + xAxis->setRange(-1, 1); + yAxis->setRange(0, 1); + rescaleAxes(false); - return true; - } + clearAxisRangeHistory(); + updateAxisRangeHistory(); - // Finally the generic case where the user point to any point *in* the - // graph + replot(); +} - for(int iter = 0; iter < keys.size(); ++iter) - { - if(keys.at(iter) > key) - { - if(iter > 0) - { - p_range->lower = keys.at(iter - 1); - p_range->upper = key; - return true; - } - else - { - p_range->lower = keys.at(0); - p_range->upper = key; - return true; - } - } - } - return false; - } +//! Insert a keyboard key code in the list of registered key. +/*! + The \c m_regQtKeyCodeMap map of keyboard keys is a register that stores + key codes of keys that have a special meaning while working on the data + plotted in the plot widgets along with the helper string. - //! Clear the history of the axis ranges. - /*! +*/ +void +AbstractPlotWidget::registerQtKeyCode(int qtKeyCode, const QString &helpText) +{ + m_regQtKeyCodeMap.insert(qtKeyCode, helpText); +} - Each time a view on a plot is modified by zooming/unzooming panning via the - axes, the new view ranges are stored. It is thus possible to rewind the axis - range history (using the backspace key). This function clears that history. -*/ - void - AbstractPlotWidget::clearAxisRangeHistory() - { - while(!m_xAxisRangeHistory.isEmpty()) - delete m_xAxisRangeHistory.takeFirst(); +/*/js/ + * .showHelpSummary() + * + * Show a tooltip with a help string summarizing the various keyboard key + * combinations. + */ - while(!m_yAxisRangeHistory.isEmpty()) - delete m_yAxisRangeHistory.takeFirst(); +//! Craft a string explaining the various key combinations for the +//! integrations. +void +AbstractPlotWidget::showHelpSummary() +{ + QString helpText; - m_lastAxisRangeHistoryIndex = -1; - } + QMapIterator iterator(m_regQtKeyCodeMap); + while(iterator.hasNext()) + { + iterator.next(); + helpText.append(iterator.value() + "\n"); + } - //! Create new axis range history items and append them to the history. - /*! + QSize widgetSize = size(); + QPoint windowPos = mp_parentWnd->pos(); + QPoint toolTipPos = + windowPos + QPoint(widgetSize.width() / 4, widgetSize.height() / 4); + QToolTip::showText(toolTipPos, helpText, this, QRect()); +} - The plot widget is queried to get the current x/y-axis ranges and the - current ranges are appended to the history for x-axis and for y-axis. -*/ - void - AbstractPlotWidget::updateAxisRangeHistory() - { - m_xAxisRangeHistory.append(new QCPRange(xAxis->range())); - m_yAxisRangeHistory.append(new QCPRange(yAxis->range())); +//! Set the \c m_pressedKeyCode to the key code in \p event. +void +AbstractPlotWidget::keyPressEvent(QKeyEvent *event) +{ + m_pressedKeyCode = event->key(); +} - // Set the indices to the current position -1; - m_lastAxisRangeHistoryIndex = m_xAxisRangeHistory.size() - 1; - // qDebug() << __FILE__ << __LINE__ - // << "AbstractPlotWidget::updateAxisRangeHistory"; - } +//! Handle specific key codes and trigger respective actions. +void +AbstractPlotWidget::keyReleaseEvent(QKeyEvent *event) +{ + m_pressedKeyCode = 0; + if(event->key() == Qt::Key_Backspace) + { + backOneAxisHistoryStep(); + + event->accept(); + } + else if(event->key() == Qt::Key_T) + { + m_tracersVisible = !m_tracersVisible; + + if(!m_tracersVisible) + hideTracers(); + else + showTracers(); + + event->accept(); + } + else if(event->key() == Qt::Key_H) + { + + // The user wants to hide/show the corresponding graph from the multi + // graph plot. If the shift key is pressed, then the user wants that all + // the target plot widgets' multigraphgraph be hidden also. + + Qt::KeyboardModifiers modifiers = + QGuiApplication::queryKeyboardModifiers(); + + if(modifiers & Qt::ShiftModifier) + emit toggleMultiGraphSignal(this, true); + else + emit toggleMultiGraphSignal(this, false); + + event->accept(); + } + else if(event->key() == Qt::Key_Delete) + { + // The user wants to destroy this plot widget. + // We do not directly handle our destruction, we delegate that + // destructino to the parent window. + + shouldDestroyPlotWidget(); + } + else if(event->key() == Qt::Key_O) + { + // The user wants to show the history (brief form) of *this widget. + showHistory(); + } +} + + +/*/js/ + * .shouldDestroyPlotWidget() + * + * Start the destruction of this plot widget. + */ - //! Go up one history element in the axis history. - /*! +//! Start the process of destroying a plot widget. +/*! - If possible, back up one history item in the axis histories and update the - plot's x/y-axis ranges to match that history item. + The process involves removing the corresponding plot from the multigraph + plot widget. Then a signal is emitted to destroy the plot widget. */ - void - AbstractPlotWidget::backOneAxisHistoryStep() - { - if(m_lastAxisRangeHistoryIndex <= 0) - return; +void +AbstractPlotWidget::shouldDestroyPlotWidget() +{ + // When a single graph plot widget is destroyed, it is necessary to + // automatically destroy the corresponding, the matching multigraph + // QGraph. This signal is connected to a slot that will handle the removal + // of the matching multigraph graph. + static_cast(mp_parentWnd)->removeMultiGraph(this); + + // This abstract plot widget does not handle its destruction by + // itself, it delegates its distruction to the main window of the + // program that will handle the slot matching this signal. + + emit destroyPlotWidget(this); +} + + +/*/js/ + * .toggleMultiGraph() + * + * If the multi-graph plot corresponding to this plot widget is visible, make + * it invisible. And vice versa. + */ - setAxisRangesWithHistoryIndex(--m_lastAxisRangeHistoryIndex); - } +//! Toggle visibility of the corresponding graph in the multigraph plot +//! widget. +void +AbstractPlotWidget::toggleMultiGraph() +{ + static_cast(mp_parentWnd)->toggleMultiGraph(this); +} - //! Get the axis histories at index \p index and update the plot ranges. - /*! +/*/js/ + * .showMultiGraph() + * + * Make the multi-graph plot corresponding to this plot widget visible. + */ +//! Make visible the corresponding graph in the multigraph plot widget. +void +AbstractPlotWidget::showMultiGraph() +{ + static_cast(mp_parentWnd)->showMultiGraph(this); +} - \param index index at which to select the axis history item. - \sa updateAxisRangeHistory(). +/*/js/ + * .hideMultiGraph() + * + * Make the multi-graph plot corresponding to this plot widget invisible. + */ +//! Make invisible the corresponding graph in the multigraph plot widget. +void +AbstractPlotWidget::hideMultiGraph() +{ + static_cast(mp_parentWnd)->hideMultiGraph(this); +} -*/ - void - AbstractPlotWidget::setAxisRangesWithHistoryIndex(int index) - { - if(index >= m_xAxisRangeHistory.size()) - return; - xAxis->setRange(*(m_xAxisRangeHistory.at(index))); - yAxis->setRange(*(m_yAxisRangeHistory.at(index))); +//! Set the plotting and decoration color for \c this plot widget. +/*! - replot(); - } + This function is called when the user wants to change the color of the plot + widget's graph and decorations (tick labels, axis names). + */ +void +AbstractPlotWidget::setPlottingColor(const QColor &newColor) +{ + if(!newColor.isValid()) + return; + // This function does not do anything if *this is a multi-graph plot + // widget. + if(m_isMultiGraph) + { + qDebug() << __FILE__ << __LINE__ + << "Returning because *this plot widget is multi-graph."; - //! Clear the plot. - /*! + return; + } - The graph is asked to clear its data, the axes are reset and the graph is - replot to update it as an empty plot. + // We want to have the color handy + m_plottingColor = newColor; -*/ - void - AbstractPlotWidget::clearPlot() - { - graph()->clearData(); + // First this single-graph widget + QPen pen; - // Set axes ranges, so we see all data: - xAxis->setRange(-1, 1); - yAxis->setRange(0, 1); - rescaleAxes(false); + // If this plot widget is hosting the color map, there is a specific + // treatement. + if(mp_colorMap != Q_NULLPTR) + { + QCPAxis *xAxis = mp_colorMap->keyAxis(); - clearAxisRangeHistory(); - updateAxisRangeHistory(); + pen = xAxis->basePen(); + pen.setColor(m_plottingColor); - replot(); - } + xAxis->setBasePen(pen); + xAxis->setLabelColor(m_plottingColor); + xAxis->setTickLabelColor(m_plottingColor); + QCPAxis *yAxis = mp_colorMap->valueAxis(); + yAxis->setBasePen(pen); + yAxis->setLabelColor(m_plottingColor); + yAxis->setTickLabelColor(m_plottingColor); - //! Insert a keyboard key code in the list of registered key. - /*! + replot(); - The \c m_regQtKeyCodeMap map of keyboard keys is a register that stores - key codes of keys that have a special meaning while working on the data - plotted in the plot widgets along with the helper string. + // There is not multi-graph replica, just return. + return; + } -*/ - void - AbstractPlotWidget::registerQtKeyCode(int qtKeyCode, const QString &helpText) - { - m_regQtKeyCodeMap.insert(qtKeyCode, helpText); - } + pen = graph()->pen(); + pen.setColor(m_plottingColor); + graph()->setPen(pen); + replot(); - /*/js/ - * .showHelpSummary() - * - * Show a tooltip with a help string summarizing the various keyboard key - * combinations. - */ - - //! Craft a string explaining the various key combinations for the integrations. - void - AbstractPlotWidget::showHelpSummary() - { - QString helpText; + return; +} - QMapIterator iterator(m_regQtKeyCodeMap); - while(iterator.hasNext()) - { - iterator.next(); +//! Change the plotting and decoration color for \c this plot widget. +/*! - helpText.append(iterator.value() + "\n"); - } + This function is called when the user wants to change the color of the plot + widget's graph and decorations (tick labels, axis names). + */ +void +AbstractPlotWidget::changePlottingColor(const QColor &newColor) +{ + if(!newColor.isValid()) + return; - QSize widgetSize = size(); - QPoint windowPos = mp_parentWnd->pos(); - QPoint toolTipPos = windowPos + QPoint(widgetSize.width() / 4, widgetSize.height() / 4); - QToolTip::showText(toolTipPos, helpText, this, QRect()); - } + // This function does not do anything if *this is a multi-graph plot + // widget. + if(m_isMultiGraph) + { + qDebug() << __FILE__ << __LINE__ + << "Returning because *this plot widget is multi-graph."; + return; + } + // We want to have the color handy + m_plottingColor = newColor; - //! Set the \c m_pressedKeyCode to the key code in \p event. - void - AbstractPlotWidget::keyPressEvent(QKeyEvent *event) - { - m_pressedKeyCode = event->key(); - } + // First this single-graph widget + QPen pen; + // If this plot widget is hosting the color map, there is a specific + // treatement. + if(mp_colorMap != Q_NULLPTR) + { + QCPAxis *xAxis = mp_colorMap->keyAxis(); - //! Handle specific key codes and trigger respective actions. - void - AbstractPlotWidget::keyReleaseEvent(QKeyEvent *event) - { - m_pressedKeyCode = 0; + pen = xAxis->basePen(); + pen.setColor(m_plottingColor); - if(event->key() == Qt::Key_Backspace) - { - backOneAxisHistoryStep(); + xAxis->setBasePen(pen); + xAxis->setLabelColor(m_plottingColor); + xAxis->setTickLabelColor(m_plottingColor); - event->accept(); - } - else if(event->key() == Qt::Key_T) - { - m_tracersVisible = !m_tracersVisible; + QCPAxis *yAxis = mp_colorMap->valueAxis(); + yAxis->setBasePen(pen); + yAxis->setLabelColor(m_plottingColor); + yAxis->setTickLabelColor(m_plottingColor); - if(!m_tracersVisible) - hideTracers(); - else - showTracers(); + replot(); - event->accept(); - } - else if(event->key() == Qt::Key_H) - { + // There is not multi-graph replica, just return. + return; + } - // The user wants to hide/show the corresponding graph from the multi - // graph plot. If the shift key is pressed, then the user wants that all - // the target plot widgets' multigraphgraph be hidden also. + pen = graph()->pen(); + pen.setColor(m_plottingColor); + graph()->setPen(pen); - Qt::KeyboardModifiers modifiers = - QGuiApplication::queryKeyboardModifiers(); + replot(); - if(modifiers & Qt::ShiftModifier) - emit toggleMultiGraphSignal(this, true); - else - emit toggleMultiGraphSignal(this, false); + // Then, the replica graph in the multi-graph plot widget - event->accept(); - } - else if(event->key() == Qt::Key_Delete) - { - // The user wants to destroy this plot widget. - // We do not directly handle our destruction, we delegate that - // destructino to the parent window. + AbstractMultiPlotWnd *parentWnd = + static_cast(mp_parentWnd); - shouldDestroyPlotWidget(); - } - else if(event->key() == Qt::Key_O) - { - // The user wants to show the history (brief form) of *this widget. - showHistory(); - } - } + QCPGraph *multiGraph = parentWnd->multiGraph(this); + // qDebug() << __FILE__ << __LINE__ + //<< "for this:" << this << "found multiGraph: " << multiGraph; - /*/js/ - * .shouldDestroyPlotWidget() - * - * Start the destruction of this plot widget. - */ + pen = multiGraph->pen(); + pen.setColor(m_plottingColor); + multiGraph->setPen(pen); + multiGraph->parentPlot()->replot(); - //! Start the process of destroying a plot widget. - /*! + return; +} - The process involves removing the corresponding plot from the multigraph - plot widget. Then a signal is emitted to destroy the plot widget. -*/ - void - AbstractPlotWidget::shouldDestroyPlotWidget() - { - // When a single graph plot widget is destroyed, it is necessary to - // automatically destroy the corresponding, the matching multigraph - // QGraph. This signal is connected to a slot that will handle the removal - // of the matching multigraph graph. - static_cast(mp_parentWnd)->removeMultiGraph(this); - - // This abstract plot widget does not handle its destruction by - // itself, it delegates its distruction to the main window of the - // program that will handle the slot matching this signal. +//! Return the pen color of \c this plot widget graph. +QColor +AbstractPlotWidget::color() const +{ + return m_plottingColor; +} - emit destroyPlotWidget(this); - } +/*/js/ + * .exportData() + * + * Open the data export configuration window. Exporting data allows exporting + * only a subset of the whole data set. It can only be performed if the + * original data were read from a SQLite3 database-formatted mass data file. + */ +//! Export data to one or more files. +/*! - /*/js/ - * .toggleMultiGraph() - * - * If the multi-graph plot corresponding to this plot widget is visible, make - * it invisible. And vice versa. - */ - - //! Toggle visibility of the corresponding graph in the multigraph plot widget. - void - AbstractPlotWidget::toggleMultiGraph() - { - static_cast(mp_parentWnd)->toggleMultiGraph(this); - } + This function starts the process. It invokes a number of other helper + functions. + When the data are initially loaded from a SQLite3 db-formatted file, they + can be exported to new files according to a number of criteria defined by + the user. + + \sa SqlMassDataSlicer
SqlMassDataSlicerWnd. + */ +void +AbstractPlotWidget::exportData() +{ + // The user asks to export data. There are different ways of doing this: + // + // 1. export all the data contained in the current plot widget view, that + // is the key axis (X axis). That is easy, choose a file and that's done. + // + // 2. export the data according to some criteria: + // a. export the data in the key range (modifiable in the dialog box) and + // slice all these data in chunks of a given size (count is deduced) or + // b. export the data in a number of chunks (size is deduced). + + // Note that the window in which the user configures the data export + // operation is owned by MainWindow, the program's main window. That + // window is available for any plot widget to use, and thus needs to be + // updated with the caller widget's data to be useful. + + if(m_isMultiGraph || mp_colorMap != Q_NULLPTR) + return; + + // At the moment, this export only works with data that are available as + // an SQLite database file (format massDb). + if(mp_massSpecDataSet->fileFormat() != + MassSpecDataFileFormat::MASS_SPEC_DATA_FILE_FORMAT_SQLITE3) + { + QMessageBox msgBox; + msgBox.setText( + "The data cannot be exported because they were not from " + "a SQLite3 database format file."); + msgBox.setStandardButtons(QMessageBox::Ok); + msgBox.exec(); + return; + } + + // Get a pointer to the configuratin window + + MainWindow *p_mainWindow = static_cast(mp_parentWnd->parent()); + SqlMassDataSlicerWnd *p_massDataSlicerWnd = + p_mainWindow->mp_sqlMassDataSlicerWnd; + + QCPAxis *xAxis = graph()->keyAxis(); + double start = xAxis->range().lower; + double end = xAxis->range().upper; + + // We want to do the data export by taking into account the history of + // the current widget. We have m_history that accounts for previous + // events, but we need to craft one new for the start and end values + // above. + + History localHistory(m_history); + + HistoryItem *histItem = new HistoryItem; + + // arbitraryIntegrationType() is pure virtual, defined in the derived class + + histItem->newIntegrationRange(arbitraryIntegrationType(), start, end); + localHistory.appendHistoryItem(histItem); + + // We want to provide the full path name to the file + + QFileInfo fileInfo(m_fileName); + + // Sanity check + if(!fileInfo.exists()) + qFatal( + "Fatal error at %s@%d -- %s(). " + "Cannot be that the plot widget has no file name member data set " + "correctly." + "Program aborted.", + __FILE__, + __LINE__, + __FUNCTION__); + + if(!fileInfo.isAbsolute()) + qFatal( + "Fatal error at %s@%d -- %s(). " + "The plot widget's member m_fileName must be an absolute file path " + "name." + "Program aborted.", + __FILE__, + __LINE__, + __FUNCTION__); + + // qDebug() << __FILE__ << __LINE__ << __FUNCTION__ << "()" + //<< "The plot widget's m_fileName:" << m_fileName; + + p_massDataSlicerWnd->initialize( + fileInfo.absoluteFilePath(), start, end, localHistory); + + p_massDataSlicerWnd->activate(); +} + + +/*/js/ + * .asXyText() + * + * Return a textual representation of \c this plot widget data. + * + * Only the data range currently displayed is processed. + */ +//! Return a textual representation of \c this plot widget. +/*! + * Only the currently visible data range is processed. + */ +QString +AbstractPlotWidget::asXyText() +{ + if(m_isMultiGraph) + return QString(); - /*/js/ - * .showMultiGraph() - * - * Make the multi-graph plot corresponding to this plot widget visible. - */ - //! Make visible the corresponding graph in the multigraph plot widget. - void - AbstractPlotWidget::showMultiGraph() - { - static_cast(mp_parentWnd)->showMultiGraph(this); - } + // Get the pointer to the x-axis (key axis). + QCPAxis *xAxis = graph()->keyAxis(); - /*/js/ - * .hideMultiGraph() - * - * Make the multi-graph plot corresponding to this plot widget invisible. - */ - //! Make invisible the corresponding graph in the multigraph plot widget. - void - AbstractPlotWidget::hideMultiGraph() - { - static_cast(mp_parentWnd)->hideMultiGraph(this); - } + double rangeStart = xAxis->range().lower; + double rangeEnd = xAxis->range().upper; + QSharedPointer p_graphDataContainer = graph()->data(); - //! Set the plotting and decoration color for \c this plot widget. - /*! + // Iterate in the keys + auto beginIt = + p_graphDataContainer->findBegin(rangeStart, /*expandedRange*/ true); + auto endIt = p_graphDataContainer->findEnd(rangeEnd, /*expandedRange*/ true); - This function is called when the user wants to change the color of the plot - widget's graph and decorations (tick labels, axis names). - */ - void - AbstractPlotWidget::setPlottingColor(const QColor& newColor) - { - if(!newColor.isValid()) - return; + QString xyString; - // This function does not do anything if *this is a multi-graph plot - // widget. - if(m_isMultiGraph) - { - qDebug() << __FILE__ << __LINE__ - << "Returning because *this plot widget is multi-graph."; + for(auto iter = beginIt; iter != endIt; ++iter) + { + xyString += QString("%1 %2\n") + .arg(iter->key, 0, 'f', 10) + .arg(iter->value, 0, 'f', 10); + } - return; - } + return xyString; +} - // We want to have the color handy - m_plottingColor = newColor; - // First this single-graph widget - QPen pen; +/*/js/ + * .exportPlot() + * + * Open a file selection dialog window to select a file in which to export + * this plot widget's data. + * + * Unlike the exportData() function, this function only exports the currently + * displayed graph data to a comma-separated value text file. + */ +//! Export plot data to a text file as a simple plot. +/*! - // If this plot widget is hosting the color map, there is a specific - // treatement. - if(mp_colorMap != Q_NULLPTR) - { - QCPAxis *xAxis = mp_colorMap->keyAxis(); + Unlike the exportData() function, this function only exports the currently + displayed graph data to a comma-separated value text file. - pen = xAxis->basePen(); - pen.setColor(m_plottingColor); + Note that only the currently selected plot ranges are exported. To export + the whole plot data, make sure to unzoom the plot. + */ +void +AbstractPlotWidget::exportPlot() +{ + if(m_isMultiGraph) + return; - xAxis->setBasePen(pen); - xAxis->setLabelColor(m_plottingColor); - xAxis->setTickLabelColor(m_plottingColor); + // The user asks that the (that is not the whole set of data), but only + // the + // x,y plot for the current plot widget. This is the easiest solution. The + // only constraint is that we only export the data corresponding to the + // current X axis range. + + QString outputFileName = m_fileName; + outputFileName += ".xy"; + + QString newFileName = + QFileDialog::getSaveFileName(this, + "Open file", + outputFileName, + tr("Ascii (x,y) files (*.txt *.xy *.asc)")); + + if(newFileName.isEmpty()) + return; + + outputFileName = newFileName; + + QString xyString = asXyText(); + + QFile file(outputFileName); + + file.open(QIODevice::WriteOnly); + QTextStream out(&file); // we will serialize the data into the file + out << xyString; + + file.close(); +} + + +/*/js/ + * .exportPlotToFile(fileName, rangeStart, rangeEnd) + * + * Export plot data to a text file as a simple plot. Limit the data range to + * export using the numerical parameters. + * + * fileName: holding the file name + * rangeStart: holding the beginning of the range to be exported + * rangeEnd holding the end of the range to be exported + */ +//! Export plot data to a text file as a simple plot. +/*! - QCPAxis *yAxis = mp_colorMap->valueAxis(); - yAxis->setBasePen(pen); - yAxis->setLabelColor(m_plottingColor); - yAxis->setTickLabelColor(m_plottingColor); + Unlike the exportPlo() function, this function takes the name of the file in + which to export the data and the range that is required to be exported. This + function is useful in scripting. + */ +void +AbstractPlotWidget::exportPlotToFile(const QString &fileName, + double start, + double end) +{ + if(m_isMultiGraph) + return; - replot(); + // The user asks that the (that is not the whole set of data), but only + // the x,y plot for the current plot widget. This is the easiest solution. + // The only constraint is that we only export the data corresponding to + // the current X axis range. - // There is not multi-graph replica, just return. - return; - } + QString outputFileName = fileName; - pen = graph()->pen(); - pen.setColor(m_plottingColor); - graph()->setPen(pen); + if(outputFileName.isEmpty()) + { + outputFileName = m_fileName; - replot(); + outputFileName += ".xy"; - return; - } + QString newFileName = QFileDialog::getSaveFileName( + this, + "Open file", + outputFileName, + tr("Ascii (x,y) files (*.txt *.xy *.asc)")); + if(newFileName.isEmpty()) + return; - //! Change the plotting and decoration color for \c this plot widget. - /*! + outputFileName = newFileName; + } - This function is called when the user wants to change the color of the plot - widget's graph and decorations (tick labels, axis names). - */ - void - AbstractPlotWidget::changePlottingColor(const QColor& newColor) - { - if(!newColor.isValid()) - return; + // Get the pointer to the x-axis (key axis). - // This function does not do anything if *this is a multi-graph plot - // widget. - if(m_isMultiGraph) - { - qDebug() << __FILE__ << __LINE__ - << "Returning because *this plot widget is multi-graph."; + QCPAxis *xAxis = graph()->keyAxis(); - return; - } + double rangeStart = start; - // We want to have the color handy - m_plottingColor = newColor; + if(qIsNaN(rangeStart)) + { + rangeStart = xAxis->range().lower; + } - // First this single-graph widget - QPen pen; + double rangeEnd = end; - // If this plot widget is hosting the color map, there is a specific - // treatement. - if(mp_colorMap != Q_NULLPTR) - { - QCPAxis *xAxis = mp_colorMap->keyAxis(); + if(qIsNaN(rangeEnd)) + { + rangeEnd = xAxis->range().upper; + } - pen = xAxis->basePen(); - pen.setColor(m_plottingColor); + QSharedPointer p_graphDataContainer = graph()->data(); - xAxis->setBasePen(pen); - xAxis->setLabelColor(m_plottingColor); - xAxis->setTickLabelColor(m_plottingColor); + // Iterate in the keys + auto beginIt = + p_graphDataContainer->findBegin(rangeStart, /*expandedRange*/ true); + auto endIt = p_graphDataContainer->findEnd(rangeEnd, /*expandedRange*/ true); - QCPAxis *yAxis = mp_colorMap->valueAxis(); - yAxis->setBasePen(pen); - yAxis->setLabelColor(m_plottingColor); - yAxis->setTickLabelColor(m_plottingColor); + QString xyString; - replot(); + for(auto iter = beginIt; iter != endIt; ++iter) + { + xyString += QString("%1 %2\n") + .arg(iter->key, 0, 'f', 10) + .arg(iter->value, 0, 'f', 10); + } - // There is not multi-graph replica, just return. - return; - } + // Now craft a header that will identify clearly the data. The '#' is a + // comment prefix. - pen = graph()->pen(); - pen.setColor(m_plottingColor); - graph()->setPen(pen); + QString header; - replot(); + QFile file(outputFileName); - // Then, the replica graph in the multi-graph plot widget + if(file.open(QIODevice::WriteOnly) == false) + { + qWarning() + << __FILE__ << __LINE__ << __FUNCTION__ + << "Failed to export the plot because the file could not be opened."; - AbstractMultiPlotWnd *parentWnd = static_cast(mp_parentWnd); + return; + } - QCPGraph *multiGraph = parentWnd->multiGraph(this); + // qWarning() << "opened file with text:" << outputString; - //qDebug() << __FILE__ << __LINE__ - //<< "for this:" << this << "found multiGraph: " << multiGraph; + QTextStream out(&file); // we will serialize the data into the file + out << xyString; - pen = multiGraph->pen(); - pen.setColor(m_plottingColor); - multiGraph->setPen(pen); - multiGraph->parentPlot()->replot(); + file.close(); +} - return; - } +/*/js/ + * .savePlotToGraphicsFile() + * + * Open the graphics export configuration dialog window. + */ +//! Open the graphics export configuration dialog window. +bool +AbstractPlotWidget::savePlotToGraphicsFile() +{ + qDebug() << __FILE__ << __LINE__ << __FUNCTION__ << "()"; - //! Return the pen color of \c this plot widget graph. - QColor - AbstractPlotWidget::color() const - { - return m_plottingColor; - } + SaveToGraphicsFileDlg dlg(this, this, "mineXpert"); + if(QDialog::Accepted == dlg.exec()) + return true; + else + return false; +} + + +/*/js/ + * .saveToPdfFile(fileName, noCosmeticPen, width, height, + * pdfCreator, title) + * + * Save this plot widget as a PDF file graphics. + * + * fileName: holding the file name + * noCosmeticPen: that tells if pen optimizations should be + * performed + * width: holding the size of the graphics file in pixels + * height: holding the size of the graphics file in pixels + * pdfCreator: holding the name of the creator of the PDF file + * title: holding the title of the graphics file + */ +//! Save this plot widget as a PDF file graphics. +bool +AbstractPlotWidget::savePlotToPdfFile(const QString &fileName, + bool noCosmeticPen, + int width, + int height, + const QString &pdfCreator, + const QString &title) +{ + return savePdf(fileName, width, height, + noCosmeticPen ? QCP::epNoCosmetic : QCP::epAllowCosmetic, pdfCreator, title); +} - /*/js/ - * .exportData() - * - * Open the data export configuration window. Exporting data allows exporting - * only a subset of the whole data set. It can only be performed if the - * original data were read from a SQLite3 database-formatted mass data file. - */ - //! Export data to one or more files. - /*! - - This function starts the process. It invokes a number of other helper functions. - - When the data are initially loaded from a SQLite3 db-formatted file, they - can be exported to new files according to a number of criteria defined by - the user. - - \sa SqlMassDataSlicer
SqlMassDataSlicerWnd. - */ - void - AbstractPlotWidget::exportData() - { - // The user asks to export data. There are different ways of doing this: - // - // 1. export all the data contained in the current plot widget view, that - // is the key axis (X axis). That is easy, choose a file and that's done. - // - // 2. export the data according to some criteria: - // a. export the data in the key range (modifiable in the dialog box) and - // slice all these data in chunks of a given size (count is deduced) or - // b. export the data in a number of chunks (size is deduced). - - // Note that the window in which the user configures the data export - // operation is owned by MainWindow, the program's main window. That - // window is available for any plot widget to use, and thus needs to be - // updated with the caller widget's data to be useful. - - if(m_isMultiGraph || mp_colorMap != Q_NULLPTR) - return; - - // At the moment, this export only works with data that are available as - // an SQLite database file (format massDb). - if(mp_massSpecDataSet->fileFormat() != - MassSpecDataFileFormat::MASS_SPEC_DATA_FILE_FORMAT_SQLITE3) - { - QMessageBox msgBox; - msgBox.setText("The data cannot be exported because they were not from " - "a SQLite3 database format file."); - msgBox.setStandardButtons(QMessageBox::Ok); - msgBox.exec(); - return; - } - // Get a pointer to the configuratin window +/*/js/ + * .keys() + * + * Return an of values representing the keys of the data + * plotted. + */ +//! Return a list of double values representing the keys of the data plotted. +QList +AbstractPlotWidget::keys() +{ + QList keyList; - MainWindow *p_mainWindow = static_cast(mp_parentWnd->parent()); - SqlMassDataSlicerWnd *p_massDataSlicerWnd = p_mainWindow->mp_sqlMassDataSlicerWnd; + if(m_isMultiGraph) + { + qDebug() << __FILE__ << __LINE__ << __FUNCTION__ + << "Cannot select keys from multiGraph plot."; - QCPAxis *xAxis = graph()->keyAxis(); - double start = xAxis->range().lower; - double end = xAxis->range().upper; + return keyList; + } - // We want to do the data export by taking into account the history of - // the current widget. We have m_history that accounts for previous - // events, but we need to craft one new for the start and end values - // above. + QSharedPointer p_graphDataContainer = graph()->data(); - History localHistory(m_history); + // Iterate in the keys + auto beginIt = p_graphDataContainer->begin(); + auto endIt = p_graphDataContainer->end(); - HistoryItem *histItem = new HistoryItem; + for(auto iter = beginIt; iter != endIt; ++iter) + keyList.append(iter->key); - // arbitraryIntegrationType() is pure virtual, defined in the derived class + // qDebug() << __FILE__ << __LINE__ << __FUNCTION__ + //<< "keys:" << keyList(); - histItem->newIntegrationRange(arbitraryIntegrationType(), start, end); - localHistory.appendHistoryItem(histItem); + return keyList; +} - // We want to provide the full path name to the file - QFileInfo fileInfo(m_fileName); +/*/js/ + * .values() + * + * Return an of values representing the values of the data + * plotted. + */ +//! Return a list of double values representing the values of the data +//! plotted. +QList +AbstractPlotWidget::values() +{ + QList valueList; - // Sanity check - if(!fileInfo.exists()) - qFatal("Fatal error at %s@%d -- %s(). " - "Cannot be that the plot widget has no file name member data set correctly." - "Program aborted.", - __FILE__, __LINE__, __FUNCTION__); - - if(!fileInfo.isAbsolute()) - qFatal("Fatal error at %s@%d -- %s(). " - "The plot widget's member m_fileName must be an absolute file path name." - "Program aborted.", - __FILE__, __LINE__, __FUNCTION__); + if(m_isMultiGraph) + { + qDebug() << __FILE__ << __LINE__ << __FUNCTION__ + << "Cannot select keys from multiGraph plot."; - //qDebug() << __FILE__ << __LINE__ << __FUNCTION__ << "()" - //<< "The plot widget's m_fileName:" << m_fileName; + return valueList; + } - p_massDataSlicerWnd->initialize(fileInfo.absoluteFilePath(), - start, end, localHistory); + QSharedPointer p_graphDataContainer = graph()->data(); - p_massDataSlicerWnd->activate(); - } + // Iterate in the keys + auto beginIt = p_graphDataContainer->begin(); + auto endIt = p_graphDataContainer->end(); + for(auto iter = beginIt; iter != endIt; ++iter) + valueList.append(iter->value); - /*/js/ - * .asXyText() - * - * Return a textual representation of \c this plot widget data. - * - * Only the data range currently displayed is processed. - */ - //! Return a textual representation of \c this plot widget. - /*! - * Only the currently visible data range is processed. - */ - QString - AbstractPlotWidget::asXyText() - { - if(m_isMultiGraph) - return QString(); + // qDebug() << __FILE__ << __LINE__ << __FUNCTION__ + //<< "values:" << valueList; - // Get the pointer to the x-axis (key axis). + return valueList; +} - QCPAxis *xAxis = graph()->keyAxis(); - double rangeStart = xAxis->range().lower; - double rangeEnd = xAxis->range().upper; +//! Set the last TIC intensity value. +void +AbstractPlotWidget::setLastTicIntensity(double value) +{ + m_lastTicIntensity = value; +} - // Remember that the data are like this in a QCPGraph: - // typedef QMap< double, QCPData > QCPDataMap - // and the double key of the map is the key of QCPData: - // QCPData(key, value). - QCPDataMap *data = graph()->data(); +/*/js/ + * .lastTicIntensity() + * + * Return the last TIC intensity value that was computed. + */ +//! Return the last TIC intensity value that was computed. +double +AbstractPlotWidget::lastTicIntensity(void) +{ + return m_lastTicIntensity; +} - QList xValueList = data->keys(); - QString xyString; +/*/js/ + * .trace() + * + * Return a Trace object initialized with the data in this plot widget. + */ +//! Return a Trace instance initialized with the data in this plot widget +msXpSlibmass::Trace +AbstractPlotWidget::trace() +{ + if(m_isMultiGraph) + { + qDebug() << __FILE__ << __LINE__ << __FUNCTION__ + << "Cannot select keys from multiGraph plot."; - for(int iter = 0; iter < xValueList.size(); ++iter) - { - double xValue = xValueList.at(iter); + return msXpSlibmass::Trace(); + } - if(xValue >= rangeStart) - { - if(xValue <= rangeEnd) - { - double yValue = data->value(xValue).value; - - xyString += QString("%1 %2\n") - .arg(xValue, 0, 'f', 10) - .arg(yValue, 0, 'f', 10); - } - else - break; - } - } + msXpSlibmass::Trace trace; - return xyString; - } + QSharedPointer p_graphDataContainer = graph()->data(); + // Iterate in the keys + auto beginIt = p_graphDataContainer->begin(); + auto endIt = p_graphDataContainer->end(); - /*/js/ - * .exportPlot() - * - * Open a file selection dialog window to select a file in which to export - * this plot widget's data. - * - * Unlike the exportData() function, this function only exports the currently - * displayed graph data to a comma-separated value text file. - */ - //! Export plot data to a text file as a simple plot. - /*! - - Unlike the exportData() function, this function only exports the currently - displayed graph data to a comma-separated value text file. - - Note that only the currently selected plot ranges are exported. To export - the whole plot data, make sure to unzoom the plot. - */ - void - AbstractPlotWidget::exportPlot() - { - if(m_isMultiGraph) - return; + for(auto iter = beginIt; iter != endIt; ++iter) + { + msXpSlibmass::DataPoint *dataPoint = + new msXpSlibmass::DataPoint(iter->key, iter->value); - // The user asks that the (that is not the whole set of data), but only - // the - // x,y plot for the current plot widget. This is the easiest solution. The - // only constraint is that we only export the data corresponding to the - // current X axis range. + trace.append(dataPoint); + } - QString outputFileName = m_fileName; - outputFileName += ".xy"; + return trace; +} - QString newFileName = - QFileDialog::getSaveFileName(this, "Open file", outputFileName, - tr("Ascii (x,y) files (*.txt *.xy *.asc)")); - if(newFileName.isEmpty()) - return; +//! Trigger a graph replot action with new x-axis and y-axis ranges. +void +AbstractPlotWidget::replotWithAxisRange(QCPRange xAxisRange, + QCPRange yAxisRange, + int whichAxis) +{ + if(whichAxis & X_AXIS) + xAxis->setRange(xAxisRange.lower, xAxisRange.upper); + if(whichAxis & Y_AXIS) + yAxis->setRange(yAxisRange.lower, yAxisRange.upper); + + replot(); + + // We do not want to update the history, because there would be way too + // much history items, since this function is called upon mouse moving + // handling and not only during mouse release events. + // updateAxisRangeHistory(); +} + + +/*/js/ + * .replotWithAxisRangeX(lower, upper) + * + * Replot this plot widget with new key (X-axis) data range. + * + * lower: holding the start value of the range + * upper: holding the end value of the range + */ +//! Trigger a graph replot action with new x-axis range. +void +AbstractPlotWidget::replotWithAxisRangeX(double lower, double upper) +{ + xAxis->setRange(lower, upper); + replot(); +} - outputFileName = newFileName; - QString xyString = asXyText(); +/*/js/ + * .replotWithAxisRangeY(lower, upper) + * + * Replot this plot widget with new value (Y-axis) data range. + * + * lower: holding the start value of the range + * upper: holding the end value of the range + */ +//! Trigger a graph replot action with new y-axis range. +void +AbstractPlotWidget::replotWithAxisRangeY(double lower, double upper) +{ + yAxis->setRange(lower, upper); + replot(); +} - QFile file(outputFileName); - file.open(QIODevice::WriteOnly); - QTextStream out(&file); // we will serialize the data into the file - out << xyString; +//! Hide the selection line, the xDelta text and the zoom rectangle items. +void +AbstractPlotWidget::hideAllPlotItems() +{ + if(m_selectLine->visible()) + m_selectLine->setVisible(false); - file.close(); - } + if(m_xDeltaText->visible()) + m_xDeltaText->setVisible(false); + m_zoomRect->setVisible(false); +} - /*/js/ - * .exportPlotToFile(fileName, rangeStart, rangeEnd) - * - * Export plot data to a text file as a simple plot. Limit the data range to - * export using the numerical parameters. - * - * fileName: holding the file name - * rangeStart: holding the beginning of the range to be exported - * rangeEnd holding the end of the range to be exported - */ - //! Export plot data to a text file as a simple plot. - /*! - - Unlike the exportPlo() function, this function takes the name of the file in - which to export the data and the range that is required to be exported. This - function is useful in scripting. -*/ - void - AbstractPlotWidget::exportPlotToFile(const QString &fileName, - double start, double end) - { - if(m_isMultiGraph) - return; - // The user asks that the (that is not the whole set of data), but only - // the x,y plot for the current plot widget. This is the easiest solution. - // The only constraint is that we only export the data corresponding to - // the current X axis range. +//! Show the traces (vertical and horizontal). +void +AbstractPlotWidget::showTracers() +{ + m_tracersVisible = true; + m_vStartTracer->setVisible(true); + m_hStartTracer->setVisible(true); + m_endTracer->setVisible(true); + + // Force a replot to make sure the action is immediately visible by the + // user, even without moving the mouse. + replot(); +} - QString outputFileName = fileName; - if(outputFileName.isEmpty()) - { - outputFileName = m_fileName; +//! Hide the traces (vertical and horizontal). +void +AbstractPlotWidget::hideTracers() +{ + m_tracersVisible = false; + m_vStartTracer->setVisible(false); + m_hStartTracer->setVisible(false); + m_endTracer->setVisible(false); - outputFileName += ".xy"; + // Force a replot to make sure the action is immediately visible by the + // user, even without moving the mouse. + replot(); +} - QString newFileName = - QFileDialog::getSaveFileName(this, "Open file", outputFileName, - tr("Ascii (x,y) files (*.txt *.xy *.asc)")); - if(newFileName.isEmpty()) - return; +//! Tell if the current selection has a rectangular shape. +/*! - outputFileName = newFileName; - } + The goal here is to establish if the user is selecting a rectangle of enough + height to make a meaningful zoom operation so that we can switch from delta + line measurement display to actual rectangle zoom display. The criterion is + that the height of the selection must be at least 10% the height of the + plot. - // Get the pointer to the x-axis (key axis). + \return true if the selection looks like a rectangle, that is it has a + height at least 10% of the plot height. - QCPAxis *xAxis = graph()->keyAxis(); +*/ +bool +AbstractPlotWidget::isSelectionARectangle() +{ + // First get the height of the plot. + double plotHeight = yAxis->range().upper - yAxis->range().lower; - double rangeStart = start; - if(qIsNaN(rangeStart)) - { - rangeStart = xAxis->range().lower; - } + double heightDiff = fabs(m_startDragPoint.y() - m_currentDragPoint.y()); - double rangeEnd = end; + double heightDiffRatio = (heightDiff / plotHeight) * 100; - if(qIsNaN(rangeEnd)) - { - rangeEnd = xAxis->range().upper; - } + if(heightDiffRatio > 10) + return true; + return false; +} - // Remember that the data are like this in a QCPGraph: - // typedef QMap< double, QCPData > QCPDataMap - // and the double key of the map is the key of QCPData: - // QCPData(key, value). - QCPDataMap *data = graph()->data(); +//! Draw the zoom rectangle and actually zoom. +/*! - QList xValueList = data->keys(); + This action is triggered when the user drags the mouse left button over the + plot area. The rectangle drawn make for the new zoomed-in view. - QString outputString; +*/ +void +AbstractPlotWidget::drawRectangleAndZoom() +{ + // The user has drawn the mouse left button on the graph, which means he is + // willing to draw a zoom rectangle. - for(int iter = 0; iter < xValueList.size(); ++iter) - { - double xValue = xValueList.at(iter); - if(xValue >= rangeStart) - { - if(xValue <= rangeEnd) - { - double yValue = data->value(xValue).value; - - outputString += QString("%1 %2\n") - .arg(xValue, 0, 'f', 10) - .arg(yValue, 0, 'f', 10); - } - else - break; - } - } + if(m_selectLine->visible()) + m_selectLine->setVisible(false); - // Now craft a header that will identify clearly the data. The '#' is a - // comment prefix. + if(m_xDeltaText->visible()) + m_xDeltaText->setVisible(false); - QString header; + m_zoomRect->topLeft->setCoords(m_startDragPoint.x(), m_startDragPoint.y()); + m_zoomRect->bottomRight->setCoords(m_currentDragPoint.x(), + m_currentDragPoint.y()); - QFile file(outputFileName); + m_zoomRect->setVisible(true); - if(file.open(QIODevice::WriteOnly) == false) - { - qWarning() << __FILE__ << __LINE__ << __FUNCTION__ - << "Failed to export the plot because the file could not be opened."; + // qDebug() << __FILE__ << __LINE__ + // << "should be drawing a rectangle:" << m_startDragPoint.x() << + // m_startDragPoint.y() + // << m_currentDragPoint.x() << m_currentDragPoint.y(); - return; - } + replot(); +} - //qWarning() << "opened file with text:" << outputString; - QTextStream out(&file); // we will serialize the data into the file - out << outputString; +//! Draw the horizontal x-delta line and write the delta value. +/*! - file.close(); - } + When the user drags the left mouse button in the horizontal direction, with + almost no vertical movement, draw the line that span the x-axis interval + spanning the mouse dragging movement and print the delta value. + This is typically used by the user willing to measure the distance between + two peaks in the graph. - /*/js/ - * .savePlotToGraphicsFile() - * - * Open the graphics export configuration dialog window. - */ - //! Open the graphics export configuration dialog window. - bool - AbstractPlotWidget::savePlotToGraphicsFile() - { - qDebug() << __FILE__ << __LINE__ << __FUNCTION__ << "()"; +*/ +void +AbstractPlotWidget::drawXDeltaLineAndMeasure() +{ + // The user has drawn the mouse left button on the graph in such a way + // that the xDelta is big and the yDelta is almost nothing, that + // means that he does not want to draw a rectangle but a line to + // measure the delta between two points of the graph. - SaveToGraphicsFileDlg dlg(this, this, "mineXpert"); + m_zoomRect->setVisible(false); - if(QDialog::Accepted == dlg.exec()) - return true; - else - return false; - } + // Note that the m_xRangeMin, m_xRangeMax and m_xDelta values were set + // in the mouse move with dragging on handler. They are *sorted* such that + // the m_xRangeMin contains systematically the lowest value. m_xDelta is + // already stored as abs(). + double m_xDeltaHalf = m_xDelta / 2; - /*/js/ - * .saveToPdfFile(fileName, noCosmeticPen, width, height, pdfCreator, title) - * - * Save this plot widget as a PDF file graphics. - * - * fileName: holding the file name - * noCosmeticPen: that tells if pen optimizations should be performed - * width: holding the size of the graphics file in pixels - * height: holding the size of the graphics file in pixels - * pdfCreator: holding the name of the creator of the PDF file - * title: holding the title of the graphics file - */ - //! Save this plot widget as a PDF file graphics. - bool - AbstractPlotWidget::savePlotToPdfFile(const QString &fileName, - bool noCosmeticPen, int width, int height, - const QString &pdfCreator, const QString &title) - { - return savePdf(fileName, noCosmeticPen, width, height, - pdfCreator, title); - } + m_xDeltaText->position->setCoords(m_xRangeMin + m_xDeltaHalf, + m_currentDragPoint.y()); + m_xDeltaText->setText(QString("%1").arg(m_xDelta, 0, 'f', 3)); + m_xDeltaText->setFont(QFont(font().family(), 7)); - /*/js/ - * .keys() - * - * Return an of values representing the keys of the data plotted. - */ - //! Return a list of double values representing the keys of the data plotted. - QList - AbstractPlotWidget::keys() - { - QList keyList; + m_xDeltaText->setVisible(true); - if(m_isMultiGraph) - { - qDebug() << __FILE__ << __LINE__ << __FUNCTION__ - << "Cannot select keys from multiGraph plot."; + // If we do not use the m_xRangeMin/Max values, it is because they are + // sorted, and we do not want, we want the user the actually see the real + // starting drag point and the real current drag point. + QString statusBarMsg = QString("(%1,%2)->(%3,%4) ; Delta: %5") + .arg(m_startDragPoint.x(), 0, 'f', 3) + .arg(m_startDragPoint.y(), 0, 'f', 3) + .arg(m_currentDragPoint.x(), 0, 'f', 3) + .arg(m_currentDragPoint.y(), 0, 'f', 3) + .arg(m_xDelta, 0, 'f', 6); - return keyList; - } + emit updateStatusBarSignal(statusBarMsg); - QCPDataMap *data = graph()->data(); + if(!m_selectLine->visible()) + m_selectLine->setVisible(true); - //qDebug() << __FILE__ << __LINE__ << __FUNCTION__ - //<< "keys:" << data->keys(); + m_selectLine->start->setCoords(m_startDragPoint.x(), m_startDragPoint.y()); + // But we want the line to be horizontal, thus we keep the original y + // value. + m_selectLine->end->setCoords(m_currentDragPoint.x(), m_startDragPoint.y()); - return data->keys(); - } + // Also, we do not want arrows, because we are not integrating anything + // here. + m_selectLine->setHead(QCPLineEnding::esNone); + m_selectLine->setTail(QCPLineEnding::esNone); + replot(); +} - /*/js/ - * .values() - * - * Return an of values representing the values of the data plotted. - */ - //! Return a list of double values representing the values of the data plotted. - QList - AbstractPlotWidget::values() - { - QList valueList; - if(m_isMultiGraph) - { - qDebug() << __FILE__ << __LINE__ << __FUNCTION__ - << "Cannot select keys from multiGraph plot."; +//! Draw the horizontal x-delta line and write the delta value. +/*! - return valueList; - } + When the user drags the right mouse button in the horizontal direction, with + almost no vertical movement, draw the line that span the x-axis interval + spanning the mouse dragging movement and print the delta value. Show line + endings for the delta measurement line because this mouse drag might be for + an integration (this is only known by looking at the \c m_pressedKeyCode + value and checking if it listed in \c m_regQtKeyCodeList. - QCPDataMap *data = graph()->data(); - QList keyList = data->keys(); + This is typically used by the user willing to integrate mass data in the + range selected. - for(int iter = 0; iter < keyList.size(); ++iter) - { - double xValue = keyList.at(iter); - valueList.append(data->value(xValue).value); - } +*/ +void +AbstractPlotWidget::drawXDeltaLineForZoomOrIntegration() +{ + // When the user draws a right-button line, then she is willing to select + // an X span to integrate. Depending on the keyboard key that is pressed + // that integration does one thing or another. This is only known when the + // mouse button is released. So we do not trigger the integration here. - //qDebug() << __FILE__ << __LINE__ << __FUNCTION__ - //<< "values:" << valueList; + m_zoomRect->setVisible(false); - return valueList; - } + // We also want to show the span as a text item. + // Note that the m_xRangeMin, m_xRangeMax and m_xDelta values were set + // in the mouse move with dragging on handler. They are *sorted* such that + // the m_xRangeMin contains systematically the lowest value. m_xDelta is + // already stored as abs(). - //! Set the last TIC intensity value. - void - AbstractPlotWidget::setLastTicIntensity(double value) - { - m_lastTicIntensity = value; - } + double m_xDeltaHalf = m_xDelta / 2; + m_xDeltaText->position->setCoords(m_xRangeMin + m_xDeltaHalf, + m_currentDragPoint.y()); + m_xDeltaText->setText(QString("%1").arg(m_xDelta, 0, 'f', 3)); - /*/js/ - * .lastTicIntensity() - * - * Return the last TIC intensity value that was computed. - */ - //! Return the last TIC intensity value that was computed. - double - AbstractPlotWidget::lastTicIntensity(void) - { - return m_lastTicIntensity; - } + m_xDeltaText->setFont(QFont(font().family(), 7)); + m_xDeltaText->setVisible(true); - /*/js/ - * .trace() - * - * Return a Trace object initialized with the data in this plot widget. - */ - //! Return a Trace instance initialized with the data in this plot widget - msXpSlibmass::Trace - AbstractPlotWidget::trace() - { - if(m_isMultiGraph) - { - qDebug() << __FILE__ << __LINE__ << __FUNCTION__ - << "Cannot select keys from multiGraph plot."; + if(!m_selectLine->visible()) + m_selectLine->setVisible(true); - return msXpSlibmass::Trace(); - } + m_selectLine->start->setCoords(m_startDragPoint.x(), m_startDragPoint.y()); - msXpSlibmass::Trace trace; + // We only want the arrows when we are preparing an integration + // operation. So check if one corresponding key is pressed. - QCPDataMap *p_data = graph()->data(); + if(m_regQtKeyCodeMap.contains(m_pressedKeyCode)) + { + m_selectLine->setHead(QCPLineEnding::esSpikeArrow); + m_selectLine->setTail(QCPLineEnding::esSpikeArrow); + } + else + { + m_selectLine->setHead(QCPLineEnding::esNone); + m_selectLine->setTail(QCPLineEnding::esNone); + } - QMapIteratori(*p_data); + // But we want the line to be horizontal, thus we keep the original y + // value. + m_selectLine->end->setCoords(m_currentDragPoint.x(), m_startDragPoint.y()); - while (i.hasNext()) - { - i.next(); + replot(); - msXpSlibmass::DataPoint *dataPoint = - new msXpSlibmass::DataPoint(i.value().key, i.value().value); + // But we also want to update the status bar with the current cursor + // positon and also the delta that the cursor drag is spanning. - trace.append(dataPoint); - } + QString statusBarMsg = QString("(%1,%2)->(%3,%4) ; Delta: %5") + .arg(m_startDragPoint.x()) + .arg(m_startDragPoint.y()) + .arg(m_currentDragPoint.x()) + .arg(m_currentDragPoint.y()) + .arg(m_xDelta, 0, 'f', 6); - return trace; - } + emit updateStatusBarSignal(statusBarMsg); +} - //! Trigger a graph replot action with new x-axis and y-axis ranges. - void - AbstractPlotWidget::replotWithAxisRange(QCPRange xAxisRange, - QCPRange yAxisRange, int whichAxis) - { - if(whichAxis & X_AXIS) - xAxis->setRange(xAxisRange.lower, xAxisRange.upper); - if(whichAxis & Y_AXIS) - yAxis->setRange(yAxisRange.lower, yAxisRange.upper); - - replot(); - - // We do not want to update the history, because there would be way too - // much history items, since this function is called upon mouse moving - // handling and not only during mouse release events. - // updateAxisRangeHistory(); - } +//! Tell if the mouse click was right the one of the axes of the plot. +bool +AbstractPlotWidget::isClickOntoAnyAxis(const QPointF &mousePoint) +{ + if(isClickOntoXAxis(mousePoint) || isClickOntoYAxis(mousePoint)) + return true; + return false; +} - /*/js/ - * .replotWithAxisRangeX(lower, upper) - * - * Replot this plot widget with new key (X-axis) data range. - * - * lower: holding the start value of the range - * upper: holding the end value of the range - */ - //! Trigger a graph replot action with new x-axis range. - void - AbstractPlotWidget::replotWithAxisRangeX(double lower, double upper) - { - xAxis->setRange(lower, upper); - replot(); - } +//! Tell if the mouse click was right on the x-axis. +bool +AbstractPlotWidget::isClickOntoXAxis(const QPointF &mousePoint) +{ + QCPLayoutElement *layoutElement = layoutElementAt(mousePoint); - /*/js/ - * .replotWithAxisRangeY(lower, upper) - * - * Replot this plot widget with new value (Y-axis) data range. - * - * lower: holding the start value of the range - * upper: holding the end value of the range - */ - //! Trigger a graph replot action with new y-axis range. - void - AbstractPlotWidget::replotWithAxisRangeY(double lower, double upper) - { - yAxis->setRange(lower, upper); - replot(); - } + if(layoutElement && + layoutElement == dynamic_cast(axisRect())) + { + // The graph is *inside* the axisRect that is the outermost envelope of + // the graph. Thus, if we want to know if the click was indeed on an + // axis, we need to check what selectable part of the the axisRect we + // were + // clicking: + QCPAxis::SelectablePart selectablePart; + + selectablePart = xAxis->getPartAt(mousePoint); + + if(selectablePart == QCPAxis::spAxisLabel || + selectablePart == QCPAxis::spAxis || + selectablePart == QCPAxis::spTickLabels) + return true; + } + return false; +} + + +//! Tell if the mouse click was right on the y-axis. +bool +AbstractPlotWidget::isClickOntoYAxis(const QPointF &mousePoint) +{ + QCPLayoutElement *layoutElement = layoutElementAt(mousePoint); - - //! Hide the selection line, the xDelta text and the zoom rectangle items. - void - AbstractPlotWidget::hideAllPlotItems() - { - if(m_selectLine->visible()) - m_selectLine->setVisible(false); - - if(m_xDeltaText->visible()) - m_xDeltaText->setVisible(false); - - m_zoomRect->setVisible(false); - } - - - //! Show the traces (vertical and horizontal). - void - AbstractPlotWidget::showTracers() - { - m_tracersVisible = true; - m_vStartTracer->setVisible(true); - m_hStartTracer->setVisible(true); - m_endTracer->setVisible(true); - - // Force a replot to make sure the action is immediately visible by the - // user, even without moving the mouse. - replot(); - } - - - //! Hide the traces (vertical and horizontal). - void - AbstractPlotWidget::hideTracers() - { - m_tracersVisible = false; - m_vStartTracer->setVisible(false); - m_hStartTracer->setVisible(false); - m_endTracer->setVisible(false); - - // Force a replot to make sure the action is immediately visible by the - // user, even without moving the mouse. - replot(); - } - - - //! Tell if the current selection has a rectangular shape. - /*! - - The goal here is to establish if the user is selecting a rectangle of enough - height to make a meaningful zoom operation so that we can switch from delta - line measurement display to actual rectangle zoom display. The criterion is - that the height of the selection must be at least 10% the height of the - plot. - - \return true if the selection looks like a rectangle, that is it has a - height at least 10% of the plot height. - -*/ - bool - AbstractPlotWidget::isSelectionARectangle() - { - // First get the height of the plot. - double plotHeight = yAxis->range().upper - yAxis->range().lower; - - double heightDiff = fabs(m_startDragPoint.y() - m_currentDragPoint.y()); - - double heightDiffRatio = (heightDiff / plotHeight) * 100; - - if(heightDiffRatio > 10) - return true; - - return false; - } - - - //! Draw the zoom rectangle and actually zoom. - /*! - - This action is triggered when the user drags the mouse left button over the - plot area. The rectangle drawn make for the new zoomed-in view. - -*/ - void - AbstractPlotWidget::drawRectangleAndZoom() - { - // The user has drawn the mouse left button on the graph, which means he is - // willing to draw a zoom rectangle. - - - if(m_selectLine->visible()) - m_selectLine->setVisible(false); - - if(m_xDeltaText->visible()) - m_xDeltaText->setVisible(false); - - m_zoomRect->topLeft->setCoords(m_startDragPoint.x(), m_startDragPoint.y()); - m_zoomRect->bottomRight->setCoords(m_currentDragPoint.x(), - m_currentDragPoint.y()); - - m_zoomRect->setVisible(true); - - // qDebug() << __FILE__ << __LINE__ - // << "should be drawing a rectangle:" << m_startDragPoint.x() << - // m_startDragPoint.y() - // << m_currentDragPoint.x() << m_currentDragPoint.y(); - - replot(); - } - - - //! Draw the horizontal x-delta line and write the delta value. - /*! - - When the user drags the left mouse button in the horizontal direction, with - almost no vertical movement, draw the line that span the x-axis interval - spanning the mouse dragging movement and print the delta value. - - This is typically used by the user willing to measure the distance between - two peaks in the graph. - -*/ - void - AbstractPlotWidget::drawXDeltaLineAndMeasure() - { - // The user has drawn the mouse left button on the graph in such a way - // that the xDelta is big and the yDelta is almost nothing, that - // means that he does not want to draw a rectangle but a line to - // measure the delta between two points of the graph. - - m_zoomRect->setVisible(false); - - // Note that the m_xRangeMin, m_xRangeMax and m_xDelta values were set - // in the mouse move with dragging on handler. They are *sorted* such that - // the m_xRangeMin contains systematically the lowest value. m_xDelta is - // already stored as abs(). - - double m_xDeltaHalf = m_xDelta / 2; - - m_xDeltaText->position->setCoords(m_xRangeMin + m_xDeltaHalf, - m_currentDragPoint.y()); - m_xDeltaText->setText(QString("%1").arg(m_xDelta, 0, 'f', 3)); - - m_xDeltaText->setFont(QFont(font().family(), 7)); - - m_xDeltaText->setVisible(true); - - // If we do not use the m_xRangeMin/Max values, it is because they are - // sorted, and we do not want, we want the user the actually see the real - // starting drag point and the real current drag point. - QString statusBarMsg = QString("(%1,%2)->(%3,%4) ; Delta: %5") - .arg(m_startDragPoint.x(), 0, 'f', 3) - .arg(m_startDragPoint.y(), 0, 'f', 3) - .arg(m_currentDragPoint.x(), 0, 'f', 3) - .arg(m_currentDragPoint.y(), 0, 'f', 3) - .arg(m_xDelta, 0, 'f', 6); - - emit updateStatusBarSignal(statusBarMsg); - - if(!m_selectLine->visible()) - m_selectLine->setVisible(true); - - m_selectLine->start->setCoords(m_startDragPoint.x(), m_startDragPoint.y()); - // But we want the line to be horizontal, thus we keep the original y - // value. - m_selectLine->end->setCoords(m_currentDragPoint.x(), m_startDragPoint.y()); - - // Also, we do not want arrows, because we are not integrating anything - // here. - m_selectLine->setHead(QCPLineEnding::esNone); - m_selectLine->setTail(QCPLineEnding::esNone); - - replot(); - } - - - //! Draw the horizontal x-delta line and write the delta value. - /*! - - When the user drags the right mouse button in the horizontal direction, with - almost no vertical movement, draw the line that span the x-axis interval - spanning the mouse dragging movement and print the delta value. Show line - endings for the delta measurement line because this mouse drag might be for - an integration (this is only known by looking at the \c m_pressedKeyCode - value and checking if it listed in \c m_regQtKeyCodeList. - - This is typically used by the user willing to integrate mass data in the - range selected. - -*/ - void - AbstractPlotWidget::drawXDeltaLineForZoomOrIntegration() - { - // When the user draws a right-button line, then she is willing to select - // an X span to integrate. Depending on the keyboard key that is pressed - // that integration does one thing or another. This is only known when the - // mouse button is released. So we do not trigger the integration here. - - m_zoomRect->setVisible(false); - - // We also want to show the span as a text item. - - // Note that the m_xRangeMin, m_xRangeMax and m_xDelta values were set - // in the mouse move with dragging on handler. They are *sorted* such that - // the m_xRangeMin contains systematically the lowest value. m_xDelta is - // already stored as abs(). - - double m_xDeltaHalf = m_xDelta / 2; - - m_xDeltaText->position->setCoords(m_xRangeMin + m_xDeltaHalf, - m_currentDragPoint.y()); - m_xDeltaText->setText(QString("%1").arg(m_xDelta, 0, 'f', 3)); - - m_xDeltaText->setFont(QFont(font().family(), 7)); - - m_xDeltaText->setVisible(true); - - if(!m_selectLine->visible()) - m_selectLine->setVisible(true); - - m_selectLine->start->setCoords(m_startDragPoint.x(), m_startDragPoint.y()); - - // We only want the arrows when we are preparing an integration - // operation. So check if one corresponding key is pressed. - - if(m_regQtKeyCodeMap.contains(m_pressedKeyCode)) - { - m_selectLine->setHead(QCPLineEnding::esSpikeArrow); - m_selectLine->setTail(QCPLineEnding::esSpikeArrow); - } - else - { - m_selectLine->setHead(QCPLineEnding::esNone); - m_selectLine->setTail(QCPLineEnding::esNone); - } - - // But we want the line to be horizontal, thus we keep the original y - // value. - m_selectLine->end->setCoords(m_currentDragPoint.x(), m_startDragPoint.y()); - - replot(); - - // But we also want to update the status bar with the current cursor - // positon and also the delta that the cursor drag is spanning. - - QString statusBarMsg = QString("(%1,%2)->(%3,%4) ; Delta: %5") - .arg(m_startDragPoint.x()) - .arg(m_startDragPoint.y()) - .arg(m_currentDragPoint.x()) - .arg(m_currentDragPoint.y()) - .arg(m_xDelta, 0, 'f', 6); - - emit updateStatusBarSignal(statusBarMsg); - } - - - //! Tell if the mouse click was right the one of the axes of the plot. - bool - AbstractPlotWidget::isClickOntoAnyAxis(const QPointF &mousePoint) - { - if(isClickOntoXAxis(mousePoint) || isClickOntoYAxis(mousePoint)) - return true; - - return false; - } - - - //! Tell if the mouse click was right on the x-axis. - bool - AbstractPlotWidget::isClickOntoXAxis(const QPointF &mousePoint) - { - QCPLayoutElement *layoutElement = layoutElementAt(mousePoint); - - if(layoutElement && - layoutElement == dynamic_cast(axisRect())) - { - // The graph is *inside* the axisRect that is the outermost envelope of - // the graph. Thus, if we want to know if the click was indeed on an - // axis, we need to check what selectable part of the the axisRect we - // were - // clicking: - QCPAxis::SelectablePart selectablePart; - - selectablePart = xAxis->getPartAt(mousePoint); - - if(selectablePart == QCPAxis::spAxisLabel || - selectablePart == QCPAxis::spAxis || - selectablePart == QCPAxis::spTickLabels) - return true; - } - return false; - } - - - //! Tell if the mouse click was right on the y-axis. - bool - AbstractPlotWidget::isClickOntoYAxis(const QPointF &mousePoint) - { - QCPLayoutElement *layoutElement = layoutElementAt(mousePoint); - - if(layoutElement && - layoutElement == dynamic_cast(axisRect())) - { - // The graph is *inside* the axisRect that is the outermost envelope of - // the graph. Thus, if we want to know if the click was indeed on an - // axis, we need to check what selectable part of the the axisRect we - // were - // clicking: - QCPAxis::SelectablePart selectablePart; - - selectablePart = yAxis->getPartAt(mousePoint); - - if(selectablePart == QCPAxis::spAxisLabel || - selectablePart == QCPAxis::spAxis || - selectablePart == QCPAxis::spTickLabels) - return true; - } - return false; - } - - - //! Calcuted delta values for both x/y axes and sort the values. - /*! - - The values are sorted so that the min value is always the lower value and - the max value is always the greater value. This is because the user might - perform a mouse dragging operation in reverse direction, that is from the - right of the plot to the left of that plot (x-axis) or from the top of the - plot to the bottom of the plot (y-axis), thus from greater values to lower - values. - -*/ - void - AbstractPlotWidget::calculateSortedDragDeltas() - { - m_xRangeMin = 0; - m_xRangeMax = 0; - - m_yRangeMin = 0; - m_yRangeMax = 0; - - double deltaX = m_currentDragPoint.x() - m_startDragPoint.x(); - if(deltaX < 0) - { - m_xRangeMin = m_currentDragPoint.x(); - m_xRangeMax = m_startDragPoint.x(); - } - else - { - m_xRangeMin = m_startDragPoint.x(); - m_xRangeMax = m_currentDragPoint.x(); - } - - double deltaY = m_currentDragPoint.y() - m_startDragPoint.y(); - if(deltaY < 0) - { - m_yRangeMin = m_currentDragPoint.y(); - m_yRangeMax = m_startDragPoint.y(); - } - else - { - m_yRangeMin = m_startDragPoint.y(); - m_yRangeMax = m_currentDragPoint.y(); - } - - return; - } - - //! Rescale the x/y axes as a result of user interaction. - /*! - - Depending on the keyboard key that is pressed, axis rescaling can be carried - over in different ways: - - - full scale on both axes - - full scale only on one of the axes + if(layoutElement && + layoutElement == dynamic_cast(axisRect())) + { + // The graph is *inside* the axisRect that is the outermost envelope of + // the graph. Thus, if we want to know if the click was indeed on an + // axis, we need to check what selectable part of the the axisRect we + // were + // clicking: + QCPAxis::SelectablePart selectablePart; + + selectablePart = yAxis->getPartAt(mousePoint); + + if(selectablePart == QCPAxis::spAxisLabel || + selectablePart == QCPAxis::spAxis || + selectablePart == QCPAxis::spTickLabels) + return true; + } + return false; +} + + +//! Calcuted delta values for both x/y axes and sort the values. +/*! + + The values are sorted so that the min value is always the lower value and + the max value is always the greater value. This is because the user might + perform a mouse dragging operation in reverse direction, that is from the + right of the plot to the left of that plot (x-axis) or from the top of the + plot to the bottom of the plot (y-axis), thus from greater values to lower + values. */ - void - AbstractPlotWidget::axisRescale() - { - // Get the current x lower/upper range. - double xLower = xAxis->range().lower; - double xUpper = xAxis->range().upper; - - // Get the current y lower/upper range. - double yLower = yAxis->range().lower; - double yUpper = yAxis->range().upper; - - - if(m_clickWasOnXAxis) - { - // We are changing the range of the X axis. - - // What is the x delta ? - double xDelta = m_currentDragPoint.x() - m_startDragPoint.x(); - - if(xDelta < 0) - { - // The dragging operation was from right to left, we are enlarging - // the range (thus, we are unzooming the view, since the widget - // always has the same size). - - xAxis->setRange(xLower, xUpper + fabs(xDelta)); - } - else - { - // The dragging operation was from left to right, we are reducing - // the range (thus, we are zooming the view, since the widget - // always has the same size). - - xAxis->setRange(xLower, xUpper - fabs(xDelta)); - } - - // We may either leave the scale of the Y axis as is (default) or - // the user may want an automatic scale of the Y axis such that the - // data displayed in the new X axis range are full scale on the Y - // axis. For this, the Shift modifier key should be pressed. - - Qt::KeyboardModifiers modifiers = - QGuiApplication::queryKeyboardModifiers(); - - if(modifiers & Qt::ShiftModifier) - { - // In this case, we want to make a rescale of the Y axis such that - // it displays full scale the data in the current X axis range only. - double min = 0; - double max = 0; - - yMinMaxOnXAxisCurrentRange(min, max); - - yAxis->setRange(min, max); - } - // else, do leave the Y axis range unchanged. - } - // End of - // if(m_clickWasOnXAxis) - else // that is, if(m_clickWasOnYAxis) - { - // We are changing the range of the Y axis. - - // What is the y delta ? - double yDelta = m_currentDragPoint.y() - m_startDragPoint.y(); - - if(yDelta < 0) - { - // The dragging operation was from top to bottom, we are enlarging - // the range (thus, we are unzooming the view, since the widget - // always has the same size). - - yAxis->setRange(yLower, yUpper + fabs(yDelta)); - } - else - { - // The dragging operation was from bottom to top, we are reducing - // the range (thus, we are zooming the view, since the widget - // always has the same size). - - yAxis->setRange(yLower, yUpper - fabs(yDelta)); - } - } - // End of - // else // that is, if(m_clickWasOnYAxis) - - replot(); - } - - - //! Determine the minimum and maximum y-axis values in the plot. - /*! - - The values are determined for the current x-axis range. +void +AbstractPlotWidget::calculateSortedDragDeltas() +{ + m_xRangeMin = 0; + m_xRangeMax = 0; - If \p g is nullptr, then graph() is used as the graph from which to read the - data. + m_yRangeMin = 0; + m_yRangeMax = 0; - \param min reference to the double value in which to set the minimum y-axis - value. + double deltaX = m_currentDragPoint.x() - m_startDragPoint.x(); + if(deltaX < 0) + { + m_xRangeMin = m_currentDragPoint.x(); + m_xRangeMax = m_startDragPoint.x(); + } + else + { + m_xRangeMin = m_startDragPoint.x(); + m_xRangeMax = m_currentDragPoint.x(); + } + + double deltaY = m_currentDragPoint.y() - m_startDragPoint.y(); + if(deltaY < 0) + { + m_yRangeMin = m_currentDragPoint.y(); + m_yRangeMax = m_startDragPoint.y(); + } + else + { + m_yRangeMin = m_startDragPoint.y(); + m_yRangeMax = m_currentDragPoint.y(); + } + + return; +} + +//! Rescale the x/y axes as a result of user interaction. +/*! + + Depending on the keyboard key that is pressed, axis rescaling can be carried + over in different ways: - \param max reference to the double value in which to set the maximum y-axis - value. + - full scale on both axes + - full scale only on one of the axes */ - void - AbstractPlotWidget::yMinMaxOnXAxisCurrentRange(double &min, double &max, - QCPGraph *g) - { - // We need to find the min and max Y values in the min->max range of the X - // axis. - QCPDataMap *data = Q_NULLPTR; - - if(g == Q_NULLPTR) - data = graph()->data(); - else - data = g->data(); - - double xAxisRangeLower = xAxis->range().lower; - double xAxisRangeUpper = xAxis->range().upper; - - // qDebug() << __FILE__ << __LINE__ - // << "xAxisRangeLower:" << xAxisRangeLower << "xAxisRangeUpper: " << - // xAxisRangeUpper; - - double tempY = 0; - double minY = 0; - double maxY = 0; - - int iteration = 0; - - QMapIterator iterator(*data); - - while(iterator.hasNext()) - { - iterator.next(); +void +AbstractPlotWidget::axisRescale() +{ + // Get the current x lower/upper range. + double xLower = xAxis->range().lower; + double xUpper = xAxis->range().upper; + + // Get the current y lower/upper range. + double yLower = yAxis->range().lower; + double yUpper = yAxis->range().upper; + + + if(m_clickWasOnXAxis) + { + // We are changing the range of the X axis. + + // What is the x delta ? + double xDelta = m_currentDragPoint.x() - m_startDragPoint.x(); + + if(xDelta < 0) + { + // The dragging operation was from right to left, we are enlarging + // the range (thus, we are unzooming the view, since the widget + // always has the same size). + + xAxis->setRange(xLower, xUpper + fabs(xDelta)); + } + else + { + // The dragging operation was from left to right, we are reducing + // the range (thus, we are zooming the view, since the widget + // always has the same size). + + xAxis->setRange(xLower, xUpper - fabs(xDelta)); + } + + // We may either leave the scale of the Y axis as is (default) or + // the user may want an automatic scale of the Y axis such that the + // data displayed in the new X axis range are full scale on the Y + // axis. For this, the Shift modifier key should be pressed. + + Qt::KeyboardModifiers modifiers = + QGuiApplication::queryKeyboardModifiers(); + + if(modifiers & Qt::ShiftModifier) + { + // In this case, we want to make a rescale of the Y axis such that + // it displays full scale the data in the current X axis range only. + double min = 0; + double max = 0; + + yMinMaxOnXAxisCurrentRange(min, max); + + yAxis->setRange(min, max); + } + // else, do leave the Y axis range unchanged. + } + // End of + // if(m_clickWasOnXAxis) + else // that is, if(m_clickWasOnYAxis) + { + // We are changing the range of the Y axis. + + // What is the y delta ? + double yDelta = m_currentDragPoint.y() - m_startDragPoint.y(); + + if(yDelta < 0) + { + // The dragging operation was from top to bottom, we are enlarging + // the range (thus, we are unzooming the view, since the widget + // always has the same size). + + yAxis->setRange(yLower, yUpper + fabs(yDelta)); + } + else + { + // The dragging operation was from bottom to top, we are reducing + // the range (thus, we are zooming the view, since the widget + // always has the same size). + + yAxis->setRange(yLower, yUpper - fabs(yDelta)); + } + } + // End of + // else // that is, if(m_clickWasOnYAxis) + + replot(); +} + + +//! Determine the minimum and maximum y-axis values in the plot. +/*! + + The values are determined for the current x-axis range. + + If \p g is nullptr, then graph() is used as the graph from which to read the + data. + + \param min reference to the double value in which to set the minimum y-axis + value. + + \param max reference to the double value in which to set the maximum y-axis + value. + +*/ +void +AbstractPlotWidget::yMinMaxOnXAxisCurrentRange(double &min, + double &max, + QCPGraph *g) +{ + // We need to find the min and max Y values in the min->max range of the X + // axis. + QSharedPointer p_graphDataContainer; - double currentKey = iterator.key(); + if(g == Q_NULLPTR) + p_graphDataContainer = graph()->data(); + else + p_graphDataContainer = g->data(); - if(currentKey < xAxisRangeLower || currentKey > xAxisRangeUpper) - continue; + double xAxisRangeLower = xAxis->range().lower; + double xAxisRangeUpper = xAxis->range().upper; - tempY = iterator.value().value; + // qDebug() << __FILE__ << __LINE__ + // << "xAxisRangeLower:" << xAxisRangeLower << "xAxisRangeUpper: " << + // xAxisRangeUpper; - // qDebug() << __FILE__ << __LINE__ - // << "currentKey: " << currentKey << "tempY: " << tempY; + double tempY = 0; + double minY = 0; + double maxY = 0; - if(!iteration) - { + bool firstIteration = true; - // This is the first iteration, use the values to seed the comparison - // system. + auto beginIt = + p_graphDataContainer->findBegin(xAxisRangeLower, /*expandedRange*/ true); + auto endIt = + p_graphDataContainer->findEnd(xAxisRangeUpper, /*expandedRange*/ true); - minY = maxY = tempY; - ++iteration; - } - else - { - if(tempY > maxY) - maxY = tempY; - else if(tempY < minY) - minY = tempY; - } - } + for(auto iter = beginIt; iter != endIt; ++iter) + { + tempY = iter->value; - min = minY; - max = maxY; - } + // qDebug() << __FILE__ << __LINE__ + // << "currentKey: " << currentKey << "tempY: " << tempY; + if(firstIteration) + { - //! Get the value corresponding to key \p k in graph \p g. - /*! + // This is the first iteration, use the values to seed the + // comparison + // system. - The \p g pointer cannot be nullptr. + minY = maxY = tempY; + firstIteration = false; + } + else + { + if(tempY > maxY) + maxY = tempY; + else if(tempY < minY) + minY = tempY; + } + } - \param k key value (x-axis value) for which to get the value (y-axis - corresponding value). + min = minY; + max = maxY; +} - \param g pointer to the graph in which to peek for the value. - \return double value containing the value corresponding to key \p k. +//! Get the value corresponding to key \p k in graph \p g. +/*! -*/ - double - AbstractPlotWidget::getYatX(double k, QCPGraph *g) - { - if(g == Q_NULLPTR) - qFatal("Fatal error at %s@%d -- %s. " - "Pointer cannot be nullptr." - "Program aborted.", - __FILE__, __LINE__, __FUNCTION__); - - QCPItemTracer tracer(this); - tracer.setGraph(g); - tracer.setInterpolating(true); - tracer.setGraphKey(k); - tracer.updatePosition(); - - return tracer.position->value(); - } + The \p g pointer cannot be nullptr. + \param k key value (x-axis value) for which to get the value (y-axis + corresponding value). - /*/js/ - * .getYatX(x) - * - * get the value at key x. - * - * x: holding the X-axis key for which the value is returned. - */ - //! Get the value corresponding to key \p k. - /*! - - The value is searched in the default graph of this plot widget: graph(). + \param g pointer to the graph in which to peek for the value. - \param k key value (x-axis value) for which to get the value (y-axis - corresponding value). + \return double value containing the value corresponding to key \p k. - \return double value containing the value corresponding to key \p k. */ - double - AbstractPlotWidget::getYatX(double x) - { - return getYatX(x, graph()); - } - - - //! Handle mouse movements, in particular record all the last visited points. - /*! - - This function is reponsible for storing at each time the last visited point - in the graph. Here, point is intended as any x/y coordinate in the plot - widget viewport, not a graph point. - - The stored values are then the basis for a large set of calculations - throughout all the plot widget. - - \param pointer to QMouseEvent from which to retrieve the coordinates of the - visited viewport points. -*/ - void - AbstractPlotWidget::mouseMoveHandler(QMouseEvent *event) - { - // Whatever happens, we want to store the plot coordinates of the current - // mouse cursor position (will be useful of the label feature). - QPointF mousePoint = event->localPos(); - - m_lastMousedPlotPoint.setX(xAxis->pixelToCoord(mousePoint.x())); - m_lastMousedPlotPoint.setY(yAxis->pixelToCoord(mousePoint.y())); - - // qDebug() << __FILE__ << __LINE__ - // << "last moused plot point: (" << m_lastMousedPlotPoint.x() - // << "," << m_lastMousedPlotPoint.y() << ")"; - - if(event->buttons() != Qt::LeftButton && - event->buttons() != Qt::RightButton) - { - m_isDragging = false; - - // We are not dragging the mouse (no button pressed), simply show the - // x,y coordinates in the status bar. - QString statusBarMsg = QString("(%1 , %2)") - .arg(m_lastMousedPlotPoint.x()) - .arg(m_lastMousedPlotPoint.y()); - - emit updateStatusBarSignal(statusBarMsg); - - // We are not dragging, so we only show the start tracer lines. - m_endTracer->setVisible(false); - - // Only bother with the tracers if the user wants them to be visible. - if(m_tracersVisible) - { - m_vStartTracer->setVisible(true); - m_vStartTracer->start->setCoords(m_lastMousedPlotPoint.x(), - yAxis->range().upper); - - m_vStartTracer->end->setCoords(m_lastMousedPlotPoint.x(), - yAxis->range().lower); - - m_hStartTracer->setVisible(true); - m_hStartTracer->start->setCoords(xAxis->range().lower, - m_lastMousedPlotPoint.y()); - - m_hStartTracer->end->setCoords(xAxis->range().upper, - m_lastMousedPlotPoint.y()); - - replot(); - } - - event->accept(); - - return; - } - - // If we are here, that means that one of the buttons was pressed, that is - // we are dragging the mouse. - // - m_isDragging = true; - - // Now store the mouse position data into the the current drag point - // member datum, that will be used in countless occasions later. - m_currentDragPoint = m_lastMousedPlotPoint; - - // Now that we know the current position, we can compute the X-axis range: - - double tempXmin = m_startDragPoint.x(); - double tempXmax = m_currentDragPoint.x(); - - // Compute the xAxis differential: - - m_xDelta = tempXmax - tempXmin; - if(m_xDelta < 0) - { - m_xRangeMin = tempXmax; - m_xRangeMax = tempXmin; - } - else - { - m_xRangeMin = tempXmin; - m_xRangeMax = tempXmax; - } - - // We do not need the delta sign anymore: - m_xDelta = fabs(m_xDelta); - - // Same with the Y-axis range: - - double tempYmin = m_startDragPoint.y(); - double tempYmax = m_currentDragPoint.y(); - - // Compute the yAxis differential: - - m_yDelta = tempYmax - tempYmin; - if(m_yDelta < 0) - { - m_yRangeMin = tempYmax; - m_yRangeMax = tempYmin; - } - else - { - m_yRangeMin = tempYmin; - m_yRangeMax = tempYmax; - } - - // We do not need the delta sign anymore: - m_yDelta = fabs(m_yDelta); - - // When we drag, either right or left-button wise, we loose the - // horizontal line of the start tracer. - m_hStartTracer->setVisible(false); - - // We we left drag the mouse with the left button pressed, we show the - // end tracer (it has only one vertical line). - - // Only bother with the tracers if the user wants them to be visible. - if(m_tracersVisible) - { - m_endTracer->start->setCoords(m_currentDragPoint.x(), - yAxis->range().upper); - - m_endTracer->end->setCoords(m_currentDragPoint.x(), - yAxis->range().lower); - - m_endTracer->setVisible(true); - } - - // Whatever the button, when we are dealing with the axes, we do not - // want to show the tracers. - if(m_clickWasOnXAxis || m_clickWasOnYAxis) - { - // We do not want to show the tracers when we are doing that axis drag - // operation. - m_hStartTracer->setVisible(false); - m_vStartTracer->setVisible(false); - m_endTracer->setVisible(false); - - // The update of the plot is automatically handled by the plot widget, - // but we may want to propagate the axis range changes if we have locked - // the x and/or y axis... When the parent window will emit the signal, - // that signal will be caught up by all the receivers (plot widgets) - // that will update the range synchronously if the user asked for - // locking the X and/or Y axis range(s). - dynamic_cast(mp_parentWnd)->emitReplotSignal(xAxis->range(), yAxis->range()); - } - - // Now deal with the BUTTON-SPECIFIC CODE. - - if(event->buttons() == Qt::LeftButton) - { - // There are two situations: - // - // 1. The drag operation is perfectly horizontal, in which case we are - // measuring the distance between one point and another. Calculate the - // distance and show it on the middle of the line. - // - // 2. The drag operation has a big vertical vector component, in which - // case we are dragging a zoom rectangle. Draw that rectangle. - - if(m_clickWasOnXAxis || m_clickWasOnYAxis) - { - // qDebug() << __FILE__ << __LINE__ - // << "Click was on one of the axes, let the plot widget " - // << "to the QCP:iRangeDrag stuff by itself."; - - // FIXME: it might be interesting to do that stuff ourselves, so - // that - // we can apply the same logic as the one we have with the - // right-button drag X axis rescale with the shift modifier key - // pressed. - - event->accept(); - - return; - } - - // Let's check if the user is actually drawing a rectangle (covering a - // real area) or is drawing a line. - - if(isSelectionARectangle()) - { - // When we draw a rectangle the tracers are of no use. - m_hStartTracer->setVisible(false); - m_vStartTracer->setVisible(false); - m_endTracer->setVisible(false); - - drawRectangleAndZoom(); - } - else - { - // Then, make sure the tracers are visible. - m_hStartTracer->setVisible(true); - m_vStartTracer->setVisible(true); - m_endTracer->setVisible(true); - - drawXDeltaLineAndMeasure(); - } - } - // End of - // if(event->buttons() == Qt::LeftButton) - else if(event->buttons() == Qt::RightButton) - { - - // There are two situations: - // - // 1. The user has clicked onto the X or Y axis. In that case, since - // this is the right button, he want to actually scale that axis up or - // down. - // - // 2. The user has clicked onto the graph. In that case, was is done is - // a line drag for a mass spectrometry integration. What integration it - // is will be known upon mouse release, because it will be defined by - // looking at the pressed keyboard key. If no integration is asked that - // line draw operation is nothing but a zoom operation with Y axis being - // kept constant (unlike the left button-based zoom operation that draws - // a rectangle). - - if(m_clickWasOnXAxis || m_clickWasOnYAxis) - { - // qDebug() << __FILE__ << __LINE__ - // << "Zoom on the clicked axis."; - - // This operation is particularly intensive, thus we want to reduce - // the number of calculations by skipping this calculation a number - // of - // times. The user can ask for this feature by clicking the 'Q' - // letter. - if(m_pressedKeyCode == Qt::Key_Q) - { - - if(m_mouseMoveHandlerSkipCount < m_mouseMoveHandlerSkipAmount) - m_mouseMoveHandlerSkipCount++; - else - { - axisRescale(); - m_mouseMoveHandlerSkipCount = 0; - } - } - else - { - axisRescale(); - } - } - // End of - // if(m_clickWasOnXAxis || m_clickWasOnYAxis) - else - { - drawXDeltaLineForZoomOrIntegration(); - // qDebug() << __FILE__ << __LINE__ - // << "Line draw for integration."; - } - } - // End of - // else if(event->buttons() == Qt::RightButton) - - // qDebug() << __FILE__ << __LINE__ - // << "Dragging from" << m_startDragPoint.x() << "-" << m_startDragPoint.y() - // << "to" << m_currentDragPoint.x() << "-" << m_currentDragPoint.y(); - } - - - void - AbstractPlotWidget::selectionChangedHandler() - { - } - - - void - AbstractPlotWidget::setFocus() - { - QCustomPlot::setFocus(); - - //qDebug() << __FILE__ << __LINE__ << __FUNCTION__ << "()" - //<< "Setting focus to this plot widget:" << this - //<< "With parent window:" << mp_parentWnd; - - // Inform the parent window that this is the last focused widget: - AbstractMultiPlotWnd *parentWnd = dynamic_cast(mp_parentWnd); - if(parentWnd == Q_NULLPTR) - qFatal("Fatal error at %s@%d. Program aborted.", __FILE__, __LINE__); - - if(parentWnd->mp_lastFocusedPlotWidget != this) - { - parentWnd->mp_lastFocusedPlotWidget = dynamic_cast(this); - parentWnd->emitRedrawPlotBackground(dynamic_cast(this)); - } - } - - - //! Record the clicks of the mouse. - void - AbstractPlotWidget::mousePressHandler(QMouseEvent *event) - { - setFocus(); - - QPointF mousePoint = event->localPos(); - - // Let's check if the click is on the axes, either X or Y, because that - // will allow us to take proper actions. - - if(isClickOntoXAxis(mousePoint)) - { - // The X axis was clicked upon, we need to document that: - // qDebug() << __FILE__ << __LINE__ - // << "Layout element is axisRect and actually on an X axis part."; - - m_clickWasOnXAxis = true; - - int currentInteractions = interactions(); - currentInteractions |= QCP::iRangeDrag; - setInteractions((QCP::Interaction)currentInteractions); - axisRect()->setRangeDrag(xAxis->orientation()); - } - else - m_clickWasOnXAxis = false; - - if(isClickOntoYAxis(mousePoint)) - { - // The Y axis was clicked upon, we need to document that: - // qDebug() << __FILE__ << __LINE__ - // << "Layout element is axisRect and actually on an Y axis part."; - - m_clickWasOnYAxis = true; - - int currentInteractions = interactions(); - currentInteractions |= QCP::iRangeDrag; - setInteractions((QCP::Interaction)currentInteractions); - axisRect()->setRangeDrag(yAxis->orientation()); - } - else - m_clickWasOnYAxis = false; - - // At this point, let's see if we need to remove the QCP::iRangeDrag bit: - - if(!m_clickWasOnXAxis && !m_clickWasOnYAxis) - { - // qDebug() << __FILE__ << __LINE__ - // << "Click outside of axes."; - - int currentInteractions = interactions(); - currentInteractions = currentInteractions & ~QCP::iRangeDrag; - setInteractions((QCP::Interaction)currentInteractions); - } - - m_startDragPoint.setX(xAxis->pixelToCoord(mousePoint.x())); - m_startDragPoint.setY(yAxis->pixelToCoord(mousePoint.y())); - } - - - //! Set the \p params MzIntegrationParams for this plot widget - void - AbstractPlotWidget::setMzIntegrationParams(MzIntegrationParams params) - { - //qDebug() << __FILE__ << __LINE__ << __FUNCTION__ << "()" - //<< "with params:" << params.asText(); - - m_history.setMzIntegrationParams(params); - } - - - //! Get the MzIntegrationParams for this plot widget - MzIntegrationParams - AbstractPlotWidget::mzIntegrationParams() const - { - return m_history.mzIntegrationParams(); - } - - - //! React to the release of the mouse buttons. - void - AbstractPlotWidget::mouseReleaseHandler(QMouseEvent *event) - { - if(!m_isDragging) - { - // Even if we are not dragging, if one of the registered keys is - // pressed, then handle the case. - if(m_regQtKeyCodeMap.contains(m_pressedKeyCode)) - { - mouseReleaseHandledEvent(event); - return; - } - - // We only want to show the context menu if the button is the right - // button. - - if(event->button() == Qt::RightButton) - { - - // We only support data export on non-multi-graph plot widgets and on - // non-color-map widgets. - - if(m_isMultiGraph) - { - event->accept(); - return; - } - - createContextMenu()->popup(QCursor::pos()); - - event->accept(); - return; - } - } - - // We cannot hide all items in one go because we rely on their visibility - // to know what kind of dragging operation we need to perform (line-only - // X-based zoom or rectangle-based X- and Y-based zoom, for example). The - // only thing we know is that we can make the text invisible. - - if(m_xDeltaText->visible()) - m_xDeltaText->setVisible(false); - - // When we release the mouse button, whatever it was, we have the - // horizontal line of the start tracer that is drawn again. - - // Only bother with the tracers if the user wants them to be visible. - if(m_tracersVisible) - { - m_hStartTracer->setVisible(true); - } - - // If we were using the "quantum" display for the rescale of the axes - // using right-click drag on any axis, then reset the count to 0. - m_mouseMoveHandlerSkipCount = 0; - - // Compute the delta values, X and Y, that correspond to the movement that - // was done by the user while pressing the mouse button, that is get the - // geometry of the drag movement. - - calculateSortedDragDeltas(); - - // Now that we have computed the useful range, we need to check what to do - // depending on the button that was pressed. - if(event->button() == Qt::RightButton) - { - // Whatever we were doing (selection with a keyboard key pressed for an - // integration operation or simple drag operation to zoom the - // selection), we need to make the selection line invisible: - if(m_selectLine->visible()) - m_selectLine->setVisible(false); - - // Now see what we need to do depending on the key pressed code or - // nothing. - if(m_regQtKeyCodeMap.contains(m_pressedKeyCode)) - { - mouseReleaseHandledEvent(event); - } - else - { - // // There are two situations: - // 1. either we are doing a zoom operation à - // la mmmass, that is, dragging a line horizontally that will - // delimit a - // x-axis-only zoom operation; - // 2. or we are terminating a x or y axis range expansion or - // restriction. - // - // We can tell because the boolean values m_clickWasOnXAxis or - // m_clickWasOnYAxis should be set if we were dragging on any of the - // axes. - - if(m_clickWasOnXAxis || m_clickWasOnYAxis) - { - - // We were doing an axis range operation which means we do not need - // to compute any thing, just let the system as is. This is because - // when the user clicks onto an axis and then right-button-drags the - // mouse, then the plot is update real-time, so we do not need to - // replot it, it is already plot fine. The only thing would be to - // change the Y axis range if the X axis was dragged-upon so as to - // maximise the zoom on the Y axis (à la mmass, in fact). - - if(m_clickWasOnXAxis) - { - - // We may either leave the scale of the Y axis as is (default) or - // the user may want an automatic scale of the Y axis such that - // the data displayed in the new X axis range are full scale on - // the Y axis. For this, the Shift modifier key should be pressed. - - Qt::KeyboardModifiers modifiers = - QGuiApplication::queryKeyboardModifiers(); - - if(modifiers & Qt::ShiftModifier) - { - // In this case, we want to make a rescale of the Y axis - // such that - // it displays full scale the data in the current X axis - // range only. - double min = 0; - double max = 0; - - yMinMaxOnXAxisCurrentRange(min, max); - - yAxis->setRange(min, max); - } - // else - // do nothing, leave the Y axis scale as is. - - // qDebug() << __FILE__ << __LINE__ - // << "min: " << min << "max: " << max; - } - } - else - { - - // We were doing a mmass-like zoom operation, so modify the X axis - // range accordingly. Then, set the Y axis full scale only for the - // data in the X axis if the user has pressed the Shift modifier - // key. - - xAxis->setRange(m_xRangeMin, m_xRangeMax); - - // We may either leave the scale of the Y axis as is (default) or - // the user may want an automatic scale of the Y axis such that the - // data displayed in the new X axis range are full scale on the Y - // axis. For this, the Shift modifier key should be pressed. - - Qt::KeyboardModifiers modifiers = - QGuiApplication::queryKeyboardModifiers(); - - if(modifiers & Qt::ShiftModifier) - { - - // In this case, we want to make a rescale of the Y axis such that - // it displays full scale the data in the current X axis range - // only. - - double min = 0; - double max = 0; - - yMinMaxOnXAxisCurrentRange(min, max); - - yAxis->setRange(min, max); - } - else - { - - // If we do not want to rescale the Y axis to display the new X - // axis range data full scale, then this is the way to do it. The - // Y axis scale is unchanged. - - yAxis->setRange(yAxis->range().lower, m_yRangeMax); - } - } - } +double +AbstractPlotWidget::getYatX(double k, QCPGraph *g) +{ + if(g == Q_NULLPTR) + qFatal( + "Fatal error at %s@%d -- %s. " + "Pointer cannot be nullptr." + "Program aborted.", + __FILE__, + __LINE__, + __FUNCTION__); + + QCPItemTracer tracer(this); + tracer.setGraph(g); + tracer.setInterpolating(true); + tracer.setGraphKey(k); + tracer.updatePosition(); + + return tracer.position->value(); +} + + +/*/js/ + * .getYatX(x) + * + * get the value at key x. + * + * x: holding the X-axis key for which the value is returned. + */ +//! Get the value corresponding to key \p k. +/*! - // We have modified the ranges, thus store their new values in the - // history. + The value is searched in the default graph of this plot widget: graph(). - updateAxisRangeHistory(); + \param k key value (x-axis value) for which to get the value (y-axis + corresponding value). - // Do not forget that we may have locked the x and/or y axis... - dynamic_cast(mp_parentWnd)->emitReplotSignal(xAxis->range(), yAxis->range()); - } - else if(event->button() == Qt::LeftButton) - { - if(m_clickWasOnXAxis || m_clickWasOnYAxis) - { - // The range is handled automatically by the plot widget, but we - // want - // to propagate to the other widgets the range change. - // Do not forget that we may have locked the x and/or y axis... - dynamic_cast(mp_parentWnd)->emitReplotSignal(xAxis->range(), yAxis->range()); - } + \return double value containing the value corresponding to key \p k. + */ +double +AbstractPlotWidget::getYatX(double x) +{ + return getYatX(x, graph()); +} - // We were dragging with the left button pressed. Either we were - // dragging to draw a rectangle, wishing to have a zoom operation - // performed or we were dragging x-axis-wise-only to have a xDelta - // measured. - if(m_zoomRect->visible()) - { - // We were selecting a region for a zoom operation. - m_zoomRect->setVisible(false); +//! Handle mouse movements, in particular record all the last visited points. +/*! - xAxis->setRange(m_xRangeMin, m_xRangeMax); - yAxis->setRange(m_yRangeMin, m_yRangeMax); + This function is reponsible for storing at each time the last visited point + in the graph. Here, point is intended as any x/y coordinate in the plot + widget viewport, not a graph point. - updateAxisRangeHistory(); + The stored values are then the basis for a large set of calculations + throughout all the plot widget. - // Do not forget that we may have locked the x and/or y axis... - dynamic_cast(mp_parentWnd)->emitReplotSignal(xAxis->range(), yAxis->range()); - } - else if(m_selectLine->visible()) - { - // We were dragging x-axis-only-wise, to get a x-axis delta - // measurement. - m_selectLine->setVisible(false); - - // And then, also erase the xDeltaText itself. - if(m_xDeltaText->visible()) - m_xDeltaText->setVisible(false); - } - } + \param pointer to QMouseEvent from which to retrieve the coordinates of the + visited viewport points. + */ +void +AbstractPlotWidget::mouseMoveHandler(QMouseEvent *event) +{ + // Whatever happens, we want to store the plot coordinates of the current + // mouse cursor position (will be useful of the label feature). + QPointF mousePoint = event->localPos(); + + m_lastMousedPlotPoint.setX(xAxis->pixelToCoord(mousePoint.x())); + m_lastMousedPlotPoint.setY(yAxis->pixelToCoord(mousePoint.y())); + + // qDebug() << __FILE__ << __LINE__ + // << "last moused plot point: (" << m_lastMousedPlotPoint.x() + // << "," << m_lastMousedPlotPoint.y() << ")"; + + if(event->buttons() != Qt::LeftButton && event->buttons() != Qt::RightButton) + { + m_isDragging = false; + + // We are not dragging the mouse (no button pressed), simply show the + // x,y coordinates in the status bar. + QString statusBarMsg = QString("(%1 , %2)") + .arg(m_lastMousedPlotPoint.x()) + .arg(m_lastMousedPlotPoint.y()); + + emit updateStatusBarSignal(statusBarMsg); + + // We are not dragging, so we only show the start tracer lines. + m_endTracer->setVisible(false); + + // Only bother with the tracers if the user wants them to be visible. + if(m_tracersVisible) + { + m_vStartTracer->setVisible(true); + m_vStartTracer->start->setCoords(m_lastMousedPlotPoint.x(), + yAxis->range().upper); + + m_vStartTracer->end->setCoords(m_lastMousedPlotPoint.x(), + yAxis->range().lower); + + m_hStartTracer->setVisible(true); + m_hStartTracer->start->setCoords(xAxis->range().lower, + m_lastMousedPlotPoint.y()); + + m_hStartTracer->end->setCoords(xAxis->range().upper, + m_lastMousedPlotPoint.y()); + + replot(); + } + + event->accept(); + + return; + } + + // If we are here, that means that one of the buttons was pressed, that is + // we are dragging the mouse. + // + m_isDragging = true; + + // Now store the mouse position data into the the current drag point + // member datum, that will be used in countless occasions later. + m_currentDragPoint = m_lastMousedPlotPoint; + + // Now that we know the current position, we can compute the X-axis range: + + double tempXmin = m_startDragPoint.x(); + double tempXmax = m_currentDragPoint.x(); + + // Compute the xAxis differential: + + m_xDelta = tempXmax - tempXmin; + if(m_xDelta < 0) + { + m_xRangeMin = tempXmax; + m_xRangeMax = tempXmin; + } + else + { + m_xRangeMin = tempXmin; + m_xRangeMax = tempXmax; + } + + // We do not need the delta sign anymore: + m_xDelta = fabs(m_xDelta); + + // Same with the Y-axis range: + + double tempYmin = m_startDragPoint.y(); + double tempYmax = m_currentDragPoint.y(); + + // Compute the yAxis differential: + + m_yDelta = tempYmax - tempYmin; + if(m_yDelta < 0) + { + m_yRangeMin = tempYmax; + m_yRangeMax = tempYmin; + } + else + { + m_yRangeMin = tempYmin; + m_yRangeMax = tempYmax; + } + + // We do not need the delta sign anymore: + m_yDelta = fabs(m_yDelta); + + // When we drag, either right or left-button wise, we loose the + // horizontal line of the start tracer. + m_hStartTracer->setVisible(false); + + // We we left drag the mouse with the left button pressed, we show the + // end tracer (it has only one vertical line). + + // Only bother with the tracers if the user wants them to be visible. + if(m_tracersVisible) + { + m_endTracer->start->setCoords(m_currentDragPoint.x(), + yAxis->range().upper); + + m_endTracer->end->setCoords(m_currentDragPoint.x(), yAxis->range().lower); + + m_endTracer->setVisible(true); + } + + // Whatever the button, when we are dealing with the axes, we do not + // want to show the tracers. + if(m_clickWasOnXAxis || m_clickWasOnYAxis) + { + // We do not want to show the tracers when we are doing that axis drag + // operation. + m_hStartTracer->setVisible(false); + m_vStartTracer->setVisible(false); + m_endTracer->setVisible(false); + + // The update of the plot is automatically handled by the plot widget, + // but we may want to propagate the axis range changes if we have locked + // the x and/or y axis... When the parent window will emit the signal, + // that signal will be caught up by all the receivers (plot widgets) + // that will update the range synchronously if the user asked for + // locking the X and/or Y axis range(s). + dynamic_cast(mp_parentWnd) + ->emitReplotSignal(xAxis->range(), yAxis->range()); + } + + // Now deal with the BUTTON-SPECIFIC CODE. + + if(event->buttons() == Qt::LeftButton) + { + // There are two situations: + // + // 1. The drag operation is perfectly horizontal, in which case we are + // measuring the distance between one point and another. Calculate the + // distance and show it on the middle of the line. + // + // 2. The drag operation has a big vertical vector component, in which + // case we are dragging a zoom rectangle. Draw that rectangle. + + if(m_clickWasOnXAxis || m_clickWasOnYAxis) + { + // qDebug() << __FILE__ << __LINE__ + // << "Click was on one of the axes, let the plot widget " + // << "to the QCP:iRangeDrag stuff by itself."; + + // FIXME: it might be interesting to do that stuff ourselves, so + // that + // we can apply the same logic as the one we have with the + // right-button drag X axis rescale with the shift modifier key + // pressed. + + event->accept(); + + return; + } + + // Let's check if the user is actually drawing a rectangle (covering a + // real area) or is drawing a line. + + if(isSelectionARectangle()) + { + // When we draw a rectangle the tracers are of no use. + m_hStartTracer->setVisible(false); + m_vStartTracer->setVisible(false); + m_endTracer->setVisible(false); + + drawRectangleAndZoom(); + } + else + { + // Then, make sure the tracers are visible. + m_hStartTracer->setVisible(true); + m_vStartTracer->setVisible(true); + m_endTracer->setVisible(true); + + drawXDeltaLineAndMeasure(); + } + } + // End of + // if(event->buttons() == Qt::LeftButton) + else if(event->buttons() == Qt::RightButton) + { + + // There are two situations: + // + // 1. The user has clicked onto the X or Y axis. In that case, since + // this is the right button, he want to actually scale that axis up or + // down. + // + // 2. The user has clicked onto the graph. In that case, was is done is + // a line drag for a mass spectrometry integration. What integration it + // is will be known upon mouse release, because it will be defined by + // looking at the pressed keyboard key. If no integration is asked that + // line draw operation is nothing but a zoom operation with Y axis being + // kept constant (unlike the left button-based zoom operation that draws + // a rectangle). + + if(m_clickWasOnXAxis || m_clickWasOnYAxis) + { + // qDebug() << __FILE__ << __LINE__ + // << "Zoom on the clicked axis."; + + // This operation is particularly intensive, thus we want to reduce + // the number of calculations by skipping this calculation a number + // of + // times. The user can ask for this feature by clicking the 'Q' + // letter. + if(m_pressedKeyCode == Qt::Key_Q) + { + + if(m_mouseMoveHandlerSkipCount < m_mouseMoveHandlerSkipAmount) + m_mouseMoveHandlerSkipCount++; + else + { + axisRescale(); + m_mouseMoveHandlerSkipCount = 0; + } + } + else + { + axisRescale(); + } + } + // End of + // if(m_clickWasOnXAxis || m_clickWasOnYAxis) + else + { + drawXDeltaLineForZoomOrIntegration(); + // qDebug() << __FILE__ << __LINE__ + // << "Line draw for integration."; + } + } + // End of + // else if(event->buttons() == Qt::RightButton) + + // qDebug() << __FILE__ << __LINE__ + // << "Dragging from" << m_startDragPoint.x() << "-" << m_startDragPoint.y() + // << "to" << m_currentDragPoint.x() << "-" << m_currentDragPoint.y(); +} - // By definition we are stopping the drag operation by releasing the mouse - // button. Whatever that mouse button was pressed before and if there was - // one pressed before. - // We cannot set that boolean value to false before this place, because we - // call a number of routines above that need to know that dragging was - // occurring. Like mouseReleaseHandledEvent(event) for example. - m_isDragging = false; - - // Replot because we want to make the graphical items invisible, be them - // line or - // rectangle. - replot(); +void +AbstractPlotWidget::selectionChangedHandler() +{ +} - event->accept(); - } +void +AbstractPlotWidget::setFocus() +{ + QCustomPlot::setFocus(); - //! React to the double-click on the x/y axes. - void - AbstractPlotWidget::axisDoubleClickHandler(QCPAxis * axis, - QCPAxis::SelectablePart part, - QMouseEvent * event) - { - Qt::KeyboardModifiers modifiers = QGuiApplication::queryKeyboardModifiers(); + // qDebug() << __FILE__ << __LINE__ << __FUNCTION__ << "()" + //<< "Setting focus to this plot widget:" << this + //<< "With parent window:" << mp_parentWnd; + + // Inform the parent window that this is the last focused widget: + AbstractMultiPlotWnd *parentWnd = + dynamic_cast(mp_parentWnd); + if(parentWnd == Q_NULLPTR) + qFatal("Fatal error at %s@%d. Program aborted.", __FILE__, __LINE__); + + if(parentWnd->mp_lastFocusedPlotWidget != this) + { + parentWnd->mp_lastFocusedPlotWidget = dynamic_cast(this); + parentWnd->emitRedrawPlotBackground(dynamic_cast(this)); + } +} + + +//! Record the clicks of the mouse. +void +AbstractPlotWidget::mousePressHandler(QMouseEvent *event) +{ + setFocus(); - // If the Ctrl modifiers is active, then both axes are to be reset. Also - // the histories are reset also. + QPointF mousePoint = event->localPos(); - if(modifiers & Qt::ControlModifier) - { - xAxis->rescale(); - yAxis->rescale(); + // Let's check if the click is on the axes, either X or Y, because that + // will allow us to take proper actions. - clearAxisRangeHistory(); - } - - if(axis == xAxis) - { - // Reset the range of the x axis to the max view possible - axis->rescale(); - // qDebug() << __FILE__ << __LINE__ - // << "X axis double click"; - replot(); - } - else if(axis == yAxis) - { - if(modifiers & Qt::ShiftModifier) - { - // The axis should be rescaled such that the view is maximised. - double min = 0; - double max = 0; - - yMinMaxOnXAxisCurrentRange(min, max); - - // Reset the range of the y axis to full scale in Y only for the - // current - // X axis range - axis->setRange(min, max); - } - else - // The axis should be rescaled to full scale of the whole plot, not - // only the range. - axis->rescale(); - // qDebug() << __FILE__ << __LINE__ - // << "Y axis double click"; - replot(); - } + if(isClickOntoXAxis(mousePoint)) + { + // The X axis was clicked upon, we need to document that: + // qDebug() << __FILE__ << __LINE__ + // << "Layout element is axisRect and actually on an X axis part."; + + m_clickWasOnXAxis = true; + + int currentInteractions = interactions(); + currentInteractions |= QCP::iRangeDrag; + setInteractions((QCP::Interaction)currentInteractions); + axisRect()->setRangeDrag(xAxis->orientation()); + } + else + m_clickWasOnXAxis = false; + + if(isClickOntoYAxis(mousePoint)) + { + // The Y axis was clicked upon, we need to document that: + // qDebug() << __FILE__ << __LINE__ + // << "Layout element is axisRect and actually on an Y axis part."; + + m_clickWasOnYAxis = true; + + int currentInteractions = interactions(); + currentInteractions |= QCP::iRangeDrag; + setInteractions((QCP::Interaction)currentInteractions); + axisRect()->setRangeDrag(yAxis->orientation()); + } + else + m_clickWasOnYAxis = false; + + // At this point, let's see if we need to remove the QCP::iRangeDrag bit: + + if(!m_clickWasOnXAxis && !m_clickWasOnYAxis) + { + // qDebug() << __FILE__ << __LINE__ + // << "Click outside of axes."; + + int currentInteractions = interactions(); + currentInteractions = currentInteractions & ~QCP::iRangeDrag; + setInteractions((QCP::Interaction)currentInteractions); + } + + m_startDragPoint.setX(xAxis->pixelToCoord(mousePoint.x())); + m_startDragPoint.setY(yAxis->pixelToCoord(mousePoint.y())); +} + + +//! Set the \p params MzIntegrationParams for this plot widget +void +AbstractPlotWidget::setMzIntegrationParams(MzIntegrationParams params) +{ + // qDebug() << __FILE__ << __LINE__ << __FUNCTION__ << "()" + //<< "with params:" << params.asText(); - updateAxisRangeHistory(); + m_history.setMzIntegrationParams(params); +} - // Do not forget that we may have locked the x and/or y axis... - dynamic_cast(mp_parentWnd)->emitReplotSignal(xAxis->range(), yAxis->range()); - event->accept(); - } +//! Get the MzIntegrationParams for this plot widget +MzIntegrationParams +AbstractPlotWidget::mzIntegrationParams() const +{ + return m_history.mzIntegrationParams(); +} - //! Redraw the background of the \p focusedPlotWidget plot widget. - void - AbstractPlotWidget::redrawPlotBackground(QWidget *focusedPlotWidget) - { - if(focusedPlotWidget == Q_NULLPTR) - qFatal("Fatal error at %s@%d. Program aborted.", __FILE__, __LINE__); +//! React to the release of the mouse buttons. +void +AbstractPlotWidget::mouseReleaseHandler(QMouseEvent *event) +{ + if(!m_isDragging) + { + // Even if we are not dragging, if one of the registered keys is + // pressed, then handle the case. + if(m_regQtKeyCodeMap.contains(m_pressedKeyCode)) + { + mouseReleaseHandledEvent(event); + return; + } + + // We only want to show the context menu if the button is the right + // button. + + if(event->button() == Qt::RightButton) + { + + // We only support data export on non-multi-graph plot widgets and + // on + // non-color-map widgets. + + if(m_isMultiGraph) + { + event->accept(); + return; + } + + createContextMenu()->popup(QCursor::pos()); + + event->accept(); + return; + } + } + + // We cannot hide all items in one go because we rely on their visibility + // to know what kind of dragging operation we need to perform (line-only + // X-based zoom or rectangle-based X- and Y-based zoom, for example). The + // only thing we know is that we can make the text invisible. + + if(m_xDeltaText->visible()) + m_xDeltaText->setVisible(false); + + // When we release the mouse button, whatever it was, we have the + // horizontal line of the start tracer that is drawn again. + + // Only bother with the tracers if the user wants them to be visible. + if(m_tracersVisible) + { + m_hStartTracer->setVisible(true); + } + + // If we were using the "quantum" display for the rescale of the axes + // using right-click drag on any axis, then reset the count to 0. + m_mouseMoveHandlerSkipCount = 0; + + // Compute the delta values, X and Y, that correspond to the movement that + // was done by the user while pressing the mouse button, that is get the + // geometry of the drag movement. + + calculateSortedDragDeltas(); + + // Now that we have computed the useful range, we need to check what to do + // depending on the button that was pressed. + if(event->button() == Qt::RightButton) + { + // Whatever we were doing (selection with a keyboard key pressed for an + // integration operation or simple drag operation to zoom the + // selection), we need to make the selection line invisible: + if(m_selectLine->visible()) + m_selectLine->setVisible(false); + + // Now see what we need to do depending on the key pressed code or + // nothing. + if(m_regQtKeyCodeMap.contains(m_pressedKeyCode)) + { + mouseReleaseHandledEvent(event); + } + else + { + // // There are two situations: + // 1. either we are doing a zoom operation à + // la mmmass, that is, dragging a line horizontally that will + // delimit a + // x-axis-only zoom operation; + // 2. or we are terminating a x or y axis range expansion or + // restriction. + // + // We can tell because the boolean values m_clickWasOnXAxis or + // m_clickWasOnYAxis should be set if we were dragging on any of the + // axes. + + if(m_clickWasOnXAxis || m_clickWasOnYAxis) + { + + // We were doing an axis range operation which means we do not + // need + // to compute any thing, just let the system as is. This is + // because + // when the user clicks onto an axis and then right-button-drags + // the + // mouse, then the plot is update real-time, so we do not need + // to + // replot it, it is already plot fine. The only thing would be + // to + // change the Y axis range if the X axis was dragged-upon so as + // to + // maximise the zoom on the Y axis (à la mmass, in fact). + + if(m_clickWasOnXAxis) + { + + // We may either leave the scale of the Y axis as is + // (default) + // or + // the user may want an automatic scale of the Y axis such + // that + // the data displayed in the new X axis range are full scale + // on + // the Y axis. For this, the Shift modifier key should be + // pressed. + + Qt::KeyboardModifiers modifiers = + QGuiApplication::queryKeyboardModifiers(); + + if(modifiers & Qt::ShiftModifier) + { + // In this case, we want to make a rescale of the Y axis + // such that + // it displays full scale the data in the current X axis + // range only. + double min = 0; + double max = 0; + + yMinMaxOnXAxisCurrentRange(min, max); + + yAxis->setRange(min, max); + } + // else + // do nothing, leave the Y axis scale as is. + + // qDebug() << __FILE__ << __LINE__ + // << "min: " << min << "max: " << max; + } + } + else + { + + // We were doing a mmass-like zoom operation, so modify the X + // axis + // range accordingly. Then, set the Y axis full scale only for + // the + // data in the X axis if the user has pressed the Shift modifier + // key. + + xAxis->setRange(m_xRangeMin, m_xRangeMax); + + // We may either leave the scale of the Y axis as is (default) + // or + // the user may want an automatic scale of the Y axis such that + // the + // data displayed in the new X axis range are full scale on the + // Y + // axis. For this, the Shift modifier key should be pressed. + + Qt::KeyboardModifiers modifiers = + QGuiApplication::queryKeyboardModifiers(); + + if(modifiers & Qt::ShiftModifier) + { + + // In this case, we want to make a rescale of the Y axis + // such + // that + // it displays full scale the data in the current X axis + // range + // only. + + double min = 0; + double max = 0; + + yMinMaxOnXAxisCurrentRange(min, max); + + yAxis->setRange(min, max); + } + else + { + + // If we do not want to rescale the Y axis to display the + // new + // X + // axis range data full scale, then this is the way to do + // it. + // The + // Y axis scale is unchanged. + + yAxis->setRange(yAxis->range().lower, m_yRangeMax); + } + } + } + + // We have modified the ranges, thus store their new values in the + // history. + + updateAxisRangeHistory(); + + // Do not forget that we may have locked the x and/or y axis... + dynamic_cast(mp_parentWnd) + ->emitReplotSignal(xAxis->range(), yAxis->range()); + } + else if(event->button() == Qt::LeftButton) + { + if(m_clickWasOnXAxis || m_clickWasOnYAxis) + { + // The range is handled automatically by the plot widget, but we + // want + // to propagate to the other widgets the range change. + // Do not forget that we may have locked the x and/or y axis... + dynamic_cast(mp_parentWnd) + ->emitReplotSignal(xAxis->range(), yAxis->range()); + } + + // We were dragging with the left button pressed. Either we were + // dragging to draw a rectangle, wishing to have a zoom operation + // performed or we were dragging x-axis-wise-only to have a xDelta + // measured. + + if(m_zoomRect->visible()) + { + // We were selecting a region for a zoom operation. + m_zoomRect->setVisible(false); + + xAxis->setRange(m_xRangeMin, m_xRangeMax); + yAxis->setRange(m_yRangeMin, m_yRangeMax); + + updateAxisRangeHistory(); + + // Do not forget that we may have locked the x and/or y axis... + dynamic_cast(mp_parentWnd) + ->emitReplotSignal(xAxis->range(), yAxis->range()); + } + else if(m_selectLine->visible()) + { + // We were dragging x-axis-only-wise, to get a x-axis delta + // measurement. + m_selectLine->setVisible(false); + + // And then, also erase the xDeltaText itself. + if(m_xDeltaText->visible()) + m_xDeltaText->setVisible(false); + } + } + + // By definition we are stopping the drag operation by releasing the mouse + // button. Whatever that mouse button was pressed before and if there was + // one pressed before. + // We cannot set that boolean value to false before this place, because we + // call a number of routines above that need to know that dragging was + // occurring. Like mouseReleaseHandledEvent(event) for example. + m_isDragging = false; + + // Replot because we want to make the graphical items invisible, be them + // line or + // rectangle. + + replot(); + + event->accept(); +} + + +//! React to the double-click on the x/y axes. +void +AbstractPlotWidget::axisDoubleClickHandler(QCPAxis *axis, + QCPAxis::SelectablePart part, + QMouseEvent *event) +{ + Qt::KeyboardModifiers modifiers = QGuiApplication::queryKeyboardModifiers(); - if(dynamic_cast(this) != focusedPlotWidget) - { - // The focused widget is not *this widget. We should make sure that - // we were not the one that had the focus, because in this case we - // need to redraw an unfocused background. + // If the Ctrl modifiers is active, then both axes are to be reset. Also + // the histories are reset also. - axisRect()->setBackground(m_unfocusedBrush); - } - else - { - axisRect()->setBackground(m_focusedBrush); - } + if(modifiers & Qt::ControlModifier) + { + xAxis->rescale(); + yAxis->rescale(); + + clearAxisRangeHistory(); + } + + if(axis == xAxis) + { + // Reset the range of the x axis to the max view possible + axis->rescale(); + // qDebug() << __FILE__ << __LINE__ + // << "X axis double click"; + replot(); + } + else if(axis == yAxis) + { + if(modifiers & Qt::ShiftModifier) + { + // The axis should be rescaled such that the view is maximised. + double min = 0; + double max = 0; + + yMinMaxOnXAxisCurrentRange(min, max); + + // Reset the range of the y axis to full scale in Y only for the + // current + // X axis range + axis->setRange(min, max); + } + else + // The axis should be rescaled to full scale of the whole plot, not + // only the range. + axis->rescale(); + // qDebug() << __FILE__ << __LINE__ + // << "Y axis double click"; + replot(); + } + + updateAxisRangeHistory(); + + // Do not forget that we may have locked the x and/or y axis... + dynamic_cast(mp_parentWnd) + ->emitReplotSignal(xAxis->range(), yAxis->range()); + + event->accept(); +} + + +//! Redraw the background of the \p focusedPlotWidget plot widget. +void +AbstractPlotWidget::redrawPlotBackground(QWidget *focusedPlotWidget) +{ + if(focusedPlotWidget == Q_NULLPTR) + qFatal("Fatal error at %s@%d. Program aborted.", __FILE__, __LINE__); - replot(); - } + if(dynamic_cast(this) != focusedPlotWidget) + { + // The focused widget is not *this widget. We should make sure that + // we were not the one that had the focus, because in this case we + // need to redraw an unfocused background. + + axisRect()->setBackground(m_unfocusedBrush); + } + else + { + axisRect()->setBackground(m_focusedBrush); + } + replot(); +} } // namespace msXpSmineXpert - diff -pruN 5.3.3-1/minexpert/gui/ColorMapPlotWidget.cpp 5.4.0-1/minexpert/gui/ColorMapPlotWidget.cpp --- 5.3.3-1/minexpert/gui/ColorMapPlotWidget.cpp 2018-06-20 15:46:39.000000000 +0000 +++ 5.4.0-1/minexpert/gui/ColorMapPlotWidget.cpp 2018-09-11 19:21:00.000000000 +0000 @@ -107,7 +107,6 @@ namespace msXpSmineXpert setupWidget(); mp_colorMap = new QCPColorMap(xAxis, yAxis); - addPlottable(mp_colorMap); } @@ -689,7 +688,7 @@ namespace msXpSmineXpert // At this point the transposition has been done. - mp_colorMap->clearData(); + mp_colorMap->data()->clear(); mp_colorMap->rescaleDataRange(true); // We must invert the bool value that indicates the orientation of the diff -pruN 5.3.3-1/minexpert/gui/DriftSpecWnd.cpp 5.4.0-1/minexpert/gui/DriftSpecWnd.cpp --- 5.3.3-1/minexpert/gui/DriftSpecWnd.cpp 2018-06-20 15:46:39.000000000 +0000 +++ 5.4.0-1/minexpert/gui/DriftSpecWnd.cpp 2018-09-11 19:21:00.000000000 +0000 @@ -689,8 +689,17 @@ namespace msXpSmineXpert // queried in another context. senderPlotWidget->setLastTicIntensity(integrator->ticIntensity()); + QString fullMsg = msg + QString(": TIC int.: %1").arg(integrator->ticIntensity()); + // Now we can dipslay the results in the status bar: - statusBar()->showMessage(msg + QString(": TIC int.: %1").arg(integrator->ticIntensity())); + statusBar()->showMessage(fullMsg); + + // And in the main console window, now , with the proper color. + + QColor color = senderPlotWidget->color(); + + MainWindow *mainWindow = static_cast(parent()); + mainWindow->logConsoleMessage(fullMsg, color, false /*overwrite*/); // Finally we can destroy the integrator. delete integrator; diff -pruN 5.3.3-1/minexpert/gui/MassSpecPlotWidget.cpp 5.4.0-1/minexpert/gui/MassSpecPlotWidget.cpp --- 5.3.3-1/minexpert/gui/MassSpecPlotWidget.cpp 2018-06-20 15:46:39.000000000 +0000 +++ 5.4.0-1/minexpert/gui/MassSpecPlotWidget.cpp 2018-09-11 19:21:00.000000000 +0000 @@ -31,8 +31,6 @@ */ - - ///////////////////////////// Qt include @@ -48,1764 +46,1820 @@ namespace msXpSmineXpert { - /*/js/ Class: MassSpecPlotWidget - * This class cannot be instantiated with the new operator. Objects - * of this class are made available to the scripting environment under the - * form of object variable names massSpecPlotWidget[index], with [index] - * being 0 for the first object created and being incremented each time a new - * MassSpecPlotWidget is created. - */ +/*/js/ Class: MassSpecPlotWidget + * This class cannot be instantiated with the new operator. Objects + * of this class are made available to the scripting environment under the + * form of object variable names massSpecPlotWidget[index], with [index] + * being 0 for the first object created and being incremented each time a new + * MassSpecPlotWidget is created. + */ - //! Construct an initialized MassSpecPlotWidget instance. - /*! +//! Construct an initialized MassSpecPlotWidget instance. +/*! - This function registers the key codes that, in conjunction to mouse button - clicks trigger specific actions, like data integrations. + This function registers the key codes that, in conjunction to mouse button + clicks trigger specific actions, like data integrations. - \param parent parent widget. + \param parent parent widget. - \param name name of the module. + \param name name of the module. - \param desc description of the wiget type. + \param desc description of the wiget type. - \param massSpecDataSet MassSpecDataSet holding the mass data. + \param massSpecDataSet MassSpecDataSet holding the mass data. - \param fileName name of the file from which the data were loaded. + \param fileName name of the file from which the data were loaded. - \param isMultiGraph tells if the widget to be instanciated is for displaying - multiple graphs. + \param isMultiGraph tells if the widget to be instanciated is for displaying + multiple graphs. */ - MassSpecPlotWidget::MassSpecPlotWidget(QWidget * parent, - const QString & name, - const QString & desc, - const MassSpecDataSet * massSpecDataSet, - const QString & fileName, - bool isMultiGraph) - : - AbstractPlotWidget{parent, name, - desc, massSpecDataSet, fileName, isMultiGraph} - { - AbstractPlotWidget::registerQtKeyCode(Qt::Key_R, - "Press R while right mouse click-drag to integrate to a XIC chromatogram"); - AbstractPlotWidget::registerQtKeyCode(Qt::Key_D, - "Press D while right mouse click-drag to integrate to a drift spectrum"); - AbstractPlotWidget::registerQtKeyCode(Qt::Key_I, - "Press I while right mouse click-drag to integrate to a TIC intensity value"); - - // Give the axes some labels: - xAxis->setLabel("m/z"); - yAxis->setLabel("counts"); - } - - - //! Destruct \c this MassSpecPlotWidget instance. - MassSpecPlotWidget::~MassSpecPlotWidget() - { - } - - - //! Create the contextual menu. - QMenu * - MassSpecPlotWidget::createContextMenu() - { - AbstractPlotWidget::createContextMenu(); - - // In the mass spectrum plot widget, exporting the data does not make - // sense because we cannot filter the mass spectra for a valid m/z range. - // So we need to hide the corresponding menu item. - - mpa_exportDataAction->setVisible(false); - - return mpa_contextMenu; - } - - - //! Deconvolute the mass peaks into charge and molecular mass. - bool - MassSpecPlotWidget::deconvolute() - { - // There are two situations: when the user is deconvoluting on the - // basis of the distance between two consecutive peaks of a same - // isotopic cluster or when the user deconvolutes on the basis of two - // different charged-stated peaks that belong to the same envelope. - - // We can tell the difference because in the first case the xDelta - // should be less than 1. In the other case, of course the difference - // is much greater than 1. - - // Note that m_xDelta is always fabs(). - - if(m_xDelta >= 0 && m_xDelta <= 1.1) - { - //qDebug() << __FILE__ << __LINE__ << __FUNCTION__ << "()" - //<< "m_xDelta:" << m_xDelta - //<< "trying isotope-based deconvolution."; - - return deconvoluteIsotopicCluster(); - } - - // If not deconvoluting on the basis of the isotopic cluster, then: - - // Let's get the spinbox value that says what is the span between the - // two charge envelope peaks that are looked into: - MassSpecWnd *wnd = dynamic_cast(mp_parentWnd); - int span = wnd->chargeSpan(); - - //qDebug() << __FILE__ << __LINE__ << __FUNCTION__ << "()" - //<< "span is:" << span; - - return deconvoluteChargedState(span); - } - - - - //! Deconvolute the mass peaks into charge and molecular mass. - /*! - - This is one of two methods to deconvolute mass data into a charge value and - a Mr value. The method implemented in this function is based on the charge - state envelope offered by the mass spectrum (most often for polymers of a - reasonable size). - - \param span value representing the number of peaks of the charge state - envelope that are spanned by the user selection. Defaults to 1, that is, the - span encompasses two \e consecutive mass peaks of a given charge state - envelope. - - Set m_lastMz, m_lastCharge and m_lastMass. - - \return true if the deconvolution could be performed, false otherwise. - */ - bool - MassSpecPlotWidget::deconvoluteChargedState(int span) - { - // We assume that we are dealing with two successive (if span is 1) mass - // peaks belonging to a given charge state family. - - // We call span the number of peaks of a given charge state envelope - // that separate the initial peak (lowerMz) from the last peak (upperMz). - // That parameter defaults to 1. - - // Note that in this case, we cannot use the m_xRangeMin and m_xRangeMax - // values, because they are sorted, and we need to know in which direction - // the user had drug the mouse, because we want to provide the Mr value - // for the peak currently under the mouse cursor, that is under - // currentDragPoint. - - double startMz = m_startDragPoint.x(); - double curMz = m_currentDragPoint.x(); - - if(startMz == curMz) - { - m_lastCharge = -1; - m_lastMz = qSNaN(); - m_lastTicIntensity = qSNaN(); - m_lastMass = qSNaN(); - - return false; - } - - // We need to be aware that the status bar of the window that contains - // this plot widget shows the cursor position realtime, and that cursor - // position is the m_currentDragPoint.x value. Thus, we need to make the - // calculations with the charge being the one of the polymer under the - // cursor position. This is tricky because it changes when the user - // switches drag senses: from left to right and right to left. - // The way z is calculated always makes it the charge of the highest mz - // value. So knowing this, depending on the drag sense we'll have to take - // curMz and apply to it either z charge (left to right drag) or (z+span) - // charge (right to left). - - // Make sure lower is actually lower, even if drag is from right to left. - // This is only to have a single charge calculation. - double lowerMz; - double upperMz; - - if(startMz < curMz) - { - lowerMz = startMz; - upperMz = curMz; - } - else - { - lowerMz = curMz; - upperMz = startMz; - } - - double chargeTemp = ((lowerMz * span) - span) / (upperMz - lowerMz); - - // Make a judicious roundup. - - double chargeIntPart; - double chargeFracPart = modf(chargeTemp, &chargeIntPart); - - // When calculating the charge of the ion, very rarely does it provide a - // perfect integer value. Most often (if deconvolution is for bona fide - // peaks belonging to the same charge state envelope) that value is with - // either a large fractional part or a very small fractional part. What we - // test here, it that fractional part. If it is greater than - // m_chargeFracPartTolerance, then we simply round up to the next integer - // value (that is, chargeIntPart = 27 and chargeFracPart 0.995, then we - // set charge to 28). If it is lesser or equal to (1 - - // m_chargeFracPartTolerance /* that is >= 0.01 */, then we let - // chargeIntPart unmodified (that is, chargeIntPart = 29 and - // chargeFracPart 0.01, then we set charge to 29). If chargeFracPart is in - // between (1 - m_chargeFracPartTolerance) and m_chargeFracPartTolerance, - // then we consider that the peaks do not belong to the same charge state - // envelope. - - //qDebug() << __FILE__ << __LINE__ << __FUNCTION__ - //<< "Charge:" << chargeIntPart - //<< "Charge fractional part: " << chargeFracPart; - - if(chargeFracPart >= (1 - m_chargeFracPartTolerance /* that is >= 0.01 */) && - chargeFracPart <= m_chargeFracPartTolerance /* that is <= 0.99 */) - { - m_lastCharge = -1; - m_lastMz = qSNaN(); - m_lastTicIntensity = qSNaN(); - m_lastMass = qSNaN(); - - //qDebug() << __FILE__ << __LINE__ - //<< "Not a charge state family peak," - //<< "returning from deconvoluteChargeState"; - - return false; - } - - if(chargeFracPart > m_chargeFracPartTolerance) - m_lastCharge = chargeIntPart + 1; - else - m_lastCharge = chargeIntPart; - - // Now, to actually compute the molecular mass based on the charge and on - // the currently displayed m/z value, we need to have some thinking: - - if(startMz < curMz) - { - // The drag was from left to right, that is curMz is greater than - // startMz. Fine, the z value is effectively the charge of the ion at - // curMz. Easy, no charge value modification here. - - // Now that we know that the values will be useful for the data analysis - // stuff, store the actual values in the proper sorted order. - m_keyRangeStart = startMz; - m_keyRangeEnd = curMz; - } - else - { - // The drag was from right to left, that is curMz is less than startMz. - // So we want to show the charge of the curMz, that is, z + span. - m_lastCharge = m_lastCharge + span; - - // Now that we know that the values will be useful for the data analysis - // stuff, store the actual values in the proper sorted order. - m_keyRangeStart = curMz; - m_keyRangeEnd = startMz; - } - - m_lastMz = curMz; - m_lastMass = (curMz * m_lastCharge) - (m_lastCharge * m_protonMass); - - //qDebug() << __FILE__ << __LINE__ - //<< "startMz:" << QString("%1").arg(startMz, 0, 'f', 6) - //<< "m_lastMz (curMz):" << QString("%1").arg(m_lastMz, 0, 'f', 6) - //<< "m_lastMass:" << QString("%1").arg(m_lastMass, 0, 'f', 6) - //<< "m_lastCharge:" << QString("%1").arg(m_lastCharge); - - return true; - } - - - //! Deconvolute the mass peaks into charge and molecular mass. - /*! - - This is one of two methods to deconvolute mass data into a charge value and - a Mr value. The method implemented in this function is based on the distance - that separates two immediately consecutive peaks of an isotopic cluster. - This method can be used as long as the instrument produced data with a - resolution sufficient to separate reasonably well the different peaks of an - isotopic cluster. - - Set m_lastMz, m_lastCharge and m_lastMass. - - \return true if the deconvolution could be performed, false otherwise. - */ - bool - MassSpecPlotWidget::deconvoluteIsotopicCluster() - { - - // m_xRangeMin and m_xRangeMax and m_xDelta (in fabs() form) have been set - // during mouve movement handling. Note that the range values *are - // sorted*. - - double chargeTemp = 1 / m_xDelta; - - // Reset the value (mz) axis range data - m_keyRangeStart = qSNaN(); - m_keyRangeEnd = qSNaN(); - - //qDebug() << __FILE__ << __LINE__ << __FUNCTION__ << "()" - //<< "m_xRangeMin:" << m_xRangeMin - //<< "m_xRangeMax:" << m_xRangeMax; - - if(m_xRangeMax == m_xRangeMin) - { - //qDebug() << __FILE__ << __LINE__ - //<< "Same m_xRangeMax and m_xRangeMin:" - //<< "returning from deconvoluteIsotopicCluster"; - - return false; - } - - // Update the start and end range values for use in another function. - m_keyRangeStart = m_xRangeMin; - m_keyRangeEnd = m_xRangeMax; - - // Make a judicious roundup. - double chargeIntPart; - double chargeFracPart = modf(chargeTemp, &chargeIntPart); - - //qDebug() << __FILE__ << __LINE__ << __FUNCTION__ << "()" - //<< "m_xDelta:" << m_xDelta - //<< "chargeTemp:" << chargeTemp - //<< "chargeIntPart:" << chargeIntPart - //<< "chargeFracPart:" << chargeFracPart - //<< "m_chargeFracPartTolerance:" << m_chargeFracPartTolerance; - - if(chargeFracPart >= (1 - m_chargeFracPartTolerance) && - chargeFracPart <= m_chargeFracPartTolerance) - { - m_lastCharge = -1; - m_lastMz = qSNaN(); - m_lastTicIntensity = qSNaN(); - m_lastMass = qSNaN(); - m_keyRangeStart = qSNaN(); - m_keyRangeEnd = qSNaN(); - - //qDebug() << __FILE__ << __LINE__ - //<< "Not in a isotopic cluster peak:" - //<< "returning from deconvoluteIsotopicCluster"; - - return false; - } - - if(chargeFracPart > m_chargeFracPartTolerance) - { - m_lastCharge = chargeIntPart + 1; - - //qDebug() << __FILE__ << __LINE__ << __FUNCTION__ << "()" - //<< "chargeFracPart > m_chargeFracPartTolerance -> m_lastCharge = " << m_lastCharge; - } - else - { - m_lastCharge = chargeIntPart; - - //qDebug() << __FILE__ << __LINE__ << __FUNCTION__ << "()" - //<< "chargeFracPart <= m_chargeFracPartTolerance -> m_lastCharge = " << m_lastCharge; - } - - // Now that we have the charge in the form of an int, we can compute the - // Mr of the lightest isotopic cluster peak (the one that has the lowest x - // value). That value is stored in m_xRangeMin. - - m_lastMz = m_xRangeMin; - - m_lastMass = (m_lastMz * m_lastCharge) - (m_lastCharge * m_protonMass); - - return true; - } - - - //! Craft a string representing the data of the peak that was analysed. - /*! - - To do so, this functions get the data format string from the parent window's - AnalysisPreferences instance. The format string is interpreted and the - relevant values are substituted to craft a stanza (a paragraph) that matches - the peak data at hand. - - \return a string containing the stanza. - */ - QString - MassSpecPlotWidget::craftAnalysisStanza(QCPGraph *theGraph, - const QString &fileName) - { - - //qDebug() << __FILE__ << __LINE__ - //<< "Entering" << __FUNCTION__"; - - // This function might be called for a graph that sits in a single-graph - // plot widget or for a graph that sits in a multi-graph plot widget. - // Depending on the parameters, we'll know what is the case. If the - // parameters are not nullptr or empty, then the plot widget is a - // multi-graph plot widget and we need to set the data in the analysis - // record only for the graph - // passed as parameter. - - QCPGraph *origGraph = nullptr; - - if(theGraph == nullptr) - origGraph = graph(); - else - origGraph = theGraph; - - QString destFileName; - - if(fileName.isEmpty()) - destFileName = m_fileName; - else - destFileName = fileName; - - - // When the mouse moves over the plot widget, its position is recorded - // real time. That position is both a m/z value and an i (intensity) - // value. We cannot rely on the i value, because it is valid only the for - // the last added graph. But the m/z value is the same whatever the graph - // we are interested in. - - // Craft the analysis stanza: - QString stanza; - - MassSpecWnd *wnd = dynamic_cast(mp_parentWnd); - if(wnd == nullptr) - qFatal("Fatal error at %s@%d. Program aborted.", __FILE__, __LINE__); - - const AnalysisPreferences *analPrefs = wnd->analysisPreferences(); - if(analPrefs == nullptr) - return stanza; - - // The way we work here is that we get a format string that specifies how - // the user wants to have the data formatted in the stanza. That format - // string is located in a DataFormatStringSpecif object as the m_format - // member. There is also a m_formatType member that indicates what is the - // format that we request (mass spec, tic chrom or drift spec). That - // format type member is an int that also is the key of the hash that is - // located in the analPrefs: QHash - // m_dataFormatStringSpecifHash. - - DataFormatStringSpecif *specif = - analPrefs->m_dataFormatStringSpecifHash.value(FormatType::MASS_SPEC); - - if(specif == nullptr) - qFatal("Fatal error at %s@%d. Program aborted.", __FILE__, __LINE__); - - // Handy local copy. - QString formatString = specif->m_format; - - QChar prevChar = ' '; - - for(int iter = 0; iter < formatString.size(); ++iter) - { - QChar curChar = formatString.at(iter); - - // qDebug() << __FILE__ << __LINE__ - // << "Current char:" << curChar; - - if(curChar == '\\') - { - if(prevChar == '\\') - { - stanza += '\\'; - prevChar = ' '; - continue; - } - else - { - prevChar = '\\'; - continue; - } - } - - if(curChar == '%') - { - if(prevChar == '\\') - { - stanza += '%'; - prevChar = ' '; - continue; - } - else - { - prevChar = '%'; - continue; - } - } - - if(curChar == 'n') - { - if(prevChar == '\\') - { - stanza += QString("\n"); - - // Because a newline only works if it is followed by something, - // and - // if the user wants a termination newline, then we need to - // duplicate that new line char if we are at the end of the - // string. - - if(iter == formatString.size() - 1) - { - // This is the last character of the line, then, duplicate - // the - // newline so that it actually creates a new line in the - // text. - - stanza += QString("\n"); - } - - prevChar = ' '; - continue; - } - } - - if(prevChar == '%') - { - // The current character might have a specific signification. - if(curChar == 'f') - { - QFileInfo fileInfo(destFileName); - if(fileInfo.exists()) - stanza += fileInfo.fileName(); - else - stanza += "Untitled"; - prevChar = ' '; - continue; - } - if(curChar == 'X') - { - stanza += QString("%1").arg(m_lastMz, 0, 'g', 6); - prevChar = ' '; - continue; - } - if(curChar == 'Y') - { - // We need to get the value of the intensity for the graph. - double intensity = getYatX(m_lastMz, origGraph); - - if(!intensity) - qDebug() << __FILE__ << __LINE__ - << "Warning, intensity for m/z " << m_lastMz - << "is zero."; - else - stanza += QString("%1").arg(intensity, 0, 'g', 6); - - prevChar = ' '; - continue; - } - if(curChar == 'x') - { - stanza += QString("%1").arg(m_xDelta, 0, 'g', 6); - prevChar = ' '; - continue; - } - if(curChar == 'y') - { - stanza += "this is the mass spec count delta y"; - - prevChar = ' '; - continue; - } - if(curChar == 'z') - { - stanza += QString("%1").arg(m_lastCharge); - - prevChar = ' '; - continue; - } - if(curChar == 'M') - { - stanza += QString("%1").arg(m_lastMass, 0, 'f', 6); - - prevChar = ' '; - continue; - } - if(curChar == 'I') - { - stanza += QString("%1").arg(m_lastTicIntensity, 0, 'g', 3); - - prevChar = ' '; - continue; - } - if(curChar == 's') - { - stanza += QString("%1").arg(m_keyRangeStart, 0, 'f', 3); - - prevChar = ' '; - continue; - } - if(curChar == 'e') - { - stanza += QString("%1").arg(m_keyRangeEnd, 0, 'f', 3); - - prevChar = ' '; - continue; - } - // At this point the '%' is not followed by any special character - // above, so we skip them both from the text. If the '%' is to be - // printed, then it needs to be escaped. - - continue; - } - // End of - // if(prevChar == '%') - - // The character prior this current one was not '%' so we just append - // the current character. - stanza += curChar; - } - // End of - // for (int iter = 0; iter < pattern.size(); ++iter) - - return stanza; - } +MassSpecPlotWidget::MassSpecPlotWidget(QWidget *parent, + const QString &name, + const QString &desc, + const MassSpecDataSet *massSpecDataSet, + const QString &fileName, + bool isMultiGraph) + : AbstractPlotWidget{ + parent, name, desc, massSpecDataSet, fileName, isMultiGraph} +{ + AbstractPlotWidget::registerQtKeyCode( + Qt::Key_R, + "Press R while right mouse click-drag to integrate to a XIC chromatogram"); + AbstractPlotWidget::registerQtKeyCode( + Qt::Key_D, + "Press D while right mouse click-drag to integrate to a drift spectrum"); + AbstractPlotWidget::registerQtKeyCode(Qt::Key_I, + "Press I while right mouse click-drag " + "to integrate to a TIC intensity " + "value"); + + // Give the axes some labels: + xAxis->setLabel("m/z"); + yAxis->setLabel("counts"); +} + + +//! Destruct \c this MassSpecPlotWidget instance. +MassSpecPlotWidget::~MassSpecPlotWidget() +{ +} + + +//! Create the contextual menu. +QMenu * +MassSpecPlotWidget::createContextMenu() +{ + AbstractPlotWidget::createContextMenu(); + + // In the mass spectrum plot widget, exporting the data does not make + // sense because we cannot filter the mass spectra for a valid m/z range. + // So we need to hide the corresponding menu item. + + mpa_exportDataAction->setVisible(false); + + return mpa_contextMenu; +} + + +//! Deconvolute the mass peaks into charge and molecular mass. +bool +MassSpecPlotWidget::deconvolute() +{ + // There are two situations: when the user is deconvoluting on the + // basis of the distance between two consecutive peaks of a same + // isotopic cluster or when the user deconvolutes on the basis of two + // different charged-stated peaks that belong to the same envelope. + + // We can tell the difference because in the first case the xDelta + // should be less than 1. In the other case, of course the difference + // is much greater than 1. + + // Note that m_xDelta is always fabs(). + + if(m_xDelta >= 0 && m_xDelta <= 1.1) + { + // qDebug() << __FILE__ << __LINE__ << __FUNCTION__ << "()" + //<< "m_xDelta:" << m_xDelta + //<< "trying isotope-based deconvolution."; + + return deconvoluteIsotopicCluster(); + } + + // If not deconvoluting on the basis of the isotopic cluster, then: + // Let's get the spinbox value that says what is the span between the + // two charge envelope peaks that are looked into: + MassSpecWnd *wnd = dynamic_cast(mp_parentWnd); + int span = wnd->chargeSpan(); - //! Mouse movement handler. - /*! + // qDebug() << __FILE__ << __LINE__ << __FUNCTION__ << "()" + //<< "span is:" << span; - This function is responsible for triggering the deconvolution functions - depending on the type (left/right) mouse button that might be pressed. + return deconvoluteChargedState(span); +} + + +//! Deconvolute the mass peaks into charge and molecular mass. +/*! + + This is one of two methods to deconvolute mass data into a charge value and + a Mr value. The method implemented in this function is based on the charge + state envelope offered by the mass spectrum (most often for polymers of a + reasonable size). + + \param span value representing the number of peaks of the charge state + envelope that are spanned by the user selection. Defaults to 1, that is, the + span encompasses two \e consecutive mass peaks of a given charge state + envelope. + + Set m_lastMz, m_lastCharge and m_lastMass. + + \return true if the deconvolution could be performed, false otherwise. + */ +bool +MassSpecPlotWidget::deconvoluteChargedState(int span) +{ + // We assume that we are dealing with two successive (if span is 1) mass + // peaks belonging to a given charge state family. + + // We call span the number of peaks of a given charge state envelope + // that separate the initial peak (lowerMz) from the last peak (upperMz). + // That parameter defaults to 1. + + // Note that in this case, we cannot use the m_xRangeMin and m_xRangeMax + // values, because they are sorted, and we need to know in which direction + // the user had drug the mouse, because we want to provide the Mr value + // for the peak currently under the mouse cursor, that is under + // currentDragPoint. + + double startMz = m_startDragPoint.x(); + double curMz = m_currentDragPoint.x(); + + if(startMz == curMz) + { + m_lastCharge = -1; + m_lastMz = qSNaN(); + m_lastTicIntensity = qSNaN(); + m_lastMass = qSNaN(); + + return false; + } + + // We need to be aware that the status bar of the window that contains + // this plot widget shows the cursor position realtime, and that cursor + // position is the m_currentDragPoint.x value. Thus, we need to make the + // calculations with the charge being the one of the polymer under the + // cursor position. This is tricky because it changes when the user + // switches drag senses: from left to right and right to left. + // The way z is calculated always makes it the charge of the highest mz + // value. So knowing this, depending on the drag sense we'll have to take + // curMz and apply to it either z charge (left to right drag) or (z+span) + // charge (right to left). + + // Make sure lower is actually lower, even if drag is from right to left. + // This is only to have a single charge calculation. + double lowerMz; + double upperMz; + + if(startMz < curMz) + { + lowerMz = startMz; + upperMz = curMz; + } + else + { + lowerMz = curMz; + upperMz = startMz; + } + + double chargeTemp = ((lowerMz * span) - span) / (upperMz - lowerMz); + + // Make a judicious roundup. + + double chargeIntPart; + double chargeFracPart = modf(chargeTemp, &chargeIntPart); + + // When calculating the charge of the ion, very rarely does it provide a + // perfect integer value. Most often (if deconvolution is for bona fide + // peaks belonging to the same charge state envelope) that value is with + // either a large fractional part or a very small fractional part. What we + // test here, it that fractional part. If it is greater than + // m_chargeFracPartTolerance, then we simply round up to the next integer + // value (that is, chargeIntPart = 27 and chargeFracPart 0.995, then we + // set charge to 28). If it is lesser or equal to (1 - + // m_chargeFracPartTolerance /* that is >= 0.01 */, then we let + // chargeIntPart unmodified (that is, chargeIntPart = 29 and + // chargeFracPart 0.01, then we set charge to 29). If chargeFracPart is in + // between (1 - m_chargeFracPartTolerance) and m_chargeFracPartTolerance, + // then we consider that the peaks do not belong to the same charge state + // envelope. + + // qDebug() << __FILE__ << __LINE__ << __FUNCTION__ + //<< "Charge:" << chargeIntPart + //<< "Charge fractional part: " << chargeFracPart; + + if(chargeFracPart >= (1 - m_chargeFracPartTolerance /* that is >= 0.01 */) && + chargeFracPart <= m_chargeFracPartTolerance /* that is <= 0.99 */) + { + m_lastCharge = -1; + m_lastMz = qSNaN(); + m_lastTicIntensity = qSNaN(); + m_lastMass = qSNaN(); + + // qDebug() << __FILE__ << __LINE__ + //<< "Not a charge state family peak," + //<< "returning from deconvoluteChargeState"; + + return false; + } + + if(chargeFracPart > m_chargeFracPartTolerance) + m_lastCharge = chargeIntPart + 1; + else + m_lastCharge = chargeIntPart; + + // Now, to actually compute the molecular mass based on the charge and on + // the currently displayed m/z value, we need to have some thinking: + + if(startMz < curMz) + { + // The drag was from left to right, that is curMz is greater than + // startMz. Fine, the z value is effectively the charge of the ion at + // curMz. Easy, no charge value modification here. + + // Now that we know that the values will be useful for the data analysis + // stuff, store the actual values in the proper sorted order. + m_keyRangeStart = startMz; + m_keyRangeEnd = curMz; + } + else + { + // The drag was from right to left, that is curMz is less than startMz. + // So we want to show the charge of the curMz, that is, z + span. + m_lastCharge = m_lastCharge + span; + + // Now that we know that the values will be useful for the data analysis + // stuff, store the actual values in the proper sorted order. + m_keyRangeStart = curMz; + m_keyRangeEnd = startMz; + } + + m_lastMz = curMz; + m_lastMass = (curMz * m_lastCharge) - (m_lastCharge * m_protonMass); + + // qDebug() << __FILE__ << __LINE__ + //<< "startMz:" << QString("%1").arg(startMz, 0, 'f', 6) + //<< "m_lastMz (curMz):" << QString("%1").arg(m_lastMz, 0, 'f', 6) + //<< "m_lastMass:" << QString("%1").arg(m_lastMass, 0, 'f', 6) + //<< "m_lastCharge:" << QString("%1").arg(m_lastCharge); + + return true; +} + + +//! Deconvolute the mass peaks into charge and molecular mass. +/*! + + This is one of two methods to deconvolute mass data into a charge value and + a Mr value. The method implemented in this function is based on the distance + that separates two immediately consecutive peaks of an isotopic cluster. + This method can be used as long as the instrument produced data with a + resolution sufficient to separate reasonably well the different peaks of an + isotopic cluster. + + Set m_lastMz, m_lastCharge and m_lastMass. + + \return true if the deconvolution could be performed, false otherwise. + */ +bool +MassSpecPlotWidget::deconvoluteIsotopicCluster() +{ + + // m_xRangeMin and m_xRangeMax and m_xDelta (in fabs() form) have been set + // during mouve movement handling. Note that the range values *are + // sorted*. + + double chargeTemp = 1 / m_xDelta; + + // Reset the value (mz) axis range data + m_keyRangeStart = qSNaN(); + m_keyRangeEnd = qSNaN(); + + // qDebug() << __FILE__ << __LINE__ << __FUNCTION__ << "()" + //<< "m_xRangeMin:" << m_xRangeMin + //<< "m_xRangeMax:" << m_xRangeMax; + + if(m_xRangeMax == m_xRangeMin) + { + // qDebug() << __FILE__ << __LINE__ + //<< "Same m_xRangeMax and m_xRangeMin:" + //<< "returning from deconvoluteIsotopicCluster"; + + return false; + } + + // Update the start and end range values for use in another function. + m_keyRangeStart = m_xRangeMin; + m_keyRangeEnd = m_xRangeMax; + + // Make a judicious roundup. + double chargeIntPart; + double chargeFracPart = modf(chargeTemp, &chargeIntPart); + + // qDebug() << __FILE__ << __LINE__ << __FUNCTION__ << "()" + //<< "m_xDelta:" << m_xDelta + //<< "chargeTemp:" << chargeTemp + //<< "chargeIntPart:" << chargeIntPart + //<< "chargeFracPart:" << chargeFracPart + //<< "m_chargeFracPartTolerance:" << m_chargeFracPartTolerance; + + if(chargeFracPart >= (1 - m_chargeFracPartTolerance) && + chargeFracPart <= m_chargeFracPartTolerance) + { + m_lastCharge = -1; + m_lastMz = qSNaN(); + m_lastTicIntensity = qSNaN(); + m_lastMass = qSNaN(); + m_keyRangeStart = qSNaN(); + m_keyRangeEnd = qSNaN(); + + // qDebug() << __FILE__ << __LINE__ + //<< "Not in a isotopic cluster peak:" + //<< "returning from deconvoluteIsotopicCluster"; + + return false; + } + + if(chargeFracPart > m_chargeFracPartTolerance) + { + m_lastCharge = chargeIntPart + 1; + + // qDebug() << __FILE__ << __LINE__ << __FUNCTION__ << "()" + //<< "chargeFracPart > m_chargeFracPartTolerance -> m_lastCharge = " << + // m_lastCharge; + } + else + { + m_lastCharge = chargeIntPart; + + // qDebug() << __FILE__ << __LINE__ << __FUNCTION__ << "()" + //<< "chargeFracPart <= m_chargeFracPartTolerance -> m_lastCharge = " << + // m_lastCharge; + } + + // Now that we have the charge in the form of an int, we can compute the + // Mr of the lightest isotopic cluster peak (the one that has the lowest x + // value). That value is stored in m_xRangeMin. + + m_lastMz = m_xRangeMin; + + m_lastMass = (m_lastMz * m_lastCharge) - (m_lastCharge * m_protonMass); + + return true; +} + + +//! Craft a string representing the data of the peak that was analysed. +/*! + + To do so, this functions get the data format string from the parent window's + AnalysisPreferences instance. The format string is interpreted and the + relevant values are substituted to craft a stanza (a paragraph) that matches + the peak data at hand. + + \return a string containing the stanza. + */ +QString +MassSpecPlotWidget::craftAnalysisStanza(QCPGraph *theGraph, + const QString &fileName) +{ + + // qDebug() << __FILE__ << __LINE__ + //<< "Entering" << __FUNCTION__"; + + // This function might be called for a graph that sits in a single-graph + // plot widget or for a graph that sits in a multi-graph plot widget. + // Depending on the parameters, we'll know what is the case. If the + // parameters are not nullptr or empty, then the plot widget is a + // multi-graph plot widget and we need to set the data in the analysis + // record only for the graph + // passed as parameter. + + QCPGraph *origGraph = nullptr; + + if(theGraph == nullptr) + origGraph = graph(); + else + origGraph = theGraph; + + QString destFileName; + + if(fileName.isEmpty()) + destFileName = m_fileName; + else + destFileName = fileName; + + + // When the mouse moves over the plot widget, its position is recorded + // real time. That position is both a m/z value and an i (intensity) + // value. We cannot rely on the i value, because it is valid only the for + // the last added graph. But the m/z value is the same whatever the graph + // we are interested in. + + // Craft the analysis stanza: + QString stanza; + + MassSpecWnd *wnd = dynamic_cast(mp_parentWnd); + if(wnd == nullptr) + qFatal("Fatal error at %s@%d. Program aborted.", __FILE__, __LINE__); + + const AnalysisPreferences *analPrefs = wnd->analysisPreferences(); + if(analPrefs == nullptr) + return stanza; + + // The way we work here is that we get a format string that specifies how + // the user wants to have the data formatted in the stanza. That format + // string is located in a DataFormatStringSpecif object as the m_format + // member. There is also a m_formatType member that indicates what is the + // format that we request (mass spec, tic chrom or drift spec). That + // format type member is an int that also is the key of the hash that is + // located in the analPrefs: QHash + // m_dataFormatStringSpecifHash. + + DataFormatStringSpecif *specif = + analPrefs->m_dataFormatStringSpecifHash.value(FormatType::MASS_SPEC); + + if(specif == nullptr) + qFatal("Fatal error at %s@%d. Program aborted.", __FILE__, __LINE__); + + // Handy local copy. + QString formatString = specif->m_format; + + QChar prevChar = ' '; + + for(int iter = 0; iter < formatString.size(); ++iter) + { + QChar curChar = formatString.at(iter); + + // qDebug() << __FILE__ << __LINE__ + // << "Current char:" << curChar; + + if(curChar == '\\') + { + if(prevChar == '\\') + { + stanza += '\\'; + prevChar = ' '; + continue; + } + else + { + prevChar = '\\'; + continue; + } + } + + if(curChar == '%') + { + if(prevChar == '\\') + { + stanza += '%'; + prevChar = ' '; + continue; + } + else + { + prevChar = '%'; + continue; + } + } + + if(curChar == 'n') + { + if(prevChar == '\\') + { + stanza += QString("\n"); + + // Because a newline only works if it is followed by something, + // and + // if the user wants a termination newline, then we need to + // duplicate that new line char if we are at the end of the + // string. + + if(iter == formatString.size() - 1) + { + // This is the last character of the line, then, duplicate + // the + // newline so that it actually creates a new line in the + // text. + + stanza += QString("\n"); + } + + prevChar = ' '; + continue; + } + } + + if(prevChar == '%') + { + // The current character might have a specific signification. + if(curChar == 'f') + { + QFileInfo fileInfo(destFileName); + if(fileInfo.exists()) + stanza += fileInfo.fileName(); + else + stanza += "Untitled"; + prevChar = ' '; + continue; + } + if(curChar == 'X') + { + stanza += QString("%1").arg(m_lastMz, 0, 'g', 6); + prevChar = ' '; + continue; + } + if(curChar == 'Y') + { + // We need to get the value of the intensity for the graph. + double intensity = getYatX(m_lastMz, origGraph); + + if(!intensity) + qDebug() << __FILE__ << __LINE__ + << "Warning, intensity for m/z " << m_lastMz + << "is zero."; + else + stanza += QString("%1").arg(intensity, 0, 'g', 6); + + prevChar = ' '; + continue; + } + if(curChar == 'x') + { + stanza += QString("%1").arg(m_xDelta, 0, 'g', 6); + prevChar = ' '; + continue; + } + if(curChar == 'y') + { + stanza += "this is the mass spec count delta y"; + + prevChar = ' '; + continue; + } + if(curChar == 'z') + { + stanza += QString("%1").arg(m_lastCharge); + + prevChar = ' '; + continue; + } + if(curChar == 'M') + { + stanza += QString("%1").arg(m_lastMass, 0, 'f', 6); + + prevChar = ' '; + continue; + } + if(curChar == 'I') + { + stanza += QString("%1").arg(m_lastTicIntensity, 0, 'g', 3); + + prevChar = ' '; + continue; + } + if(curChar == 's') + { + stanza += QString("%1").arg(m_keyRangeStart, 0, 'f', 3); + + prevChar = ' '; + continue; + } + if(curChar == 'e') + { + stanza += QString("%1").arg(m_keyRangeEnd, 0, 'f', 3); + + prevChar = ' '; + continue; + } + // At this point the '%' is not followed by any special character + // above, so we skip them both from the text. If the '%' is to be + // printed, then it needs to be escaped. + + continue; + } + // End of + // if(prevChar == '%') + + // The character prior this current one was not '%' so we just append + // the current character. + stanza += curChar; + } + // End of + // for (int iter = 0; iter < pattern.size(); ++iter) + + return stanza; +} + + +//! Mouse movement handler. +/*! + + This function is responsible for triggering the deconvolution functions + depending on the type (left/right) mouse button that might be pressed. */ - void - MassSpecPlotWidget::mouseMoveHandler(QMouseEvent *event) - { - // This function is in charge of setting the *ordered* m_xRangeMin/Max and - // m_yRangeMin/Max and fabs(m_xDelta) and fabs(m_yDelta) values, which - // thus are up-to-data for use here. - - AbstractPlotWidget::mouseMoveHandler(event); - - // if(m_isMultiGraph) - // qDebug() << __FILE__ << __LINE__ - // << "Multi-graph"; - // else - // qDebug() << __FILE__ << __LINE__ - // << "Not multi-graph"; - - // if the is text is available that means that the base class function has - // done the work. - if(!hasItem(m_xDeltaText)) - { - event->accept(); - return; - } - - // If we are here, that means that we have something - // derived-class-specific to do. - if(event->buttons() == Qt::LeftButton) - { - // We know that we are willing to inform the user on the xDelta and - // thus on the charge of the ion of which the distance between peaks - // of the corresponding isotopic cluster is being measure if there is - // the m_xDeltaText item associated to the plot. - - //qDebug() << __FILE__ << __LINE__ << __FUNCTION__ << "()" - //<< QDateTime().currentDateTime() << "now trying a deconvolution"; - - if(!deconvolute()) - return; - - // Get the message that is already displayed in the parent main window, - // as the base class mouse move handler displays the coordinates of the - // moving cursor. But we want to add the ion specifs. - - // Handy cast pointer. - QMainWindow *parentWnd = static_cast(mp_parentWnd); - QString currentMessage = parentWnd->statusBar()->currentMessage(); - - parentWnd->statusBar()->showMessage( - currentMessage + - QString(" ; range [%1-%2]: z = %3 ; Mr = %4)") - .arg(m_keyRangeStart, 0, 'f', 3) - .arg(m_keyRangeEnd, 0, 'f', 3) - .arg(m_lastCharge) - .arg(m_lastMass, 0, 'f', 6)); - } - - event->accept(); - return; - } - - - //! Handler for the mouse release event. - /*! - - This function checks for the pressed keyboard key code and, depending on - that key code, triggers specific actions, like integrating data to drift - spectrum or to retention time (XIC) or to single TIC intensity value. +void +MassSpecPlotWidget::mouseMoveHandler(QMouseEvent *event) +{ + // This function is in charge of setting the *ordered* m_xRangeMin/Max and + // m_yRangeMin/Max and fabs(m_xDelta) and fabs(m_yDelta) values, which + // thus are up-to-data for use here. + + AbstractPlotWidget::mouseMoveHandler(event); + + // if(m_isMultiGraph) + // qDebug() << __FILE__ << __LINE__ + // << "Multi-graph"; + // else + // qDebug() << __FILE__ << __LINE__ + // << "Not multi-graph"; + + // if the is text is available that means that the base class function has + // done the work. + if(!hasItem(m_xDeltaText)) + { + event->accept(); + return; + } + + // If we are here, that means that we have something + // derived-class-specific to do. + if(event->buttons() == Qt::LeftButton) + { + // We know that we are willing to inform the user on the xDelta and + // thus on the charge of the ion of which the distance between peaks + // of the corresponding isotopic cluster is being measure if there is + // the m_xDeltaText item associated to the plot. + + // qDebug() << __FILE__ << __LINE__ << __FUNCTION__ << "()" + //<< QDateTime().currentDateTime() << "now trying a deconvolution"; + + if(!deconvolute()) + return; + + // Get the message that is already displayed in the parent main window, + // as the base class mouse move handler displays the coordinates of the + // moving cursor. But we want to add the ion specifs. + + // Handy cast pointer. + QMainWindow *parentWnd = static_cast(mp_parentWnd); + QString currentMessage = parentWnd->statusBar()->currentMessage(); + + parentWnd->statusBar()->showMessage( + currentMessage + + QString(" ; range [%1-%2]: z = %3 ; Mr = %4)") + .arg(m_keyRangeStart, 0, 'f', 3) + .arg(m_keyRangeEnd, 0, 'f', 3) + .arg(m_lastCharge) + .arg(m_lastMass, 0, 'f', 6)); + } + + event->accept(); + return; +} + + +//! Handler for the mouse release event. +/*! + + This function checks for the pressed keyboard key code and, depending on + that key code, triggers specific actions, like integrating data to drift + spectrum or to retention time (XIC) or to single TIC intensity value. */ - void - MassSpecPlotWidget::mouseReleaseHandledEvent(QMouseEvent *event) - { - if(m_isMultiGraph) - // All the actions below can only be performed if the plot widget has a - // knowledge of the mass spec data set. Thus, if *this plot widget is a - // multi-graph plot widget we need to return immediately. - return; - - if(m_pressedKeyCode == Qt::Key_D && event->button() == Qt::RightButton) - { - integrateToDt(xRangeMin(), xRangeMax()); - } - - if(m_pressedKeyCode == Qt::Key_R && event->button() == Qt::RightButton) - { - integrateToRt(xRangeMin(), xRangeMax()); - } - - if(m_pressedKeyCode == Qt::Key_I && event->button() == Qt::RightButton) - { - integrateToTicIntensity(xRangeMin(), xRangeMax()); - } - } - - - //! Perform a ranged [\p lower -- \p upper] data integration to a drift spectrum. - void - MassSpecPlotWidget::integrateToDt(double lower, double upper) - { - // Get the pointer to the x-axis (key axis). - - QCPAxis *xAxis = graph()->keyAxis(); - - double rangeStart = lower; - if(qIsNaN(rangeStart)) - { - rangeStart = xAxis->range().lower; - } - - double rangeEnd = upper; - - if(qIsNaN(rangeEnd)) - { - rangeEnd = xAxis->range().upper; - } - - History localHistory = m_history; - HistoryItem *histItem = new HistoryItem; - histItem->newIntegrationRange(IntegrationType::MZ_TO_DT, rangeStart, rangeEnd); - - // Aggreate the new item to the local history copy we made. - localHistory.appendHistoryItem(histItem); - - emit newDriftSpectrum(mp_massSpecDataSet, "Calculating drift spectrum.", - localHistory, m_plottingColor); - } - - - /*/js/ - * MassSpecPlotWidget.jsIntegrateToDt(lower, upper) - * - * Starts an integration of mass spectra data to a drift spectrum limiting the - * data range specified with the numerical arguments. - * - * lower, upper: retention time values limiting the integration. If no values - * are provided, there is no limitation to the integration. - * - * This function creates a new plot widget to display the obtained results. - */ - void - MassSpecPlotWidget::jsIntegrateToDt(double lower, double upper) - { - // Get the pointer to the x-axis (key axis). - - QCPAxis *xAxis = graph()->keyAxis(); - - double rangeStart = lower; - if(qIsNaN(rangeStart)) - { - rangeStart = xAxis->range().lower; - } - - double rangeEnd = upper; - - if(qIsNaN(rangeEnd)) - { - rangeEnd = xAxis->range().upper; - } - - History localHistory = m_history; - HistoryItem *histItem = new HistoryItem; - histItem->newIntegrationRange(IntegrationType::MZ_TO_DT, rangeStart, rangeEnd); - - // Aggreate the new item to the local history copy we made. - localHistory.appendHistoryItem(histItem); - - emit jsNewDriftSpectrum(mp_massSpecDataSet, "Calculating drift spectrum.", - localHistory, m_plottingColor); - } - - - //! Perform a ranged [\p lower -- \p upper] data integration to a TIC chromatogram. - void - MassSpecPlotWidget::integrateToRt(double lower, double upper) - { - // Get the pointer to the x-axis (key axis). - - QCPAxis *xAxis = graph()->keyAxis(); - - double rangeStart = lower; - if(qIsNaN(rangeStart)) - { - rangeStart = xAxis->range().lower; - } - - double rangeEnd = upper; - - if(qIsNaN(rangeEnd)) - { - rangeEnd = xAxis->range().upper; - } - - History localHistory = m_history; - HistoryItem *histItem = new HistoryItem; - histItem->newIntegrationRange(IntegrationType::MZ_TO_RT, rangeStart, rangeEnd); - - // Aggreate the new item to the local history copy we made. - localHistory.appendHistoryItem(histItem); - - // The signal is emitted, but the connection to the receiver exists only - // if this plot widget is NOT multi-graph. So, even if mp_massSpecDataSet - // is nullptr, there is no risk. - emit newTicChromatogram(mp_massSpecDataSet, "Calculating extracted ion chromatogram.", - localHistory, m_plottingColor); - } - - - /*/js/ - * MassSpecPlotWidget.jsIntegrateToRt(lower, upper) - * - * Starts an integration of mass spectra data to a XIC chromatogram limiting the - * data range specified with the numerical arguments. - * - * lower, upper: retention time values limiting the integration. If no values - * are provided, there is no limitation to the integration. - * - * This function creates a new plot widget to display the obtained results. - */ - void - MassSpecPlotWidget::jsIntegrateToRt(double lower, double upper) - { - // Get the pointer to the x-axis (key axis). - - QCPAxis *xAxis = graph()->keyAxis(); - - double rangeStart = lower; - if(qIsNaN(rangeStart)) - { - rangeStart = xAxis->range().lower; - } - - double rangeEnd = upper; - - if(qIsNaN(rangeEnd)) - { - rangeEnd = xAxis->range().upper; - } - - History localHistory = m_history; - HistoryItem *histItem = new HistoryItem; - histItem->newIntegrationRange(IntegrationType::MZ_TO_RT, rangeStart, rangeEnd); - - // Aggreate the new item to the local history copy we made. - localHistory.appendHistoryItem(histItem); - - // The signal is emitted, but the connection to the receiver exists only - // if this plot widget is NOT multi-graph. So, even if mp_massSpecDataSet - // is nullptr, there is no risk. - emit jsNewTicChromatogram(mp_massSpecDataSet, "Calculating extracted ion chromatogram.", - localHistory, m_plottingColor); - } - - - //! Perform a ranged [\p lower -- \p upper] data integration to a single TIC intensity value. - void - MassSpecPlotWidget::integrateToTicIntensity(double lower, double upper) - { - if(m_isMultiGraph) - // We cannot perform the action, because this plot widget has not mass - // spec data set pointer, it is a graph-only plot widget to display all - // the graphs overlaid. - return; - - // Get the pointer to the x-axis (key axis). - - QCPAxis *xAxis = graph()->keyAxis(); - - double rangeStart = lower; - if(qIsNaN(rangeStart)) - { - rangeStart = xAxis->range().lower; - } - - double rangeEnd = upper; - if(qIsNaN(rangeEnd)) - { - rangeEnd = xAxis->range().upper; - } - - // Reset the axis range data because we may return prematurely and we want - // to craft a stanza with proper values (even if they are qINan()). - m_keyRangeStart = qSNaN(); - m_keyRangeEnd = qSNaN(); - - // Also reset the other datum that might hold invalid values. - m_lastTicIntensity = qSNaN(); - - if(rangeStart == rangeEnd) - { - return; - } - - // Slot for sorting stuff. - double tempVal; - - // Set the values in sorted order for later stanza crafting. - if(rangeStart > rangeEnd) - { - tempVal = rangeStart; - rangeStart = rangeEnd; - rangeStart = tempVal; - } - - History localHistory = m_history; - HistoryItem *histItem = new HistoryItem; - histItem->newIntegrationRange(IntegrationType::MZ_TO_TIC_INT, rangeStart, rangeEnd); - - // At this point store the range data so that the user may use it in - // analysis reporting. - m_keyRangeStart = rangeStart; - m_keyRangeEnd = rangeEnd; - - // Aggreate the new item to the local history copy we made. - localHistory.appendHistoryItem(histItem); - - // Sanity check. It is not possible that this plot widget is not - // multi-graph and that at the same time, the mass spec data set pointer - // is nullptr. - if(!m_isMultiGraph && mp_massSpecDataSet == Q_NULLPTR) - qFatal("Fatal error at %s@%d -- %s(). " - "Programming error." - "Program aborted.", - __FILE__, __LINE__, __FUNCTION__); - - // Capture immediately the text that is located in the status bar - // because if the computation is long that text will have disappeared - // and we won't be able to show it in the TIC int text. - - QMainWindow *parentWnd = static_cast(mp_parentWnd); - QString currentMessage = parentWnd->statusBar()->currentMessage(); - - if(currentMessage.isEmpty()) - currentMessage = QString("range [%1-%2]") - .arg(m_keyRangeStart, 0, 'f', 3) - .arg(m_keyRangeEnd, 0, 'f', 3); - else - currentMessage += QString(" ; range [%1-%2]") - .arg(m_keyRangeStart, 0, 'f', 3) - .arg(m_keyRangeEnd, 0, 'f', 3); - - qDebug() << __FILE__ << __LINE__ << __FUNCTION__ << "()" - << "Emitting ticIntensitySignal"; - - emit ticIntensitySignal(mp_massSpecDataSet, currentMessage, localHistory); - } - - - /*/js/ - * MassSpecPlotWidget.jsIntegrateToTicIntensity(lower, upper) - * - * Starts an integration of mass spectra data to a TIC intensity single value - * limiting the data range specified with the numerical arguments. - * - * lower, upper: retention time values limiting the integration. If no values - * are provided, there is no limitation to the integration. - * - * The TIC intensity value is returned - */ - double - MassSpecPlotWidget::jsIntegrateToTicIntensity(double lower, double upper) - { - if(m_isMultiGraph) - // We cannot perform the action, because this plot widget has not mass - // spec data set pointer, it is a graph-only plot widget to display all - // the graphs overlaid. - return 0; - - // Get the pointer to the x-axis (key axis). - - QCPAxis *xAxis = graph()->keyAxis(); - - double rangeStart = lower; - if(qIsNaN(rangeStart)) - { - rangeStart = xAxis->range().lower; - } - - double rangeEnd = upper; - if(qIsNaN(rangeEnd)) - { - rangeEnd = xAxis->range().upper; - } - - // Reset the axis range data because we may return prematurely and we want - // to craft a stanza with proper values (even if they are qINan()). - m_keyRangeStart = qSNaN(); - m_keyRangeEnd = qSNaN(); - - // Also reset the other datum that might hold invalid values. - m_lastTicIntensity = qSNaN(); - - if(rangeStart == rangeEnd) - { - return false; - } - - // Slot for sorting stuff. - double tempVal; - - // Set the values in sorted order for later stanza crafting. - if(rangeStart > rangeEnd) - { - tempVal = rangeStart; - rangeStart = rangeEnd; - rangeStart = tempVal; - } - - History localHistory = m_history; - HistoryItem *histItem = new HistoryItem; - histItem->newIntegrationRange(IntegrationType::MZ_TO_TIC_INT, rangeStart, rangeEnd); - - // At this point store the range data so that the user may use it in - // analysis reporting. - m_keyRangeStart = rangeStart; - m_keyRangeEnd = rangeEnd; - - // Aggreate the new item to the local history copy we made. - localHistory.appendHistoryItem(histItem); - - MassSpecWnd *parentWnd = static_cast(mp_parentWnd); - - // Capture immediately the text that is located in the status bar - // because if the computation is long that text will have disappeared - // and we won't be able to show it in the TIC int text. - - QString currentMessage = parentWnd->statusBar()->currentMessage(); - - QApplication::setOverrideCursor(QCursor(Qt::BusyCursor)); - - // Sanity check. It is not possible that this plot widget is not - // multi-graph and that at the same time, the mass spec data set pointer - // is nullptr. - - if(!m_isMultiGraph && mp_massSpecDataSet == Q_NULLPTR) - qFatal("Fatal error at %s@%d -- %s(). " - "Programming error." - "Program aborted.", - __FILE__, __LINE__, __FUNCTION__); - - MassDataIntegrator integrator(mp_massSpecDataSet, localHistory); - - integrator.integrateToTicIntensity(); - - m_lastTicIntensity = integrator.ticIntensity(); - - QApplication::restoreOverrideCursor(); - - if(currentMessage.isEmpty()) - parentWnd->statusBar()->showMessage(QString("range [%1-%2]: TIC I = %3") - .arg(m_keyRangeStart, 0, 'f', 3) - .arg(m_keyRangeEnd, 0, 'f', 3) - .arg(m_lastTicIntensity, 0, 'g', 3)); - else - parentWnd->statusBar()->showMessage(currentMessage + - QString(" ; range [%1-%2]: TIC I = %3") - .arg(m_keyRangeStart, 0, 'f', 3) - .arg(m_keyRangeEnd, 0, 'f', 3) - .arg(m_lastTicIntensity, 0, 'g', 3)); - - return m_lastTicIntensity; - } - - - /*/js/ - * MassSpecPlotWidget.massSpectrum(lower, upper) - * - * Creates a new object limiting the data to the lower and - * upper range limits. The data used to craft the new MassSpectrum are this - * plot widget data. That is, the object is not created by - * looking into the internal mass spectral data set. - * - * lower, upper: m/z values limiting the integration. If no values - * are provided, there is no limitation to the integration and all the points - * in this plot widget are used. - * - * Return a new MassSpectrum object. - */ - //! Return a MassSpectrum crafted from the plot data. - msXpSlibmass::MassSpectrum - MassSpecPlotWidget::massSpectrum(double lower, double upper) - { - msXpSlibmass::MassSpectrum massSpectrum; - - // Iterate in the map and for each map item craft a MassPeak that is - // appended to the returned MassSpectrum. - - if(m_isMultiGraph) - return msXpSlibmass::MassSpectrum(); - - QCPDataMap *data = graph()->data(); - - QList keyList = data->keys(); - - for(int iter = 0; iter < keyList.size(); ++iter) - { - double mz = keyList.at(iter); - double i = data->value(mz).value; - - if(!qIsNaN(lower)) - { - if(mz < lower) - continue; - } - if(!qIsNaN(upper)) - { - - // plot data are sorted, so we can break for this condition. - - if(mz > upper) - break; - } - - // At this point, we are in the range, if one was defined. - - massSpectrum.append(new msXpSlibmass::DataPoint(mz, i)); - } - - return massSpectrum; - } - - - /*/js/ - * MassSpecPlotWidget.newPlot(trace) - * - * Create a new MassSpecPlotWidget using trace for the initialization - * of the data. - * - * This function creates a new plot widget to display the data. - */ - - //! Create a new plot. This function is useful in the scripting environment. - void - MassSpecPlotWidget::newPlot() - { - - // We only work on this if *this plot widget is *not* multigraph - - if(m_isMultiGraph) - return; - - MainWindow *mainWindow = static_cast(mp_parentWnd->parent()); - QScriptContext *ctx = mainWindow->mp_scriptingWnd->m_scriptEngine.currentContext(); - - int argCount = ctx->argumentCount(); - //qDebug() << __FILE__ << __LINE__ << __FUNCTION__ << "()" - //<< "argCount:" << argCount; - - if(argCount != 1) - { - ctx->throwError("Syntax error: function newPlot() takes one Trace object as argument."); - return; - } - - QScriptValue arg = ctx->argument(0); - QVariant variant = arg.data().toVariant(); - - if(!variant.isValid()) - { - ctx->throwError("Syntax error: function newPlot() takes one Trace object as argument."); - return; - } - - if(variant.userType() == QMetaType::type("msXpSlibmass::Trace")) - { - msXpSlibmass::Trace trace(qscriptvalue_cast(arg)); - - static_cast(mp_parentWnd)->newPlot(this, mp_massSpecDataSet, - QVector::fromList(trace.keyList()), - QVector::fromList(trace.valList()), - "Trace from scripting environment.", m_history, m_plottingColor); - } - else - { - ctx->throwError("Syntax error: function newPlot() takes one Trace object as argument."); - return; - } - } - - - - //! Key release event handler. - /*! - - Depending on the type of plot widget (multigraph or not), the actions - triggered in this function will differ. - - For example, the space key will trigger the crafting of an analysis stanza - (see craftAnalysisStanza()). The 'L' key triggers the printout of the - currently pointed graph point data to the console window. The TAB key will - trigger the cycling of the selected item in the open spectra dialog window - (see OpenSpectraDlg). +void +MassSpecPlotWidget::mouseReleaseHandledEvent(QMouseEvent *event) +{ + if(m_isMultiGraph) + // All the actions below can only be performed if the plot widget has a + // knowledge of the mass spec data set. Thus, if *this plot widget is a + // multi-graph plot widget we need to return immediately. + return; + + if(m_pressedKeyCode == Qt::Key_D && event->button() == Qt::RightButton) + { + integrateToDt(xRangeMin(), xRangeMax()); + } + + if(m_pressedKeyCode == Qt::Key_R && event->button() == Qt::RightButton) + { + integrateToRt(xRangeMin(), xRangeMax()); + } + + if(m_pressedKeyCode == Qt::Key_I && event->button() == Qt::RightButton) + { + integrateToTicIntensity(xRangeMin(), xRangeMax()); + } +} + + +//! Perform a ranged [\p lower -- \p upper] data integration to a drift +//! spectrum. +void +MassSpecPlotWidget::integrateToDt(double lower, double upper) +{ + // Get the pointer to the x-axis (key axis). + + QCPAxis *xAxis = graph()->keyAxis(); + + double rangeStart = lower; + if(qIsNaN(rangeStart)) + { + rangeStart = xAxis->range().lower; + } + + double rangeEnd = upper; + + if(qIsNaN(rangeEnd)) + { + rangeEnd = xAxis->range().upper; + } + + History localHistory = m_history; + HistoryItem *histItem = new HistoryItem; + histItem->newIntegrationRange( + IntegrationType::MZ_TO_DT, rangeStart, rangeEnd); + + // Aggreate the new item to the local history copy we made. + localHistory.appendHistoryItem(histItem); + + emit newDriftSpectrum(mp_massSpecDataSet, + "Calculating drift spectrum.", + localHistory, + m_plottingColor); +} + + +/*/js/ + * MassSpecPlotWidget.jsIntegrateToDt(lower, upper) + * + * Starts an integration of mass spectra data to a drift spectrum limiting the + * data range specified with the numerical arguments. + * + * lower, upper: retention time values limiting the integration. If no values + * are provided, there is no limitation to the integration. + * + * This function creates a new plot widget to display the obtained results. + */ +void +MassSpecPlotWidget::jsIntegrateToDt(double lower, double upper) +{ + // Get the pointer to the x-axis (key axis). + + QCPAxis *xAxis = graph()->keyAxis(); + + double rangeStart = lower; + if(qIsNaN(rangeStart)) + { + rangeStart = xAxis->range().lower; + } + + double rangeEnd = upper; + + if(qIsNaN(rangeEnd)) + { + rangeEnd = xAxis->range().upper; + } + + History localHistory = m_history; + HistoryItem *histItem = new HistoryItem; + histItem->newIntegrationRange( + IntegrationType::MZ_TO_DT, rangeStart, rangeEnd); + + // Aggreate the new item to the local history copy we made. + localHistory.appendHistoryItem(histItem); + + emit jsNewDriftSpectrum(mp_massSpecDataSet, + "Calculating drift spectrum.", + localHistory, + m_plottingColor); +} + + +//! Perform a ranged [\p lower -- \p upper] data integration to a TIC +//! chromatogram. +void +MassSpecPlotWidget::integrateToRt(double lower, double upper) +{ + // Get the pointer to the x-axis (key axis). + + QCPAxis *xAxis = graph()->keyAxis(); + + double rangeStart = lower; + if(qIsNaN(rangeStart)) + { + rangeStart = xAxis->range().lower; + } + + double rangeEnd = upper; + + if(qIsNaN(rangeEnd)) + { + rangeEnd = xAxis->range().upper; + } + + History localHistory = m_history; + HistoryItem *histItem = new HistoryItem; + histItem->newIntegrationRange( + IntegrationType::MZ_TO_RT, rangeStart, rangeEnd); + + // Aggreate the new item to the local history copy we made. + localHistory.appendHistoryItem(histItem); + + // The signal is emitted, but the connection to the receiver exists only + // if this plot widget is NOT multi-graph. So, even if mp_massSpecDataSet + // is nullptr, there is no risk. + emit newTicChromatogram(mp_massSpecDataSet, + "Calculating extracted ion chromatogram.", + localHistory, + m_plottingColor); +} + + +/*/js/ + * MassSpecPlotWidget.jsIntegrateToRt(lower, upper) + * + * Starts an integration of mass spectra data to a XIC chromatogram limiting the + * data range specified with the numerical arguments. + * + * lower, upper: retention time values limiting the integration. If no values + * are provided, there is no limitation to the integration. + * + * This function creates a new plot widget to display the obtained results. + */ +void +MassSpecPlotWidget::jsIntegrateToRt(double lower, double upper) +{ + // Get the pointer to the x-axis (key axis). + + QCPAxis *xAxis = graph()->keyAxis(); + + double rangeStart = lower; + if(qIsNaN(rangeStart)) + { + rangeStart = xAxis->range().lower; + } + + double rangeEnd = upper; + + if(qIsNaN(rangeEnd)) + { + rangeEnd = xAxis->range().upper; + } + + History localHistory = m_history; + HistoryItem *histItem = new HistoryItem; + histItem->newIntegrationRange( + IntegrationType::MZ_TO_RT, rangeStart, rangeEnd); + + // Aggreate the new item to the local history copy we made. + localHistory.appendHistoryItem(histItem); + + // The signal is emitted, but the connection to the receiver exists only + // if this plot widget is NOT multi-graph. So, even if mp_massSpecDataSet + // is nullptr, there is no risk. + emit jsNewTicChromatogram(mp_massSpecDataSet, + "Calculating extracted ion chromatogram.", + localHistory, + m_plottingColor); +} + + +//! Perform a ranged [\p lower -- \p upper] data integration to a single TIC +//! intensity value. +void +MassSpecPlotWidget::integrateToTicIntensity(double lower, double upper) +{ + if(m_isMultiGraph) + // We cannot perform the action, because this plot widget has not mass + // spec data set pointer, it is a graph-only plot widget to display all + // the graphs overlaid. + return; + + // Get the pointer to the x-axis (key axis). + + QCPAxis *xAxis = graph()->keyAxis(); + + double rangeStart = lower; + if(qIsNaN(rangeStart)) + { + rangeStart = xAxis->range().lower; + } + + double rangeEnd = upper; + if(qIsNaN(rangeEnd)) + { + rangeEnd = xAxis->range().upper; + } + + // Reset the axis range data because we may return prematurely and we want + // to craft a stanza with proper values (even if they are qINan()). + m_keyRangeStart = qSNaN(); + m_keyRangeEnd = qSNaN(); + + // Also reset the other datum that might hold invalid values. + m_lastTicIntensity = qSNaN(); + + if(rangeStart == rangeEnd) + { + return; + } + + // Slot for sorting stuff. + double tempVal; + + // Set the values in sorted order for later stanza crafting. + if(rangeStart > rangeEnd) + { + tempVal = rangeStart; + rangeStart = rangeEnd; + rangeStart = tempVal; + } + + History localHistory = m_history; + HistoryItem *histItem = new HistoryItem; + histItem->newIntegrationRange( + IntegrationType::MZ_TO_TIC_INT, rangeStart, rangeEnd); + + // At this point store the range data so that the user may use it in + // analysis reporting. + m_keyRangeStart = rangeStart; + m_keyRangeEnd = rangeEnd; + + // Aggreate the new item to the local history copy we made. + localHistory.appendHistoryItem(histItem); + + // Sanity check. It is not possible that this plot widget is not + // multi-graph and that at the same time, the mass spec data set pointer + // is nullptr. + if(!m_isMultiGraph && mp_massSpecDataSet == Q_NULLPTR) + qFatal( + "Fatal error at %s@%d -- %s(). " + "Programming error." + "Program aborted.", + __FILE__, + __LINE__, + __FUNCTION__); + + // Capture immediately the text that is located in the status bar + // because if the computation is long that text will have disappeared + // and we won't be able to show it in the TIC int text. + + QMainWindow *parentWnd = static_cast(mp_parentWnd); + QString currentMessage = parentWnd->statusBar()->currentMessage(); + + if(currentMessage.isEmpty()) + currentMessage = QString("range [%1-%2]") + .arg(m_keyRangeStart, 0, 'f', 3) + .arg(m_keyRangeEnd, 0, 'f', 3); + else + currentMessage += QString(" ; range [%1-%2]") + .arg(m_keyRangeStart, 0, 'f', 3) + .arg(m_keyRangeEnd, 0, 'f', 3); + + qDebug() << __FILE__ << __LINE__ << __FUNCTION__ << "()" + << "Emitting ticIntensitySignal"; + + emit ticIntensitySignal(mp_massSpecDataSet, currentMessage, localHistory); +} + + +/*/js/ + * MassSpecPlotWidget.jsIntegrateToTicIntensity(lower, upper) + * + * Starts an integration of mass spectra data to a TIC intensity single value + * limiting the data range specified with the numerical arguments. + * + * lower, upper: retention time values limiting the integration. If no values + * are provided, there is no limitation to the integration. + * + * The TIC intensity value is returned + */ +double +MassSpecPlotWidget::jsIntegrateToTicIntensity(double lower, double upper) +{ + if(m_isMultiGraph) + // We cannot perform the action, because this plot widget has not mass + // spec data set pointer, it is a graph-only plot widget to display all + // the graphs overlaid. + return 0; + + // Get the pointer to the x-axis (key axis). + + QCPAxis *xAxis = graph()->keyAxis(); + + double rangeStart = lower; + if(qIsNaN(rangeStart)) + { + rangeStart = xAxis->range().lower; + } + + double rangeEnd = upper; + if(qIsNaN(rangeEnd)) + { + rangeEnd = xAxis->range().upper; + } + + // Reset the axis range data because we may return prematurely and we want + // to craft a stanza with proper values (even if they are qINan()). + m_keyRangeStart = qSNaN(); + m_keyRangeEnd = qSNaN(); + + // Also reset the other datum that might hold invalid values. + m_lastTicIntensity = qSNaN(); + + if(rangeStart == rangeEnd) + { + return false; + } + + // Slot for sorting stuff. + double tempVal; + + // Set the values in sorted order for later stanza crafting. + if(rangeStart > rangeEnd) + { + tempVal = rangeStart; + rangeStart = rangeEnd; + rangeStart = tempVal; + } + + History localHistory = m_history; + HistoryItem *histItem = new HistoryItem; + histItem->newIntegrationRange( + IntegrationType::MZ_TO_TIC_INT, rangeStart, rangeEnd); + + // At this point store the range data so that the user may use it in + // analysis reporting. + m_keyRangeStart = rangeStart; + m_keyRangeEnd = rangeEnd; + + // Aggreate the new item to the local history copy we made. + localHistory.appendHistoryItem(histItem); + + MassSpecWnd *parentWnd = static_cast(mp_parentWnd); + + // Capture immediately the text that is located in the status bar + // because if the computation is long that text will have disappeared + // and we won't be able to show it in the TIC int text. + + QString currentMessage = parentWnd->statusBar()->currentMessage(); + + QApplication::setOverrideCursor(QCursor(Qt::BusyCursor)); + + // Sanity check. It is not possible that this plot widget is not + // multi-graph and that at the same time, the mass spec data set pointer + // is nullptr. + + if(!m_isMultiGraph && mp_massSpecDataSet == Q_NULLPTR) + qFatal( + "Fatal error at %s@%d -- %s(). " + "Programming error." + "Program aborted.", + __FILE__, + __LINE__, + __FUNCTION__); + + MassDataIntegrator integrator(mp_massSpecDataSet, localHistory); + + integrator.integrateToTicIntensity(); + + m_lastTicIntensity = integrator.ticIntensity(); + + QApplication::restoreOverrideCursor(); + + if(currentMessage.isEmpty()) + parentWnd->statusBar()->showMessage(QString("range [%1-%2]: TIC I = %3") + .arg(m_keyRangeStart, 0, 'f', 3) + .arg(m_keyRangeEnd, 0, 'f', 3) + .arg(m_lastTicIntensity, 0, 'g', 3)); + else + parentWnd->statusBar()->showMessage(currentMessage + + QString(" ; range [%1-%2]: TIC I = %3") + .arg(m_keyRangeStart, 0, 'f', 3) + .arg(m_keyRangeEnd, 0, 'f', 3) + .arg(m_lastTicIntensity, 0, 'g', 3)); + + return m_lastTicIntensity; +} + + +/*/js/ + * MassSpecPlotWidget.massSpectrum(lower, upper) + * + * Creates a new object limiting the data to the lower and + * upper range limits. The data used to craft the new MassSpectrum are this + * plot widget data. That is, the object is not created by + * looking into the internal mass spectral data set. + * + * lower, upper: m/z values limiting the integration. If no values + * are provided, there is no limitation to the integration and all the points + * in this plot widget are used. + * + * Return a new MassSpectrum object. + */ +//! Return a MassSpectrum crafted from the plot data. +msXpSlibmass::MassSpectrum +MassSpecPlotWidget::massSpectrum(double lower, double upper) +{ + msXpSlibmass::MassSpectrum massSpectrum; + + // Iterate in the map and for each map item craft a MassPeak that is + // appended to the returned MassSpectrum. + + if(m_isMultiGraph) + return msXpSlibmass::MassSpectrum(); + + QSharedPointer p_graphDataContainer = graph()->data(); + + auto beginIt = p_graphDataContainer->findBegin(lower, /*expandedRange*/ true); + auto endIt = p_graphDataContainer->findEnd(upper, /*expandedRange*/ true); + + for(auto iter = beginIt; iter != endIt; ++iter) + { + double mz = iter->key; + + if(!qIsNaN(lower)) + { + if(mz < lower) + continue; + } + + if(!qIsNaN(upper)) + { + + // plot data are sorted, so we can break for this condition. + + if(mz > upper) + break; + } + + // At this point, we are in the range, if one was defined. + + msXpSlibmass::DataPoint *dataPoint = + new msXpSlibmass::DataPoint(mz, iter->value); + + massSpectrum.append(dataPoint); + } + + return massSpectrum; +} + + +/*/js/ + * MassSpecPlotWidget.newPlot(trace) + * + * Create a new MassSpecPlotWidget using trace for the initialization + * of the data. + * + * This function creates a new plot widget to display the data. + */ + +//! Create a new plot. This function is useful in the scripting environment. +void +MassSpecPlotWidget::newPlot() +{ + + // We only work on this if *this plot widget is *not* multigraph + + if(m_isMultiGraph) + return; + + MainWindow *mainWindow = static_cast(mp_parentWnd->parent()); + QScriptContext *ctx = + mainWindow->mp_scriptingWnd->m_scriptEngine.currentContext(); + + int argCount = ctx->argumentCount(); + // qDebug() << __FILE__ << __LINE__ << __FUNCTION__ << "()" + //<< "argCount:" << argCount; + + if(argCount != 1) + { + ctx->throwError( + "Syntax error: function newPlot() takes one Trace object as argument."); + return; + } + + QScriptValue arg = ctx->argument(0); + QVariant variant = arg.data().toVariant(); + + if(!variant.isValid()) + { + ctx->throwError( + "Syntax error: function newPlot() takes one Trace object as argument."); + return; + } + + if(variant.userType() == QMetaType::type("msXpSlibmass::Trace")) + { + msXpSlibmass::Trace trace(qscriptvalue_cast(arg)); + + static_cast(mp_parentWnd) + ->newPlot(this, + mp_massSpecDataSet, + QVector::fromList(trace.keyList()), + QVector::fromList(trace.valList()), + "Trace from scripting environment.", + m_history, + m_plottingColor); + } + else + { + ctx->throwError( + "Syntax error: function newPlot() takes one Trace object as argument."); + return; + } +} + + +//! Key release event handler. +/*! + + Depending on the type of plot widget (multigraph or not), the actions + triggered in this function will differ. + + For example, the space key will trigger the crafting of an analysis stanza + (see craftAnalysisStanza()). The 'L' key triggers the printout of the + currently pointed graph point data to the console window. The TAB key will + trigger the cycling of the selected item in the open spectra dialog window + (see OpenSpectraDlg). */ - void - MassSpecPlotWidget::keyReleaseEvent(QKeyEvent *event) - { - MassSpecWnd *parentWnd = static_cast(mp_parentWnd); - MainWindow * mainWindow = static_cast(parentWnd->parent()); - - // First, check if the space bar was pressed. - if(event->key() == Qt::Key_Space) - { - // The handling of the stanza creation is different in these two - // situations: - // 1. the plot widget where this event occurred is a conventional - // mono-graph plot widget that sits in the lower part of the window. In - // this case, the filename of the spectrum data file is available. - // 2. the plot widget is a multi-graph plot widget that sits in the - // upper part of the multi plot window. In that case, it is more - // difficult to know what is the file that initially contained the data - // plotted. We want to know what graph corresponds to what list widget - // item that is selected (or not) in the open mass spectra dialog window - // (see MainWindow). - - QString stanza; - if(m_isMultiGraph) - { - - // The event occurred in the multi-graph plot widget where many graphs - // are displayed. We need to craft a stanza for each graph that - // replicates the data of a plot that is proxied in the list widget of - // the OpenSpectraDlg. Only handle the spectra of which the list - // widget item is currently selected and for which the corresponding - // mass multi-graph plot is visible. - - for(int iter = 0; iter < graphCount(); ++iter) - { - QCPGraph *iterGraph = graph(iter); - - // Only work on this graph if it is visible: - if(!iterGraph->visible()) - continue; - - // Get a handle to the conventional plot widget of which this - // multi-graph plot widget's graph is a replica. - AbstractPlotWidget *massSpecPlotWidget = - parentWnd->monoGraphPlot(iterGraph); - - // Now use that pointer to get a handle to the tic chromatogram plot - // widget whence the data in this plot widget came: - - // // Old version: - // AbstractPlotWidget *ticChromPlotWidget = - // mainWindow->m_ticChromVersusMassSpecMultiMap.key(massSpecPlotWidget); - - // New version: - DataPlotWidgetRelation *p_rootRelation = Q_NULLPTR; - AbstractPlotWidget *ticChromPlotWidget = - mainWindow->m_dataPlotWidgetRelationer.rootPlotWidget(massSpecPlotWidget, &p_rootRelation); - - if(ticChromPlotWidget == nullptr) - { - qFatal("Fatal error at %s@%d -- %s. " - "Cannot be that a multiGraph plot widget has no root plot widget." - "Program aborted.", - __FILE__, __LINE__, __FUNCTION__); - } - - // At this point, we know what plot widget in the Tic chrom window - // is at the origin of the graph currently iterated into. We need to - // know if that plot widget has a corresponding item in the open - // spectrum dialog list widget that is currently selected. - - if(mainWindow->mp_openSpectraDlg->isPlotWidgetSelected(ticChromPlotWidget)) - { - - // This means that we have to get the filename out of this tic - // chrom plot widget's mass spec data set: - - QString fileName = - static_cast(ticChromPlotWidget)->massSpecDataSet()->fileName(); - - stanza = craftAnalysisStanza(iterGraph, fileName); - - if(stanza.isEmpty()) - { - parentWnd->statusBar()->showMessage( - "Failed to craft an analysis stanza. " - "Please set the analysis preferences."); - - event->accept(); - - return; - } - else - { - // qDebug() << __FILE__ << __LINE__ - // << "Stanza: " << stanza; - - emit recordAnalysisStanza(stanza, m_plottingColor); - } - } - } - // End of - // for(int iter = 0; iter < graphCount(); ++iter) - } - // End of - // if(m_isMultiGraph) - else - { - // We are in a plot widget that is a single-graph plot widget, the - // situation is easier: - - // stanza = craftAnalysisStanza(); - stanza = craftAnalysisStanza(); - - if(stanza.isEmpty()) - { - parentWnd->statusBar()->showMessage( - "Failed to craft an analysis stanza. " - "Please set the analysis preferences."); - - event->accept(); - return; - } - else - { - - // Send the stanza to the console window, so that we can make a copy - // paste. - - emit recordAnalysisStanza(stanza, m_plottingColor); - } - } - - event->accept(); - return; - } - // End of - // if(event->key() == Qt::Key_Space) - else if(event->key() == Qt::Key_Tab) - { - // qDebug() << __FILE__ << __LINE__ - // << "MassSpecPlotWidget::keyReleaseEvent - // AbstractPlotWidgetevent->key() == Qt::Key_Tab"; - - if(!m_isMultiGraph) - { - // We do not want to handle the TAB key because it will try to cycle - // into the - // various plot widgets of the lower part of the window. - - // qDebug() << __FILE__ << __LINE__ - // << "Mass spec plot widget is not multi-graph"; - - event->accept(); - return; - } - - // When this key event occurs in a multigraph plot widget, that means - // that the user wants to cycle in the graphs, most probably because she - // is in an analysis procedure. - // - // The OpenSpectraDlg list widget's items reflect all the mass specra - // opened. For each open spectrum, there is a corresponding list widget - // item, colored the same as the corresponding tic chrom plot widget - // that show the TIC chromatogram. - // - // Note that there might be list widget items that we are not going to - // deal with because they have no mass spec plot widget (and thus not - // multi-graph plot widget graph neither) because the user has opened - // the mass file but not yet performed any mass spectrum combination. - // - // Also, the TAB key cycling only works when one list widget item is - // selected. If there are more than one item selected, then deselect all - // the item but the first of the selected ones, to seed the cycling - // conditions. - - int iCount = mainWindow->mp_openSpectraDlg->itemCount(); - int siCount = mainWindow->mp_openSpectraDlg->selectedItemCount(); - - AbstractPlotWidget *ticChromPlotWidget; - - if(!siCount) - { - // qDebug() << __FILE__ << __LINE__ - // << "Not a single list widget item is selected. There are" - // << iCount << "items in the list widget"; - - // Not a single list widget item is selected. We want to select the - // first one that has a corresponding graph in this multi-graph plot - // widget. - for(int iter = 0; iter < iCount; ++iter) - { - ticChromPlotWidget = - mainWindow->mp_openSpectraDlg->plotWidgetAt(iter); - - // Get to the corresponding mass spec plot widget. - // Because a single tic chrom plot widget might generated many - // different mass spec plot widgets, we get a list: - // QListmassSpecPlotWidgetList = - // mainWindow->m_ticChromVersusMassSpecMultiMap.values(ticChromPlotWidget); - - QList massSpecPlotWidgetList; - mainWindow->m_dataPlotWidgetRelationer.targets( - ticChromPlotWidget, &massSpecPlotWidgetList); - - // As long as there is at least one item, we are ok. - if(massSpecPlotWidgetList.size()) - { - // qDebug() << __FILE__ << __LINE__ - // << "List widget at index " << iter << "will be - // selected."; - - // Select that item right away. - mainWindow->mp_openSpectraDlg->deselectAllPlotWidgetsButOne( - ticChromPlotWidget); - break; - } - } - } - else if(siCount == 1) - { - // qDebug() << __FILE__ << __LINE__ - // << "Only one item is selected in the list widget. There are" - // << iCount << "items in the list widget"; - - // There is only one item that is selected. Just get to the next - // one, - // if possible, or cycle back to the next possible starting from the - // top. - int siIndex; - ticChromPlotWidget = - mainWindow->mp_openSpectraDlg->firstSelectedPlotWidget(&siIndex); - - - // qDebug() << __FILE__ << __LINE__ - // << "The item that is selected is at index " << siIndex; - - // The item that is selected is at index siIndex. Now, iterate in - // the - // various items of the list widget, starting at index siIndex + 1, - // or - // 0 and check if the iterated item has a corresponding mass spec - // window plot widget. If so, just select it. - - if(iCount == 1) - { - - // qDebug() << __FILE__ << __LINE__ - // << "The is only one item in the list widget, thus nothing to - // do."; - - // There is one item selected and only one item. Nothing to do. - event->accept(); - return; - } - - // There are multiple items, so iterate into each of them and see if - // we can select it, if it has a corresponding plot widget here. - // Start iterating at the next index, since we want to cycle through - // the various items. - - // If the currently selected item is the last of the list widget, - // then - // loop over to the first. - if(++siIndex > iCount - 1) - siIndex = 0; - - // qDebug() << __FILE__ << __LINE__ - // << "Starting iteration in the list widget at index " << siIndex; - - int iter = siIndex; - bool hasLooped = false; - - while(true) - { - // We cannot use the for loop below, because we want to loop - // over - // the end of the widget list if siIndex is in the middle of it, - // for example. - // for(int iter = siIndex; iter < iCount; ++iter) - - // qDebug() << __FILE__ << __LINE__ - // << "Iterating with iter: " << iter; - - ticChromPlotWidget = - mainWindow->mp_openSpectraDlg->plotWidgetAt(iter); - - // Get to the corresponding mass spec plot widget. - // Because a single tic chrom plot widget might generated many - // different mass spec plot widgets, we get a list: - // QListmassSpecPlotWidgetList = - // mainWindow->m_ticChromVersusMassSpecMultiMap.values(ticChromPlotWidget); - - QList massSpecPlotWidgetList; - mainWindow->m_dataPlotWidgetRelationer.targets( - ticChromPlotWidget, &massSpecPlotWidgetList); - - // As long as there is at least one item, we are ok. - if(massSpecPlotWidgetList.size()) - { - // qDebug() << __FILE__ << __LINE__ - // << "The item at index " << iter << "is going to be - // selected."; - - // Select that item right away. - mainWindow->mp_openSpectraDlg->deselectAllPlotWidgetsButOne( - ticChromPlotWidget); - break; - } - - // qDebug() << __FILE__ << __LINE__ - // << "Iterated in list widget item index " << iter; - - if(++iter >= iCount) - { - // qDebug() << __FILE__ << __LINE__ - // << "iter :" << iter << "is >= iCount, reset to 0"; - - iter = 0; - - // We will need to know that we looped over the last widget - // list - // item, such that we can test if we are going past the - // first - // index that we iterated over. - hasLooped = true; - - continue; - } - - // But we do not want to loop forever: - if(hasLooped && iter >= siIndex) - { - // qDebug() << __FILE__ << __LINE__ - // << "We looped already and iter is:" << iter << "so we - // break the loop."; - - break; - } - } - // End of - // while(true) - - // qDebug() << __FILE__ << __LINE__ - // << "Out of for loop iterating in the list widget items."; - - event->accept(); - return; - } - else - { - // The number of selected items is more than one. We want to only - // have - // one item selected, that has a corresponding mass spec plot - // widget. - // Then, next TAB key strokes will cycle through the list widget - // items. - int siIndex = - mainWindow->mp_openSpectraDlg->firstSelectedPlotWidgetIndex(); - - // If the currently selected item is the last of the list widget, - // then - // loop over to the first. - if(++siIndex >= iCount - 1) - siIndex = 0; - - for(int iter = siIndex; iter < iCount; ++iter) - { - ticChromPlotWidget = - mainWindow->mp_openSpectraDlg->plotWidgetAt(iter); - - // Get to the corresponding mass spec plot widget. - // Because a single tic chrom plot widget might generated many - // different mass spec plot widgets, we get a list: - // QListmassSpecPlotWidgetList = - // mainWindow->m_ticChromVersusMassSpecMultiMap.values(ticChromPlotWidget); - - QList massSpecPlotWidgetList; - mainWindow->m_dataPlotWidgetRelationer.targets( - ticChromPlotWidget, &massSpecPlotWidgetList); - - // As long as there is at least one item, we are ok. - if(massSpecPlotWidgetList.size()) - { - // Select that item right away. - mainWindow->mp_openSpectraDlg->deselectAllPlotWidgetsButOne( - ticChromPlotWidget); - break; - } - } - - event->accept(); - return; - } - // End of else that is, there are more than one list widget item - // selected. - } - // End of else if(event->key() == Qt::Key_Tab) - else if(event->key() == Qt::Key_L) - { - // The user wants to copy the current cursor location to the console - // window, such that it remains available after having moved the cursor. - // The handling of the text creation is different in these two - // situations: - // - // 1. the plot widget where this event occurred is a conventional - // mono-graph plot widget that sits in the lower part of the window. In - // this case, the color to be used to display the data label in the - // console window is easily gotten from the graph's pen. - // - // 2. the plot widget is a multi-graph plot widget that sits in the - // upper part of the multi plot window. In that case, it is more - // difficult to know what is the proper color to use, because we need to - // go to the open spectra dialog and get the list of selected files that - // initially contained the data plotted. We want to know what graph - // corresponds to what list widget item that is selected (or not) in the - // open mass spectra dialog window (see MainWindow). - - QString label; - if(m_isMultiGraph) - { - - // The event occurred in the multi-graph plot widget where many graphs - // are displayed. We need to craft a label for each graph that - // replicates the data of a plot that is proxied in the list widget of - // the OpenSpectraDlg. Only handle the spectra of which the list - // widget item is currently selected and for which the corresponding - // mass multi-graph plot is visible. - - for(int iter = 0; iter < graphCount(); ++iter) - { - QCPGraph *iterGraph = graph(iter); - - // Only work on this graph if it is visible: - - if(!iterGraph->visible()) - continue; - - // Get a handle to the conventional plot widget of which this - // multi-graph plot widget's graph is a replica. - - AbstractPlotWidget *massSpecPlotWidget = - parentWnd->monoGraphPlot(iterGraph); - - // Now use that pointer to get a handle to the tic chromatogram plot - // widget whence the data in this plot widget came: AbstractPlotWidget - // *ticChromPlotWidget = - // mainWindow->m_ticChromVersusMassSpecMultiMap.key(massSpecPlotWidget); - - DataPlotWidgetRelation *p_rootRelation = Q_NULLPTR; - AbstractPlotWidget *ticChromPlotWidget = - mainWindow->m_dataPlotWidgetRelationer.rootPlotWidget(massSpecPlotWidget, - &p_rootRelation); - - if(ticChromPlotWidget == nullptr) - { - qFatal("Fatal error at %s@%d -- %s. " - "Cannot be that a multiGraph plot widget has no root plot widget." - "Program aborted.", - __FILE__, __LINE__, __FUNCTION__); - } - - // At this point, we know what plot widget in the Tic chrom window - // is the root plot of the graph currently iterated into. We need to - // know if that plot widget has a corresponding item in the open - // spectrum dialog list widget that is currently selected. - - if(mainWindow->mp_openSpectraDlg->isPlotWidgetSelected( - ticChromPlotWidget)) - { - // We can craft the label text to send to the console - // window, and - // that, with the proper color. - - label = QString("MZ(%1,%2)\n") - .arg(m_lastMousedPlotPoint.x()) - .arg(m_lastMousedPlotPoint.y()); - - if(label.isEmpty()) - { - parentWnd->statusBar()->showMessage( - "Failed to craft a text label."); - - event->accept(); - return; - } - else - { - // Send the label to the console window, so that we can - // make a copy - // paste. - mainWindow->logConsoleMessage(label, m_plottingColor); - } - } - } - // End of - // for(int iter = 0; iter < graphCount(); ++iter) - } - // End of - // if(m_isMultiGraph) - else - { - // We are in a plot widget that is a single-graph plot widget, the - // situation is easier: - - label = QString("MZ(%1,%2)\n") - .arg(m_lastMousedPlotPoint.x()) - .arg(m_lastMousedPlotPoint.y()); - - if(label.isEmpty()) - { - parentWnd->statusBar()->showMessage( - "Failed to craft a text label. "); - - event->accept(); - return; - } - else - { - // Send the label to the console window, so that we can make a - // copy - // paste. - - mainWindow->logConsoleMessage(label, m_plottingColor); - } - } - - event->accept(); - return; - } - // End of - // else if(event->key() == Qt::Key_L) - - // Now let the base class do its work if needed. - AbstractPlotWidget::keyReleaseEvent(event); - } - - - //! Return the arbitrary integration type that this plot widget can handle - int - MassSpecPlotWidget::arbitraryIntegrationType() - { - return IntegrationType::MZ_TO_XXX; - } +void +MassSpecPlotWidget::keyReleaseEvent(QKeyEvent *event) +{ + MassSpecWnd *parentWnd = static_cast(mp_parentWnd); + MainWindow *mainWindow = static_cast(parentWnd->parent()); + + // First, check if the space bar was pressed. + if(event->key() == Qt::Key_Space) + { + // The handling of the stanza creation is different in these two + // situations: + // 1. the plot widget where this event occurred is a conventional + // mono-graph plot widget that sits in the lower part of the window. In + // this case, the filename of the spectrum data file is available. + // 2. the plot widget is a multi-graph plot widget that sits in the + // upper part of the multi plot window. In that case, it is more + // difficult to know what is the file that initially contained the data + // plotted. We want to know what graph corresponds to what list widget + // item that is selected (or not) in the open mass spectra dialog window + // (see MainWindow). + + QString stanza; + if(m_isMultiGraph) + { + + // The event occurred in the multi-graph plot widget where many graphs + // are displayed. We need to craft a stanza for each graph that + // replicates the data of a plot that is proxied in the list widget of + // the OpenSpectraDlg. Only handle the spectra of which the list + // widget item is currently selected and for which the corresponding + // mass multi-graph plot is visible. + + for(int iter = 0; iter < graphCount(); ++iter) + { + QCPGraph *iterGraph = graph(iter); + + // Only work on this graph if it is visible: + if(!iterGraph->visible()) + continue; + + // Get a handle to the conventional plot widget of which this + // multi-graph plot widget's graph is a replica. + AbstractPlotWidget *massSpecPlotWidget = + parentWnd->monoGraphPlot(iterGraph); + + // Now use that pointer to get a handle to the tic chromatogram + // plot + // widget whence the data in this plot widget came: + + // // Old version: + // AbstractPlotWidget *ticChromPlotWidget = + // mainWindow->m_ticChromVersusMassSpecMultiMap.key(massSpecPlotWidget); + + // New version: + DataPlotWidgetRelation *p_rootRelation = Q_NULLPTR; + AbstractPlotWidget *ticChromPlotWidget = + mainWindow->m_dataPlotWidgetRelationer.rootPlotWidget( + massSpecPlotWidget, &p_rootRelation); + + if(ticChromPlotWidget == nullptr) + { + qFatal( + "Fatal error at %s@%d -- %s. " + "Cannot be that a multiGraph plot widget has no root plot " + "widget." + "Program aborted.", + __FILE__, + __LINE__, + __FUNCTION__); + } + + // At this point, we know what plot widget in the Tic chrom window + // is at the origin of the graph currently iterated into. We need + // to + // know if that plot widget has a corresponding item in the open + // spectrum dialog list widget that is currently selected. + + if(mainWindow->mp_openSpectraDlg->isPlotWidgetSelected( + ticChromPlotWidget)) + { + + // This means that we have to get the filename out of this tic + // chrom plot widget's mass spec data set: + + QString fileName = + static_cast(ticChromPlotWidget) + ->massSpecDataSet() + ->fileName(); + + stanza = craftAnalysisStanza(iterGraph, fileName); + + if(stanza.isEmpty()) + { + parentWnd->statusBar()->showMessage( + "Failed to craft an analysis stanza. " + "Please set the analysis preferences."); + + event->accept(); + + return; + } + else + { + // qDebug() << __FILE__ << __LINE__ + // << "Stanza: " << stanza; + + emit recordAnalysisStanza(stanza, m_plottingColor); + } + } + } + // End of + // for(int iter = 0; iter < graphCount(); ++iter) + } + // End of + // if(m_isMultiGraph) + else + { + // We are in a plot widget that is a single-graph plot widget, the + // situation is easier: + + // stanza = craftAnalysisStanza(); + stanza = craftAnalysisStanza(); + + if(stanza.isEmpty()) + { + parentWnd->statusBar()->showMessage( + "Failed to craft an analysis stanza. " + "Please set the analysis preferences."); + + event->accept(); + return; + } + else + { + + // Send the stanza to the console window, so that we can make a + // copy + // paste. + + emit recordAnalysisStanza(stanza, m_plottingColor); + } + } + + event->accept(); + return; + } + // End of + // if(event->key() == Qt::Key_Space) + else if(event->key() == Qt::Key_Tab) + { + // qDebug() << __FILE__ << __LINE__ + // << "MassSpecPlotWidget::keyReleaseEvent + // AbstractPlotWidgetevent->key() == Qt::Key_Tab"; + + if(!m_isMultiGraph) + { + // We do not want to handle the TAB key because it will try to cycle + // into the + // various plot widgets of the lower part of the window. + + // qDebug() << __FILE__ << __LINE__ + // << "Mass spec plot widget is not multi-graph"; + + event->accept(); + return; + } + + // When this key event occurs in a multigraph plot widget, that means + // that the user wants to cycle in the graphs, most probably because she + // is in an analysis procedure. + // + // The OpenSpectraDlg list widget's items reflect all the mass specra + // opened. For each open spectrum, there is a corresponding list widget + // item, colored the same as the corresponding tic chrom plot widget + // that show the TIC chromatogram. + // + // Note that there might be list widget items that we are not going to + // deal with because they have no mass spec plot widget (and thus not + // multi-graph plot widget graph neither) because the user has opened + // the mass file but not yet performed any mass spectrum combination. + // + // Also, the TAB key cycling only works when one list widget item is + // selected. If there are more than one item selected, then deselect all + // the item but the first of the selected ones, to seed the cycling + // conditions. + + int iCount = mainWindow->mp_openSpectraDlg->itemCount(); + int siCount = mainWindow->mp_openSpectraDlg->selectedItemCount(); + + AbstractPlotWidget *ticChromPlotWidget; + + if(!siCount) + { + // qDebug() << __FILE__ << __LINE__ + // << "Not a single list widget item is selected. There are" + // << iCount << "items in the list widget"; + + // Not a single list widget item is selected. We want to select the + // first one that has a corresponding graph in this multi-graph plot + // widget. + for(int iter = 0; iter < iCount; ++iter) + { + ticChromPlotWidget = + mainWindow->mp_openSpectraDlg->plotWidgetAt(iter); + + // Get to the corresponding mass spec plot widget. + // Because a single tic chrom plot widget might generated many + // different mass spec plot widgets, we get a list: + // QListmassSpecPlotWidgetList = + // mainWindow->m_ticChromVersusMassSpecMultiMap.values(ticChromPlotWidget); + + QList massSpecPlotWidgetList; + mainWindow->m_dataPlotWidgetRelationer.targets( + ticChromPlotWidget, &massSpecPlotWidgetList); + + // As long as there is at least one item, we are ok. + if(massSpecPlotWidgetList.size()) + { + // qDebug() << __FILE__ << __LINE__ + // << "List widget at index " << iter << "will be + // selected."; + + // Select that item right away. + mainWindow->mp_openSpectraDlg->deselectAllPlotWidgetsButOne( + ticChromPlotWidget); + break; + } + } + } + else if(siCount == 1) + { + // qDebug() << __FILE__ << __LINE__ + // << "Only one item is selected in the list widget. There are" + // << iCount << "items in the list widget"; + + // There is only one item that is selected. Just get to the next + // one, + // if possible, or cycle back to the next possible starting from the + // top. + int siIndex; + ticChromPlotWidget = + mainWindow->mp_openSpectraDlg->firstSelectedPlotWidget(&siIndex); + + + // qDebug() << __FILE__ << __LINE__ + // << "The item that is selected is at index " << siIndex; + + // The item that is selected is at index siIndex. Now, iterate in + // the + // various items of the list widget, starting at index siIndex + 1, + // or + // 0 and check if the iterated item has a corresponding mass spec + // window plot widget. If so, just select it. + + if(iCount == 1) + { + + // qDebug() << __FILE__ << __LINE__ + // << "The is only one item in the list widget, thus nothing to + // do."; + + // There is one item selected and only one item. Nothing to do. + event->accept(); + return; + } + + // There are multiple items, so iterate into each of them and see if + // we can select it, if it has a corresponding plot widget here. + // Start iterating at the next index, since we want to cycle through + // the various items. + + // If the currently selected item is the last of the list widget, + // then + // loop over to the first. + if(++siIndex > iCount - 1) + siIndex = 0; + + // qDebug() << __FILE__ << __LINE__ + // << "Starting iteration in the list widget at index " << siIndex; + + int iter = siIndex; + bool hasLooped = false; + + while(true) + { + // We cannot use the for loop below, because we want to loop + // over + // the end of the widget list if siIndex is in the middle of it, + // for example. + // for(int iter = siIndex; iter < iCount; ++iter) + + // qDebug() << __FILE__ << __LINE__ + // << "Iterating with iter: " << iter; + + ticChromPlotWidget = + mainWindow->mp_openSpectraDlg->plotWidgetAt(iter); + + // Get to the corresponding mass spec plot widget. + // Because a single tic chrom plot widget might generated many + // different mass spec plot widgets, we get a list: + // QListmassSpecPlotWidgetList = + // mainWindow->m_ticChromVersusMassSpecMultiMap.values(ticChromPlotWidget); + + QList massSpecPlotWidgetList; + mainWindow->m_dataPlotWidgetRelationer.targets( + ticChromPlotWidget, &massSpecPlotWidgetList); + + // As long as there is at least one item, we are ok. + if(massSpecPlotWidgetList.size()) + { + // qDebug() << __FILE__ << __LINE__ + // << "The item at index " << iter << "is going to be + // selected."; + + // Select that item right away. + mainWindow->mp_openSpectraDlg->deselectAllPlotWidgetsButOne( + ticChromPlotWidget); + break; + } + + // qDebug() << __FILE__ << __LINE__ + // << "Iterated in list widget item index " << iter; + + if(++iter >= iCount) + { + // qDebug() << __FILE__ << __LINE__ + // << "iter :" << iter << "is >= iCount, reset to 0"; + + iter = 0; + + // We will need to know that we looped over the last widget + // list + // item, such that we can test if we are going past the + // first + // index that we iterated over. + hasLooped = true; + + continue; + } + + // But we do not want to loop forever: + if(hasLooped && iter >= siIndex) + { + // qDebug() << __FILE__ << __LINE__ + // << "We looped already and iter is:" << iter << "so we + // break the loop."; + + break; + } + } + // End of + // while(true) + + // qDebug() << __FILE__ << __LINE__ + // << "Out of for loop iterating in the list widget items."; + + event->accept(); + return; + } + else + { + // The number of selected items is more than one. We want to only + // have + // one item selected, that has a corresponding mass spec plot + // widget. + // Then, next TAB key strokes will cycle through the list widget + // items. + int siIndex = + mainWindow->mp_openSpectraDlg->firstSelectedPlotWidgetIndex(); + + // If the currently selected item is the last of the list widget, + // then + // loop over to the first. + if(++siIndex >= iCount - 1) + siIndex = 0; + + for(int iter = siIndex; iter < iCount; ++iter) + { + ticChromPlotWidget = + mainWindow->mp_openSpectraDlg->plotWidgetAt(iter); + + // Get to the corresponding mass spec plot widget. + // Because a single tic chrom plot widget might generated many + // different mass spec plot widgets, we get a list: + // QListmassSpecPlotWidgetList = + // mainWindow->m_ticChromVersusMassSpecMultiMap.values(ticChromPlotWidget); + + QList massSpecPlotWidgetList; + mainWindow->m_dataPlotWidgetRelationer.targets( + ticChromPlotWidget, &massSpecPlotWidgetList); + + // As long as there is at least one item, we are ok. + if(massSpecPlotWidgetList.size()) + { + // Select that item right away. + mainWindow->mp_openSpectraDlg->deselectAllPlotWidgetsButOne( + ticChromPlotWidget); + break; + } + } + + event->accept(); + return; + } + // End of else that is, there are more than one list widget item + // selected. + } + // End of else if(event->key() == Qt::Key_Tab) + else if(event->key() == Qt::Key_L) + { + // The user wants to copy the current cursor location to the console + // window, such that it remains available after having moved the cursor. + // The handling of the text creation is different in these two + // situations: + // + // 1. the plot widget where this event occurred is a conventional + // mono-graph plot widget that sits in the lower part of the window. In + // this case, the color to be used to display the data label in the + // console window is easily gotten from the graph's pen. + // + // 2. the plot widget is a multi-graph plot widget that sits in the + // upper part of the multi plot window. In that case, it is more + // difficult to know what is the proper color to use, because we need to + // go to the open spectra dialog and get the list of selected files that + // initially contained the data plotted. We want to know what graph + // corresponds to what list widget item that is selected (or not) in the + // open mass spectra dialog window (see MainWindow). + + QString label; + if(m_isMultiGraph) + { + + // The event occurred in the multi-graph plot widget where many graphs + // are displayed. We need to craft a label for each graph that + // replicates the data of a plot that is proxied in the list widget of + // the OpenSpectraDlg. Only handle the spectra of which the list + // widget item is currently selected and for which the corresponding + // mass multi-graph plot is visible. + + for(int iter = 0; iter < graphCount(); ++iter) + { + QCPGraph *iterGraph = graph(iter); + + // Only work on this graph if it is visible: + + if(!iterGraph->visible()) + continue; + + // Get a handle to the conventional plot widget of which this + // multi-graph plot widget's graph is a replica. + + AbstractPlotWidget *massSpecPlotWidget = + parentWnd->monoGraphPlot(iterGraph); + + // Now use that pointer to get a handle to the tic chromatogram + // plot + // widget whence the data in this plot widget came: + // AbstractPlotWidget + // *ticChromPlotWidget = + // mainWindow->m_ticChromVersusMassSpecMultiMap.key(massSpecPlotWidget); + + DataPlotWidgetRelation *p_rootRelation = Q_NULLPTR; + AbstractPlotWidget *ticChromPlotWidget = + mainWindow->m_dataPlotWidgetRelationer.rootPlotWidget( + massSpecPlotWidget, &p_rootRelation); + + if(ticChromPlotWidget == nullptr) + { + qFatal( + "Fatal error at %s@%d -- %s. " + "Cannot be that a multiGraph plot widget has no root plot " + "widget." + "Program aborted.", + __FILE__, + __LINE__, + __FUNCTION__); + } + + // At this point, we know what plot widget in the Tic chrom window + // is the root plot of the graph currently iterated into. We need + // to + // know if that plot widget has a corresponding item in the open + // spectrum dialog list widget that is currently selected. + + if(mainWindow->mp_openSpectraDlg->isPlotWidgetSelected( + ticChromPlotWidget)) + { + // We can craft the label text to send to the console + // window, and + // that, with the proper color. + + label = QString("MZ(%1,%2)\n") + .arg(m_lastMousedPlotPoint.x()) + .arg(m_lastMousedPlotPoint.y()); + + if(label.isEmpty()) + { + parentWnd->statusBar()->showMessage( + "Failed to craft a text label."); + + event->accept(); + return; + } + else + { + // Send the label to the console window, so that we can + // make a copy + // paste. + mainWindow->logConsoleMessage(label, m_plottingColor); + } + } + } + // End of + // for(int iter = 0; iter < graphCount(); ++iter) + } + // End of + // if(m_isMultiGraph) + else + { + // We are in a plot widget that is a single-graph plot widget, the + // situation is easier: + + label = QString("MZ(%1,%2)\n") + .arg(m_lastMousedPlotPoint.x()) + .arg(m_lastMousedPlotPoint.y()); + + if(label.isEmpty()) + { + parentWnd->statusBar()->showMessage( + "Failed to craft a text label. "); + + event->accept(); + return; + } + else + { + // Send the label to the console window, so that we can make a + // copy + // paste. + + mainWindow->logConsoleMessage(label, m_plottingColor); + } + } + + event->accept(); + return; + } + // End of + // else if(event->key() == Qt::Key_L) + + // Now let the base class do its work if needed. + AbstractPlotWidget::keyReleaseEvent(event); +} + + +//! Return the arbitrary integration type that this plot widget can handle +int +MassSpecPlotWidget::arbitraryIntegrationType() +{ + return IntegrationType::MZ_TO_XXX; +} } // namespace msXpSmineXpert diff -pruN 5.3.3-1/minexpert/gui/MassSpecWnd.cpp 5.4.0-1/minexpert/gui/MassSpecWnd.cpp --- 5.3.3-1/minexpert/gui/MassSpecWnd.cpp 2018-06-20 15:46:39.000000000 +0000 +++ 5.4.0-1/minexpert/gui/MassSpecWnd.cpp 2018-09-11 19:21:00.000000000 +0000 @@ -691,8 +691,16 @@ namespace msXpSmineXpert // queried in another context. senderPlotWidget->setLastTicIntensity(integrator->ticIntensity()); + QString fullMsg = msg + QString(": TIC int.: %1").arg(integrator->ticIntensity()); // Now we can dipslay the results in the status bar: - statusBar()->showMessage(msg + QString(": TIC int.: %1").arg(integrator->ticIntensity())); + statusBar()->showMessage(fullMsg); + + // And in the main console window, now , with the proper color. + + QColor color = senderPlotWidget->color(); + + MainWindow *mainWindow = static_cast(parent()); + mainWindow->logConsoleMessage(fullMsg, color, false /*overwrite*/); // Finally we can destroy the integrator. delete integrator; diff -pruN 5.3.3-1/minexpert/gui/SaveToGraphicsFileDlg.cpp 5.4.0-1/minexpert/gui/SaveToGraphicsFileDlg.cpp --- 5.3.3-1/minexpert/gui/SaveToGraphicsFileDlg.cpp 2018-06-20 15:46:39.000000000 +0000 +++ 5.4.0-1/minexpert/gui/SaveToGraphicsFileDlg.cpp 2018-09-11 19:21:00.000000000 +0000 @@ -207,7 +207,7 @@ namespace msXpSmineXpert creator = m_ui.creatorLineEdit->text(); title = m_ui.titleLineEdit->text(); - mp_plot->savePdf(m_fileName, false, width, height, creator, title); + mp_plot->savePdf(m_fileName, width, height, QCP::epNoCosmetic, creator, title); break; case GraphicsFormat::GRAPHICS_FORMAT_PNG: diff -pruN 5.3.3-1/minexpert/gui/TicChromWnd.cpp 5.4.0-1/minexpert/gui/TicChromWnd.cpp --- 5.3.3-1/minexpert/gui/TicChromWnd.cpp 2018-06-20 15:46:39.000000000 +0000 +++ 5.4.0-1/minexpert/gui/TicChromWnd.cpp 2018-09-11 19:21:00.000000000 +0000 @@ -1170,8 +1170,17 @@ namespace msXpSmineXpert // queried in another context. senderPlotWidget->setLastTicIntensity(integrator->ticIntensity()); + QString fullMsg = msg + QString(": TIC int.: %1").arg(integrator->ticIntensity()); + // Now we can dipslay the results in the status bar: - statusBar()->showMessage(msg + QString(": TIC int.: %1").arg(integrator->ticIntensity())); + statusBar()->showMessage(fullMsg); + + // And in the main console window, now , with the proper color. + + QColor color = senderPlotWidget->color(); + + MainWindow *mainWindow = static_cast(parent()); + mainWindow->logConsoleMessage(fullMsg, color, false /*overwrite*/); // Finally we can destroy the integrator. delete integrator; diff -pruN 5.3.3-1/minexpert/minexpert.appstream 5.4.0-1/minexpert/minexpert.appstream --- 5.3.3-1/minexpert/minexpert.appstream 1970-01-01 00:00:00.000000000 +0000 +++ 5.4.0-1/minexpert/minexpert.appstream 2018-09-11 19:21:00.000000000 +0000 @@ -0,0 +1,62 @@ + + + + org.msxpertsuite.massxpert + GPL-3.0+ + GPL-3.0+ + Mass spectrometry software + Visualize and mine mass spec data + + Filippo Rusconi + + + +

+ + minexpert is a program used to visualize and mine mass spectral data, like mass spectra. + +

+ +

The program has the following features::

+
    + +
  • Open any number of mzML-formatted mass spec data files;
    • + +
  • The program compute the TIC chromatogram and the mz=ft(dt) color map if data are for an ion mobility mass spectrometry experiment;
    • + +
  • Any number of integrations (combinations) can be performed in any direction;
    • + +
  • Navigation through the data is intuitive, flexible yet powerful;
    • + +
+ + + + org.msxpertsuite.minexpert.desktop + + + + + Multiple mass spectra opened at the same time + http://msxpertsuite.org/screenshots/minexpert/minexpert-multiple-plots-massspecwnd.png + + + + Color map show ion mobility mass data + http://msxpertsuite.org/screenshots/minexpert/minexpert-colormap-wnd-shows-full-tool-bar.png + + + + Scripting console + http://msxpertsuite.org/screenshots/minexpert/minexpert-scripting-window-history-tab.png + + + + + http://www.msxpertsuite.org + + + minexpert + + + diff -pruN 5.3.3-1/minexpert/minexpert.desktop 5.4.0-1/minexpert/minexpert.desktop --- 5.3.3-1/minexpert/minexpert.desktop 2018-06-20 15:46:39.000000000 +0000 +++ 5.4.0-1/minexpert/minexpert.desktop 1970-01-01 00:00:00.000000000 +0000 @@ -1,14 +0,0 @@ -[Desktop Entry] -Version=1.0 -Name=mineXpert -Comment=Mass spectrometry data analysis (mass spectrum analysis) -GenericName=Mass spectrometry data analysis -GenericName[fr]=Analyse de données de spectrométrie de masse -GenericName[it]=Analisi dati di spettrometria di massa -TryExec=minexpert -Exec=minexpert -Terminal=true -Icon=msxpertsuite-icon-32 -Type=Application -Categories=Education;Science;Chemistry;Biology;Qt -Keywords=Mass spectrometry;Chemistry diff -pruN 5.3.3-1/minexpert/nongui/MassDataIntegrator.cpp 5.4.0-1/minexpert/nongui/MassDataIntegrator.cpp --- 5.3.3-1/minexpert/nongui/MassDataIntegrator.cpp 2018-06-20 15:46:39.000000000 +0000 +++ 5.4.0-1/minexpert/nongui/MassDataIntegrator.cpp 2018-09-11 19:21:00.000000000 +0000 @@ -1721,7 +1721,7 @@ namespace msXpSmineXpert int rtListSize = rtList.size(); - QString msg("Integrating to TIC intensity"); + QString msg = QString("Integrating to TIC intensity"); m_progressFeedbackStartValue = 0; m_progressFeedbackEndValue = rtListSize; @@ -1800,7 +1800,7 @@ namespace msXpSmineXpert if(omp_get_thread_num() == 0) emit updateFeedbackSignal(msg, iterationCount, true /* setVisible */, - LogType::LOG_TO_BOTH, m_progressFeedbackStartValue, m_progressFeedbackEndValue); + LogType::LOG_TO_STATUS_BAR, m_progressFeedbackStartValue, m_progressFeedbackEndValue); } } // End of diff -pruN 5.3.3-1/minexpert/nongui/MassSpecDataFileLoaderPwiz.cpp 5.4.0-1/minexpert/nongui/MassSpecDataFileLoaderPwiz.cpp --- 5.3.3-1/minexpert/nongui/MassSpecDataFileLoaderPwiz.cpp 2018-06-20 15:46:39.000000000 +0000 +++ 5.4.0-1/minexpert/nongui/MassSpecDataFileLoaderPwiz.cpp 2018-09-11 19:21:00.000000000 +0000 @@ -539,9 +539,10 @@ namespace msXpSmineXpert if(qIsNaN(m_curDriftTime) || qIsInf(m_curDriftTime)) { - //qDebug() << __FILE__ << __LINE__ << __FUNCTION__ - //<< "Found a NaN drift time at index " << m_spectrumIndex << ". Ignoring it."; + qDebug() << __FILE__ << __LINE__ << __FUNCTION__ + << "Found a NaN drift time at index " << m_spectrumIndex << ". Ignoring it."; + m_curDriftTime = -1; wasNanOrInf = true; break; } diff -pruN 5.3.3-1/minexpert/org.msxpertsuite.minexpert.desktop 5.4.0-1/minexpert/org.msxpertsuite.minexpert.desktop --- 5.3.3-1/minexpert/org.msxpertsuite.minexpert.desktop 1970-01-01 00:00:00.000000000 +0000 +++ 5.4.0-1/minexpert/org.msxpertsuite.minexpert.desktop 2018-09-11 19:21:00.000000000 +0000 @@ -0,0 +1,21 @@ +[Desktop Entry] +Encoding=UTF-8 +Version=1.1 + +Type=Application +Name=mineXpert + +GenericName=Mass spectrometry +GenericName[fr]=Spectrométrie de masse +GenericName[it]=Spettrometria di massa +Comment=Mass spectrometry data analysis and mining (mass spectrum analysis) +Comment[fr]=Analyse et fouille de données de données de spectrométrie de masse +Comment[it]=Analisi di dati di spettrometria di massa + +Exec=minexpert + +Terminal=true +Icon=msxpertsuite-icon-32 + +Categories=Science;Chemistry;Biology;Qt +Keywords=Mass spectrometry;Biology;Chemistry diff -pruN 5.3.3-1/minexpert/user-manual/devdoc-javascript-reference.txt 5.4.0-1/minexpert/user-manual/devdoc-javascript-reference.txt --- 5.3.3-1/minexpert/user-manual/devdoc-javascript-reference.txt 2018-06-20 15:46:39.000000000 +0000 +++ 5.4.0-1/minexpert/user-manual/devdoc-javascript-reference.txt 2018-09-11 19:21:00.000000000 +0000 @@ -1826,12 +1826,14 @@ AbstractPlotWidget Open the graphics export configuration dialog window. - .saveToPdfFile(fileName, noCosmeticPen, width, height, pdfCreator, title) + .saveToPdfFile(fileName, noCosmeticPen, width, height, + pdfCreator, title) Save this plot widget as a PDF file graphics. fileName: holding the file name - noCosmeticPen: that tells if pen optimizations should be performed + noCosmeticPen: that tells if pen optimizations should be + performed width: holding the size of the graphics file in pixels height: holding the size of the graphics file in pixels pdfCreator: holding the name of the creator of the PDF file @@ -1840,12 +1842,14 @@ AbstractPlotWidget .keys() - Return an of values representing the keys of the data plotted. + Return an of values representing the keys of the data + plotted. .values() - Return an of values representing the values of the data plotted. + Return an of values representing the values of the data + plotted. .lastTicIntensity() Binary files 5.3.3-1/minexpert/user-manual/figures/splashscreen.png and 5.4.0-1/minexpert/user-manual/figures/splashscreen.png differ diff -pruN 5.3.3-1/minexpert/user-manual/msxpertsuite-macros.tex 5.4.0-1/minexpert/user-manual/msxpertsuite-macros.tex --- 5.3.3-1/minexpert/user-manual/msxpertsuite-macros.tex 2018-06-20 15:46:39.000000000 +0000 +++ 5.4.0-1/minexpert/user-manual/msxpertsuite-macros.tex 2018-09-11 19:21:00.000000000 +0000 @@ -2,7 +2,7 @@ \newcommand{\msxpshrefbase}[2]{\href{http://www.msxpertsuite.org/#1}{#2}} %%% Version of the software suite -\newcommand{\ver}{5.3.3} +\newcommand{\ver}{5.4.0} \newcommand{\msXpsver}{\emph{msXpertSuite} version \ver} %%% msXpertSuite diff -pruN 5.3.3-1/todo 5.4.0-1/todo --- 5.3.3-1/todo 2018-06-20 15:46:39.000000000 +0000 +++ 5.4.0-1/todo 2018-09-11 19:21:00.000000000 +0000 @@ -1,3 +1,7 @@ +minexpert: create a new statistics main menu to compute the statistics on the +whole data set or on only the first spectrum. That should be useful when +scrutinizing the m/z integration parameters. + minexpert : changing the plot color only works if a mass spectrum was already integrated, not if only the TIC chrom plot is available. That's a bug. diff -pruN 5.3.3-1/user-manual-common/texfiles/msxpertsuite-macros.tex 5.4.0-1/user-manual-common/texfiles/msxpertsuite-macros.tex --- 5.3.3-1/user-manual-common/texfiles/msxpertsuite-macros.tex 2018-06-20 15:46:39.000000000 +0000 +++ 5.4.0-1/user-manual-common/texfiles/msxpertsuite-macros.tex 2018-09-11 19:21:00.000000000 +0000 @@ -2,7 +2,7 @@ \newcommand{\msxpshrefbase}[2]{\href{http://www.msxpertsuite.org/#1}{#2}} %%% Version of the software suite -\newcommand{\ver}{5.3.3} +\newcommand{\ver}{5.4.0} \newcommand{\msXpsver}{\emph{msXpertSuite} version \ver} %%% msXpertSuite diff -pruN 5.3.3-1/winInstaller/msxpertsuite-mingw64-win7+.iss 5.4.0-1/winInstaller/msxpertsuite-mingw64-win7+.iss --- 5.3.3-1/winInstaller/msxpertsuite-mingw64-win7+.iss 2018-06-20 15:46:39.000000000 +0000 +++ 5.4.0-1/winInstaller/msxpertsuite-mingw64-win7+.iss 2018-09-11 19:21:00.000000000 +0000 @@ -2,7 +2,7 @@ AppName=msXpertSuite ; Set version number below -#define public version "5.3.3" +#define public version "5.4.0" AppVersion={#version} #define public arch "mingw64"