diff --git a/src/main/java/net/sf/mzmine/desktop/impl/projecttree/ProjectTreeMouseHandler.java b/src/main/java/net/sf/mzmine/desktop/impl/projecttree/ProjectTreeMouseHandler.java index 49f7f8939..8791e83d4 100644 --- a/src/main/java/net/sf/mzmine/desktop/impl/projecttree/ProjectTreeMouseHandler.java +++ b/src/main/java/net/sf/mzmine/desktop/impl/projecttree/ProjectTreeMouseHandler.java @@ -35,12 +35,12 @@ import net.sf.mzmine.datamodel.RawDataFile; import net.sf.mzmine.datamodel.Scan; import net.sf.mzmine.main.MZmineCore; -import net.sf.mzmine.modules.peaklistmethods.orderpeaklists.OrderPeakListsModule; -import net.sf.mzmine.modules.peaklistmethods.orderpeaklists.OrderPeakListsParameters; +import net.sf.mzmine.modules.peaklistmethods.sortpeaklists.SortPeakListsModule; +import net.sf.mzmine.modules.peaklistmethods.sortpeaklists.SortPeakListsParameters; import net.sf.mzmine.modules.rawdatamethods.exportscans.ExportScansModule; -import net.sf.mzmine.modules.rawdatamethods.orderdatafiles.OrderDataFilesModule; -import net.sf.mzmine.modules.rawdatamethods.orderdatafiles.OrderDataFilesParameters; import net.sf.mzmine.modules.rawdatamethods.rawdataexport.RawDataExportModule; +import net.sf.mzmine.modules.rawdatamethods.sortdatafiles.SortDataFilesModule; +import net.sf.mzmine.modules.rawdatamethods.sortdatafiles.SortDataFilesParameters; import net.sf.mzmine.modules.visualization.infovisualizer.InfoVisualizerModule; import net.sf.mzmine.modules.visualization.peaklisttable.PeakListTableModule; import net.sf.mzmine.modules.visualization.peaksummary.PeakSummaryVisualizerModule; @@ -169,10 +169,10 @@ public void actionPerformed(ActionEvent e) { // save current selection TreePath savedSelection[] = tree.getSelectionPaths(); RawDataFile selectedFiles[] = tree.getSelectedObjects(RawDataFile.class); - OrderDataFilesModule module = MZmineCore.getModuleInstance(OrderDataFilesModule.class); + SortDataFilesModule module = MZmineCore.getModuleInstance(SortDataFilesModule.class); ParameterSet params = - MZmineCore.getConfiguration().getModuleParameters(OrderDataFilesModule.class); - params.getParameter(OrderDataFilesParameters.dataFiles) + MZmineCore.getConfiguration().getModuleParameters(SortDataFilesModule.class); + params.getParameter(SortDataFilesParameters.dataFiles) .setValue(RawDataFilesSelectionType.SPECIFIC_FILES, selectedFiles); module.runModule(MZmineCore.getProjectManager().getCurrentProject(), params, new ArrayList()); @@ -304,10 +304,10 @@ public void actionPerformed(ActionEvent e) { // save current selection TreePath savedSelection[] = tree.getSelectionPaths(); PeakList selectedPeakLists[] = tree.getSelectedObjects(PeakList.class); - OrderPeakListsModule module = MZmineCore.getModuleInstance(OrderPeakListsModule.class); + SortPeakListsModule module = MZmineCore.getModuleInstance(SortPeakListsModule.class); ParameterSet params = - MZmineCore.getConfiguration().getModuleParameters(OrderPeakListsModule.class); - params.getParameter(OrderPeakListsParameters.peakLists) + MZmineCore.getConfiguration().getModuleParameters(SortPeakListsModule.class); + params.getParameter(SortPeakListsParameters.peakLists) .setValue(PeakListsSelectionType.SPECIFIC_PEAKLISTS, selectedPeakLists); module.runModule(MZmineCore.getProjectManager().getCurrentProject(), params, new ArrayList()); diff --git a/src/main/java/net/sf/mzmine/main/MZmineModulesList.java b/src/main/java/net/sf/mzmine/main/MZmineModulesList.java index 4b129714f..5fcd3ceed 100644 --- a/src/main/java/net/sf/mzmine/main/MZmineModulesList.java +++ b/src/main/java/net/sf/mzmine/main/MZmineModulesList.java @@ -77,13 +77,13 @@ import net.sf.mzmine.modules.peaklistmethods.normalization.linear.LinearNormalizerModule; import net.sf.mzmine.modules.peaklistmethods.normalization.rtnormalizer.RTNormalizerModule; import net.sf.mzmine.modules.peaklistmethods.normalization.standardcompound.StandardCompoundNormalizerModule; -import net.sf.mzmine.modules.peaklistmethods.orderpeaklists.OrderPeakListsModule; import net.sf.mzmine.modules.peaklistmethods.peakpicking.adap3decompositionV1_5.ADAP3DecompositionV1_5Module; import net.sf.mzmine.modules.peaklistmethods.peakpicking.adap3decompositionV2.ADAP3DecompositionV2Module; import net.sf.mzmine.modules.peaklistmethods.peakpicking.deconvolution.DeconvolutionModule; import net.sf.mzmine.modules.peaklistmethods.peakpicking.peakextender.PeakExtenderModule; import net.sf.mzmine.modules.peaklistmethods.peakpicking.shapemodeler.ShapeModelerModule; import net.sf.mzmine.modules.peaklistmethods.peakpicking.smoothing.SmoothingModule; +import net.sf.mzmine.modules.peaklistmethods.sortpeaklists.SortPeakListsModule; import net.sf.mzmine.modules.projectmethods.projectclose.ProjectCloseModule; import net.sf.mzmine.modules.projectmethods.projectload.ProjectLoadModule; import net.sf.mzmine.modules.projectmethods.projectsave.ProjectSaveAsModule; @@ -97,7 +97,6 @@ import net.sf.mzmine.modules.rawdatamethods.filtering.scanfilters.ScanFiltersModule; import net.sf.mzmine.modules.rawdatamethods.filtering.scansmoothing.ScanSmoothingModule; import net.sf.mzmine.modules.rawdatamethods.merge.RawFileMergeModule; -import net.sf.mzmine.modules.rawdatamethods.orderdatafiles.OrderDataFilesModule; import net.sf.mzmine.modules.rawdatamethods.peakpicking.gridmass.GridMassModule; import net.sf.mzmine.modules.rawdatamethods.peakpicking.manual.ManualPeakPickerModule; import net.sf.mzmine.modules.rawdatamethods.peakpicking.massdetection.MassDetectionModule; @@ -105,6 +104,7 @@ import net.sf.mzmine.modules.rawdatamethods.peakpicking.targetedpeakdetection.TargetedPeakDetectionModule; import net.sf.mzmine.modules.rawdatamethods.rawdataexport.RawDataExportModule; import net.sf.mzmine.modules.rawdatamethods.rawdataimport.RawDataImportModule; +import net.sf.mzmine.modules.rawdatamethods.sortdatafiles.SortDataFilesModule; import net.sf.mzmine.modules.tools.isotopepatternpreview.IsotopePatternPreviewModule; import net.sf.mzmine.modules.tools.msmsspectramerge.MsMsSpectraMergeModule; import net.sf.mzmine.modules.tools.mzrangecalculator.MzRangeFormulaCalculatorModule; @@ -158,10 +158,10 @@ public class MZmineModulesList { // Not ready for prime time: ADAP3DModule.class, GridMassModule.class, ManualPeakPickerModule.class, MsMsPeakPickerModule.class, ScanFiltersModule.class, CropFilterModule.class, BaselineCorrectionModule.class, - AlignScansModule.class, ScanSmoothingModule.class, OrderDataFilesModule.class, + AlignScansModule.class, ScanSmoothingModule.class, SortDataFilesModule.class, // Alignment - OrderPeakListsModule.class, JoinAlignerModule.class, HierarAlignerGcModule.class, + SortPeakListsModule.class, JoinAlignerModule.class, HierarAlignerGcModule.class, RansacAlignerModule.class, ADAP3AlignerModule.class, // PathAlignerModule.class, diff --git a/src/main/java/net/sf/mzmine/modules/peaklistmethods/orderpeaklists/OrderPeakListsModule.java b/src/main/java/net/sf/mzmine/modules/peaklistmethods/sortpeaklists/SortPeakListsModule.java similarity index 91% rename from src/main/java/net/sf/mzmine/modules/peaklistmethods/orderpeaklists/OrderPeakListsModule.java rename to src/main/java/net/sf/mzmine/modules/peaklistmethods/sortpeaklists/SortPeakListsModule.java index 5e4140d0a..07a3d2f48 100644 --- a/src/main/java/net/sf/mzmine/modules/peaklistmethods/orderpeaklists/OrderPeakListsModule.java +++ b/src/main/java/net/sf/mzmine/modules/peaklistmethods/sortpeaklists/SortPeakListsModule.java @@ -16,7 +16,7 @@ * USA */ -package net.sf.mzmine.modules.peaklistmethods.orderpeaklists; +package net.sf.mzmine.modules.peaklistmethods.sortpeaklists; import java.util.ArrayList; import java.util.Arrays; @@ -45,12 +45,12 @@ * This is a very simple module which reorders feature lists alphabetically * */ -public class OrderPeakListsModule implements MZmineProcessingModule { +public class SortPeakListsModule implements MZmineProcessingModule { private Logger logger = Logger.getLogger(this.getClass().getName()); - private static final String MODULE_NAME = "Order feature lists"; - private static final String MODULE_DESCRIPTION = "Order selected feature lists alphabetically"; + private static final String MODULE_NAME = "Sort feature lists"; + private static final String MODULE_DESCRIPTION = "Sort selected feature lists alphabetically"; @Override public @Nonnull String getName() { @@ -68,7 +68,7 @@ public ExitCode runModule(@Nonnull MZmineProject project, @Nonnull ParameterSet @Nonnull Collection tasks) { List peakLists = Arrays.asList(parameters - .getParameter(OrderPeakListsParameters.peakLists).getValue().getMatchingPeakLists()); + .getParameter(SortPeakListsParameters.peakLists).getValue().getMatchingPeakLists()); PeakListTreeModel model = null; @@ -133,7 +133,7 @@ public int compare(DefaultMutableTreeNode o1, DefaultMutableTreeNode o2) { @Override public @Nonnull Class getParameterSetClass() { - return OrderPeakListsParameters.class; + return SortPeakListsParameters.class; } } diff --git a/src/main/java/net/sf/mzmine/modules/peaklistmethods/orderpeaklists/OrderPeakListsParameters.java b/src/main/java/net/sf/mzmine/modules/peaklistmethods/sortpeaklists/SortPeakListsParameters.java similarity index 86% rename from src/main/java/net/sf/mzmine/modules/peaklistmethods/orderpeaklists/OrderPeakListsParameters.java rename to src/main/java/net/sf/mzmine/modules/peaklistmethods/sortpeaklists/SortPeakListsParameters.java index ce7727e89..7f7fcf9f4 100644 --- a/src/main/java/net/sf/mzmine/modules/peaklistmethods/orderpeaklists/OrderPeakListsParameters.java +++ b/src/main/java/net/sf/mzmine/modules/peaklistmethods/sortpeaklists/SortPeakListsParameters.java @@ -16,17 +16,17 @@ * USA */ -package net.sf.mzmine.modules.peaklistmethods.orderpeaklists; +package net.sf.mzmine.modules.peaklistmethods.sortpeaklists; import net.sf.mzmine.parameters.Parameter; import net.sf.mzmine.parameters.impl.SimpleParameterSet; import net.sf.mzmine.parameters.parametertypes.selectors.PeakListsParameter; -public class OrderPeakListsParameters extends SimpleParameterSet { +public class SortPeakListsParameters extends SimpleParameterSet { public static final PeakListsParameter peakLists = new PeakListsParameter(); - public OrderPeakListsParameters() { + public SortPeakListsParameters() { super(new Parameter[] {peakLists}); } diff --git a/src/main/java/net/sf/mzmine/modules/rawdatamethods/orderdatafiles/OrderDataFilesModule.java b/src/main/java/net/sf/mzmine/modules/rawdatamethods/sortdatafiles/SortDataFilesModule.java similarity index 90% rename from src/main/java/net/sf/mzmine/modules/rawdatamethods/orderdatafiles/OrderDataFilesModule.java rename to src/main/java/net/sf/mzmine/modules/rawdatamethods/sortdatafiles/SortDataFilesModule.java index f8210e32b..a88bdecaf 100644 --- a/src/main/java/net/sf/mzmine/modules/rawdatamethods/orderdatafiles/OrderDataFilesModule.java +++ b/src/main/java/net/sf/mzmine/modules/rawdatamethods/sortdatafiles/SortDataFilesModule.java @@ -16,7 +16,7 @@ * USA */ -package net.sf.mzmine.modules.rawdatamethods.orderdatafiles; +package net.sf.mzmine.modules.rawdatamethods.sortdatafiles; import java.util.ArrayList; import java.util.Arrays; @@ -43,10 +43,10 @@ /** * This is a very simple module which reorders data files alphabetically */ -public class OrderDataFilesModule implements MZmineProcessingModule { +public class SortDataFilesModule implements MZmineProcessingModule { - private static final String MODULE_NAME = "Order raw data files"; - private static final String MODULE_DESCRIPTION = "Order selected raw data files alphabetically"; + private static final String MODULE_NAME = "Sort raw data files"; + private static final String MODULE_DESCRIPTION = "Sort selected raw data files alphabetically"; @Override public @Nonnull String getName() { @@ -64,7 +64,7 @@ public ExitCode runModule(@Nonnull MZmineProject project, @Nonnull ParameterSet @Nonnull Collection tasks) { List dataFiles = Arrays.asList(parameters - .getParameter(OrderDataFilesParameters.dataFiles).getValue().getMatchingRawDataFiles()); + .getParameter(SortDataFilesParameters.dataFiles).getValue().getMatchingRawDataFiles()); RawDataTreeModel model = null; @@ -128,7 +128,7 @@ public int compare(DefaultMutableTreeNode o1, DefaultMutableTreeNode o2) { @Override public @Nonnull Class getParameterSetClass() { - return OrderDataFilesParameters.class; + return SortDataFilesParameters.class; } } diff --git a/src/main/java/net/sf/mzmine/modules/rawdatamethods/orderdatafiles/OrderDataFilesParameters.java b/src/main/java/net/sf/mzmine/modules/rawdatamethods/sortdatafiles/SortDataFilesParameters.java similarity index 87% rename from src/main/java/net/sf/mzmine/modules/rawdatamethods/orderdatafiles/OrderDataFilesParameters.java rename to src/main/java/net/sf/mzmine/modules/rawdatamethods/sortdatafiles/SortDataFilesParameters.java index 75ebaf2b2..d900ebd02 100644 --- a/src/main/java/net/sf/mzmine/modules/rawdatamethods/orderdatafiles/OrderDataFilesParameters.java +++ b/src/main/java/net/sf/mzmine/modules/rawdatamethods/sortdatafiles/SortDataFilesParameters.java @@ -16,17 +16,17 @@ * USA */ -package net.sf.mzmine.modules.rawdatamethods.orderdatafiles; +package net.sf.mzmine.modules.rawdatamethods.sortdatafiles; import net.sf.mzmine.parameters.Parameter; import net.sf.mzmine.parameters.impl.SimpleParameterSet; import net.sf.mzmine.parameters.parametertypes.selectors.RawDataFilesParameter; -public class OrderDataFilesParameters extends SimpleParameterSet { +public class SortDataFilesParameters extends SimpleParameterSet { public static final RawDataFilesParameter dataFiles = new RawDataFilesParameter(); - public OrderDataFilesParameters() { + public SortDataFilesParameters() { super(new Parameter[] {dataFiles}); }