Index: src/main/java/net/sf/mzmine/desktop/preferences/MZminePreferences.java =================================================================== --- src/main/java/net/sf/mzmine/desktop/preferences/MZminePreferences.java (revision 3347) +++ src/main/java/net/sf/mzmine/desktop/preferences/MZminePreferences.java (working copy) @@ -21,8 +21,6 @@ import java.text.DecimalFormat; -import org.w3c.dom.Element; - import net.sf.mzmine.main.MZmineCore; import net.sf.mzmine.parameters.Parameter; import net.sf.mzmine.parameters.ParameterSet; @@ -30,6 +28,8 @@ import net.sf.mzmine.parameters.parametertypes.OptionalModuleParameter; import net.sf.mzmine.util.ExitCode; +import org.w3c.dom.Element; + public class MZminePreferences extends SimpleParameterSet { public static final NumberFormatParameter mzFormat = new NumberFormatParameter( Index: src/main/java/net/sf/mzmine/modules/batchmode/BatchQueueParameter.java =================================================================== --- src/main/java/net/sf/mzmine/modules/batchmode/BatchQueueParameter.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/batchmode/BatchQueueParameter.java (working copy) @@ -19,6 +19,8 @@ package net.sf.mzmine.modules.batchmode; +import java.util.Collection; + import net.sf.mzmine.modules.MZmineProcessingStep; import net.sf.mzmine.parameters.Parameter; import net.sf.mzmine.parameters.ParameterSet; @@ -25,10 +27,9 @@ import net.sf.mzmine.parameters.UserParameter; import net.sf.mzmine.parameters.parametertypes.PeakListsParameter; import net.sf.mzmine.parameters.parametertypes.RawDataFilesParameter; + import org.w3c.dom.Element; -import java.util.Collection; - /** * Batch queue parameter. */ Index: src/main/java/net/sf/mzmine/modules/masslistmethods/chromatogrambuilder/ChromatogramBuilderParameters.java =================================================================== --- src/main/java/net/sf/mzmine/modules/masslistmethods/chromatogrambuilder/ChromatogramBuilderParameters.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/masslistmethods/chromatogrambuilder/ChromatogramBuilderParameters.java (working copy) @@ -22,9 +22,9 @@ import net.sf.mzmine.main.MZmineCore; import net.sf.mzmine.parameters.Parameter; import net.sf.mzmine.parameters.impl.SimpleParameterSet; +import net.sf.mzmine.parameters.parametertypes.DoubleParameter; import net.sf.mzmine.parameters.parametertypes.MZToleranceParameter; import net.sf.mzmine.parameters.parametertypes.MassListParameter; -import net.sf.mzmine.parameters.parametertypes.DoubleParameter; import net.sf.mzmine.parameters.parametertypes.RawDataFilesParameter; import net.sf.mzmine.parameters.parametertypes.StringParameter; Index: src/main/java/net/sf/mzmine/modules/peaklistmethods/alignment/path/functions/ScoreAligner.java =================================================================== --- src/main/java/net/sf/mzmine/modules/peaklistmethods/alignment/path/functions/ScoreAligner.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/peaklistmethods/alignment/path/functions/ScoreAligner.java (working copy) @@ -18,8 +18,6 @@ */ package net.sf.mzmine.modules.peaklistmethods.alignment.path.functions; -import net.sf.mzmine.modules.peaklistmethods.alignment.path.scorer.RTScore; - import java.util.ArrayList; import java.util.Arrays; import java.util.Collections; @@ -38,6 +36,7 @@ import net.sf.mzmine.datamodel.RawDataFile; import net.sf.mzmine.datamodel.impl.SimplePeakList; import net.sf.mzmine.modules.peaklistmethods.alignment.path.PathAlignerParameters; +import net.sf.mzmine.modules.peaklistmethods.alignment.path.scorer.RTScore; import net.sf.mzmine.parameters.ParameterSet; public class ScoreAligner implements Aligner { Index: src/main/java/net/sf/mzmine/modules/peaklistmethods/alignment/ransac/AlignmentPreviewTooltipGenerator.java =================================================================== --- src/main/java/net/sf/mzmine/modules/peaklistmethods/alignment/ransac/AlignmentPreviewTooltipGenerator.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/peaklistmethods/alignment/ransac/AlignmentPreviewTooltipGenerator.java (working copy) @@ -21,7 +21,9 @@ package net.sf.mzmine.modules.peaklistmethods.alignment.ransac; import java.text.NumberFormat; + import net.sf.mzmine.main.MZmineCore; + import org.jfree.chart.labels.XYToolTipGenerator; import org.jfree.data.xy.XYDataset; Index: src/main/java/net/sf/mzmine/modules/peaklistmethods/dataanalysis/rtmzplots/logratioplot/LogratioPlotModule.java =================================================================== --- src/main/java/net/sf/mzmine/modules/peaklistmethods/dataanalysis/rtmzplots/logratioplot/LogratioPlotModule.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/peaklistmethods/dataanalysis/rtmzplots/logratioplot/LogratioPlotModule.java (working copy) @@ -25,7 +25,6 @@ import javax.annotation.Nonnull; import net.sf.mzmine.datamodel.PeakList; -import net.sf.mzmine.main.MZmineCore; import net.sf.mzmine.modules.MZmineModuleCategory; import net.sf.mzmine.modules.MZmineProcessingModule; import net.sf.mzmine.modules.peaklistmethods.dataanalysis.rtmzplots.RTMZAnalyzerWindow; Index: src/main/java/net/sf/mzmine/modules/peaklistmethods/filtering/duplicatefilter/DuplicateFilterTask.java =================================================================== --- src/main/java/net/sf/mzmine/modules/peaklistmethods/filtering/duplicatefilter/DuplicateFilterTask.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/peaklistmethods/filtering/duplicatefilter/DuplicateFilterTask.java (working copy) @@ -26,8 +26,8 @@ import net.sf.mzmine.datamodel.Feature; import net.sf.mzmine.datamodel.MZmineProject; import net.sf.mzmine.datamodel.PeakList; +import net.sf.mzmine.datamodel.PeakList.PeakListAppliedMethod; import net.sf.mzmine.datamodel.PeakListRow; -import net.sf.mzmine.datamodel.PeakList.PeakListAppliedMethod; import net.sf.mzmine.datamodel.impl.SimpleFeature; import net.sf.mzmine.datamodel.impl.SimplePeakList; import net.sf.mzmine.datamodel.impl.SimplePeakListAppliedMethod; Index: src/main/java/net/sf/mzmine/modules/peaklistmethods/filtering/rowsfilter/RowsFilterTask.java =================================================================== --- src/main/java/net/sf/mzmine/modules/peaklistmethods/filtering/rowsfilter/RowsFilterTask.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/peaklistmethods/filtering/rowsfilter/RowsFilterTask.java (working copy) @@ -38,9 +38,9 @@ import net.sf.mzmine.datamodel.IsotopePattern; import net.sf.mzmine.datamodel.MZmineProject; import net.sf.mzmine.datamodel.PeakList; +import net.sf.mzmine.datamodel.PeakList.PeakListAppliedMethod; import net.sf.mzmine.datamodel.PeakListRow; import net.sf.mzmine.datamodel.RawDataFile; -import net.sf.mzmine.datamodel.PeakList.PeakListAppliedMethod; import net.sf.mzmine.datamodel.impl.SimpleFeature; import net.sf.mzmine.datamodel.impl.SimplePeakList; import net.sf.mzmine.datamodel.impl.SimplePeakListAppliedMethod; Index: src/main/java/net/sf/mzmine/modules/peaklistmethods/gapfilling/peakfinder/Gap.java =================================================================== --- src/main/java/net/sf/mzmine/modules/peaklistmethods/gapfilling/peakfinder/Gap.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/peaklistmethods/gapfilling/peakfinder/Gap.java (working copy) @@ -23,10 +23,10 @@ import java.util.Vector; import net.sf.mzmine.datamodel.DataPoint; +import net.sf.mzmine.datamodel.Feature.FeatureStatus; import net.sf.mzmine.datamodel.PeakListRow; import net.sf.mzmine.datamodel.RawDataFile; import net.sf.mzmine.datamodel.Scan; -import net.sf.mzmine.datamodel.Feature.FeatureStatus; import net.sf.mzmine.datamodel.impl.SimpleDataPoint; import net.sf.mzmine.datamodel.impl.SimpleFeature; import net.sf.mzmine.util.Range; Index: src/main/java/net/sf/mzmine/modules/peaklistmethods/identification/adductsearch/AddAdductsAction.java =================================================================== --- src/main/java/net/sf/mzmine/modules/peaklistmethods/identification/adductsearch/AddAdductsAction.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/peaklistmethods/identification/adductsearch/AddAdductsAction.java (working copy) @@ -23,6 +23,15 @@ package net.sf.mzmine.modules.peaklistmethods.identification.adductsearch; +import java.awt.Component; +import java.awt.event.ActionEvent; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Collection; + +import javax.swing.AbstractAction; +import javax.swing.SwingUtilities; + import net.sf.mzmine.main.MZmineCore; import net.sf.mzmine.parameters.Parameter; import net.sf.mzmine.parameters.ParameterSet; @@ -33,13 +42,6 @@ import net.sf.mzmine.parameters.parametertypes.StringParameter; import net.sf.mzmine.util.ExitCode; -import javax.swing.*; -import java.awt.*; -import java.awt.event.ActionEvent; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.Collection; - /** * An action to add custom adducts. * Index: src/main/java/net/sf/mzmine/modules/peaklistmethods/identification/adductsearch/AdductSearchParameters.java =================================================================== --- src/main/java/net/sf/mzmine/modules/peaklistmethods/identification/adductsearch/AdductSearchParameters.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/peaklistmethods/identification/adductsearch/AdductSearchParameters.java (working copy) @@ -21,7 +21,11 @@ import net.sf.mzmine.parameters.Parameter; import net.sf.mzmine.parameters.impl.SimpleParameterSet; -import net.sf.mzmine.parameters.parametertypes.*; +import net.sf.mzmine.parameters.parametertypes.AdductsParameter; +import net.sf.mzmine.parameters.parametertypes.MZToleranceParameter; +import net.sf.mzmine.parameters.parametertypes.PeakListsParameter; +import net.sf.mzmine.parameters.parametertypes.PercentParameter; +import net.sf.mzmine.parameters.parametertypes.RTToleranceParameter; public class AdductSearchParameters extends SimpleParameterSet { Index: src/main/java/net/sf/mzmine/modules/peaklistmethods/identification/adductsearch/AdductSearchTask.java =================================================================== --- src/main/java/net/sf/mzmine/modules/peaklistmethods/identification/adductsearch/AdductSearchTask.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/peaklistmethods/identification/adductsearch/AdductSearchTask.java (working copy) @@ -18,6 +18,11 @@ */ package net.sf.mzmine.modules.peaklistmethods.identification.adductsearch; +import static net.sf.mzmine.modules.peaklistmethods.identification.adductsearch.AdductSearchParameters.ADDUCTS; +import static net.sf.mzmine.modules.peaklistmethods.identification.adductsearch.AdductSearchParameters.MAX_ADDUCT_HEIGHT; +import static net.sf.mzmine.modules.peaklistmethods.identification.adductsearch.AdductSearchParameters.MZ_TOLERANCE; +import static net.sf.mzmine.modules.peaklistmethods.identification.adductsearch.AdductSearchParameters.RT_TOLERANCE; + import java.util.Arrays; import java.util.logging.Level; import java.util.logging.Logger; @@ -34,7 +39,6 @@ import net.sf.mzmine.util.PeakListRowSorter; import net.sf.mzmine.util.SortingDirection; import net.sf.mzmine.util.SortingProperty; -import static net.sf.mzmine.modules.peaklistmethods.identification.adductsearch.AdductSearchParameters.*; public class AdductSearchTask extends AbstractTask { Index: src/main/java/net/sf/mzmine/modules/peaklistmethods/identification/adductsearch/AdductType.java =================================================================== --- src/main/java/net/sf/mzmine/modules/peaklistmethods/identification/adductsearch/AdductType.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/peaklistmethods/identification/adductsearch/AdductType.java (working copy) @@ -19,10 +19,10 @@ package net.sf.mzmine.modules.peaklistmethods.identification.adductsearch; +import java.util.Arrays; + import net.sf.mzmine.main.MZmineCore; -import java.util.Arrays; - public class AdductType { // Default adducts. Index: src/main/java/net/sf/mzmine/modules/peaklistmethods/identification/adductsearch/DefaultAdductsAction.java =================================================================== --- src/main/java/net/sf/mzmine/modules/peaklistmethods/identification/adductsearch/DefaultAdductsAction.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/peaklistmethods/identification/adductsearch/DefaultAdductsAction.java (working copy) @@ -23,12 +23,14 @@ package net.sf.mzmine.modules.peaklistmethods.identification.adductsearch; +import java.awt.Component; +import java.awt.event.ActionEvent; + +import javax.swing.AbstractAction; +import javax.swing.SwingUtilities; + import net.sf.mzmine.parameters.parametertypes.AdductsComponent; -import javax.swing.*; -import java.awt.*; -import java.awt.event.ActionEvent; - /** * An action to handle resetting the adducts list. * Index: src/main/java/net/sf/mzmine/modules/peaklistmethods/identification/adductsearch/ExportAdductsAction.java =================================================================== --- src/main/java/net/sf/mzmine/modules/peaklistmethods/identification/adductsearch/ExportAdductsAction.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/peaklistmethods/identification/adductsearch/ExportAdductsAction.java (working copy) @@ -23,14 +23,7 @@ package net.sf.mzmine.modules.peaklistmethods.identification.adductsearch; -import com.Ostermiller.util.CSVPrinter; -import net.sf.mzmine.main.MZmineCore; -import net.sf.mzmine.parameters.parametertypes.AdductsComponent; -import net.sf.mzmine.util.dialogs.LoadSaveFileChooser; - -import javax.swing.*; -import javax.swing.filechooser.FileNameExtensionFilter; -import java.awt.*; +import java.awt.Component; import java.awt.event.ActionEvent; import java.io.File; import java.io.FileWriter; @@ -38,6 +31,16 @@ import java.util.logging.Level; import java.util.logging.Logger; +import javax.swing.AbstractAction; +import javax.swing.SwingUtilities; +import javax.swing.filechooser.FileNameExtensionFilter; + +import net.sf.mzmine.main.MZmineCore; +import net.sf.mzmine.parameters.parametertypes.AdductsComponent; +import net.sf.mzmine.util.dialogs.LoadSaveFileChooser; + +import com.Ostermiller.util.CSVPrinter; + /** * An action to handle exporting adducts to a file. * Index: src/main/java/net/sf/mzmine/modules/peaklistmethods/identification/adductsearch/ImportAdductsAction.java =================================================================== --- src/main/java/net/sf/mzmine/modules/peaklistmethods/identification/adductsearch/ImportAdductsAction.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/peaklistmethods/identification/adductsearch/ImportAdductsAction.java (working copy) @@ -23,14 +23,7 @@ package net.sf.mzmine.modules.peaklistmethods.identification.adductsearch; -import com.Ostermiller.util.CSVParser; -import net.sf.mzmine.main.MZmineCore; -import net.sf.mzmine.parameters.parametertypes.AdductsComponent; -import net.sf.mzmine.util.dialogs.LoadSaveFileChooser; - -import javax.swing.*; -import javax.swing.filechooser.FileNameExtensionFilter; -import java.awt.*; +import java.awt.Component; import java.awt.event.ActionEvent; import java.io.File; import java.io.FileReader; @@ -40,6 +33,16 @@ import java.util.logging.Level; import java.util.logging.Logger; +import javax.swing.AbstractAction; +import javax.swing.SwingUtilities; +import javax.swing.filechooser.FileNameExtensionFilter; + +import net.sf.mzmine.main.MZmineCore; +import net.sf.mzmine.parameters.parametertypes.AdductsComponent; +import net.sf.mzmine.util.dialogs.LoadSaveFileChooser; + +import com.Ostermiller.util.CSVParser; + /** * An action to handle importing adducts from a file. * Index: src/main/java/net/sf/mzmine/modules/peaklistmethods/identification/camera/CameraSearchModule.java =================================================================== --- src/main/java/net/sf/mzmine/modules/peaklistmethods/identification/camera/CameraSearchModule.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/peaklistmethods/identification/camera/CameraSearchModule.java (working copy) @@ -23,6 +23,10 @@ package net.sf.mzmine.modules.peaklistmethods.identification.camera; +import java.util.Collection; + +import javax.annotation.Nonnull; + import net.sf.mzmine.datamodel.PeakList; import net.sf.mzmine.modules.MZmineModuleCategory; import net.sf.mzmine.modules.MZmineProcessingModule; @@ -30,10 +34,6 @@ import net.sf.mzmine.taskcontrol.Task; import net.sf.mzmine.util.ExitCode; -import javax.annotation.Nonnull; - -import java.util.Collection; - /** * Uses CAMERA to form pseudo-spectra. * Index: src/main/java/net/sf/mzmine/modules/peaklistmethods/identification/camera/CameraSearchParameters.java =================================================================== --- src/main/java/net/sf/mzmine/modules/peaklistmethods/identification/camera/CameraSearchParameters.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/peaklistmethods/identification/camera/CameraSearchParameters.java (working copy) @@ -23,12 +23,16 @@ package net.sf.mzmine.modules.peaklistmethods.identification.camera; +import java.text.NumberFormat; + import net.sf.mzmine.parameters.Parameter; import net.sf.mzmine.parameters.impl.SimpleParameterSet; -import net.sf.mzmine.parameters.parametertypes.*; +import net.sf.mzmine.parameters.parametertypes.DoubleParameter; +import net.sf.mzmine.parameters.parametertypes.IntegerParameter; +import net.sf.mzmine.parameters.parametertypes.MZToleranceParameter; +import net.sf.mzmine.parameters.parametertypes.PeakListsParameter; +import net.sf.mzmine.parameters.parametertypes.PercentParameter; -import java.text.NumberFormat; - /** * Parameters for a CameraSearchTask. * Index: src/main/java/net/sf/mzmine/modules/peaklistmethods/identification/camera/CameraSearchTask.java =================================================================== --- src/main/java/net/sf/mzmine/modules/peaklistmethods/identification/camera/CameraSearchTask.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/peaklistmethods/identification/camera/CameraSearchTask.java (working copy) @@ -23,7 +23,21 @@ package net.sf.mzmine.modules.peaklistmethods.identification.camera; -import net.sf.mzmine.datamodel.*; +import java.util.HashMap; +import java.util.Map; +import java.util.Set; +import java.util.TreeSet; +import java.util.logging.Level; +import java.util.logging.Logger; +import java.util.regex.Matcher; +import java.util.regex.Pattern; + +import net.sf.mzmine.datamodel.DataPoint; +import net.sf.mzmine.datamodel.Feature; +import net.sf.mzmine.datamodel.PeakIdentity; +import net.sf.mzmine.datamodel.PeakList; +import net.sf.mzmine.datamodel.RawDataFile; +import net.sf.mzmine.datamodel.Scan; import net.sf.mzmine.datamodel.impl.SimpleDataPoint; import net.sf.mzmine.datamodel.impl.SimplePeakIdentity; import net.sf.mzmine.main.MZmineCore; @@ -40,15 +54,6 @@ import org.rosuda.JRI.REXP; import org.rosuda.JRI.Rengine; -import java.util.HashMap; -import java.util.Map; -import java.util.Set; -import java.util.TreeSet; -import java.util.logging.Level; -import java.util.logging.Logger; -import java.util.regex.Matcher; -import java.util.regex.Pattern; - /** * A task to perform a CAMERA search. * Index: src/main/java/net/sf/mzmine/modules/peaklistmethods/identification/dbsearch/SingleRowIdentificationParameters.java =================================================================== --- src/main/java/net/sf/mzmine/modules/peaklistmethods/identification/dbsearch/SingleRowIdentificationParameters.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/peaklistmethods/identification/dbsearch/SingleRowIdentificationParameters.java (working copy) @@ -22,7 +22,11 @@ import net.sf.mzmine.modules.peaklistmethods.isotopes.isotopepatternscore.IsotopePatternScoreParameters; import net.sf.mzmine.parameters.Parameter; import net.sf.mzmine.parameters.impl.SimpleParameterSet; -import net.sf.mzmine.parameters.parametertypes.*; +import net.sf.mzmine.parameters.parametertypes.IntegerParameter; +import net.sf.mzmine.parameters.parametertypes.MZToleranceParameter; +import net.sf.mzmine.parameters.parametertypes.ModuleComboParameter; +import net.sf.mzmine.parameters.parametertypes.NeutralMassParameter; +import net.sf.mzmine.parameters.parametertypes.OptionalModuleParameter; public class SingleRowIdentificationParameters extends SimpleParameterSet { Index: src/main/java/net/sf/mzmine/modules/peaklistmethods/identification/formulapredictionpeaklist/FormulaPredictionPeakListParameters.java =================================================================== --- src/main/java/net/sf/mzmine/modules/peaklistmethods/identification/formulapredictionpeaklist/FormulaPredictionPeakListParameters.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/peaklistmethods/identification/formulapredictionpeaklist/FormulaPredictionPeakListParameters.java (working copy) @@ -26,7 +26,11 @@ import net.sf.mzmine.modules.peaklistmethods.msms.msmsscore.MSMSScoreParameters; import net.sf.mzmine.parameters.Parameter; import net.sf.mzmine.parameters.impl.SimpleParameterSet; -import net.sf.mzmine.parameters.parametertypes.*; +import net.sf.mzmine.parameters.parametertypes.ComboParameter; +import net.sf.mzmine.parameters.parametertypes.IntegerParameter; +import net.sf.mzmine.parameters.parametertypes.MZToleranceParameter; +import net.sf.mzmine.parameters.parametertypes.OptionalModuleParameter; +import net.sf.mzmine.parameters.parametertypes.PeakListsParameter; public class FormulaPredictionPeakListParameters extends SimpleParameterSet { Index: src/main/java/net/sf/mzmine/modules/peaklistmethods/identification/formulapredictionpeaklist/FormulaPredictionPeakListTask.java =================================================================== --- src/main/java/net/sf/mzmine/modules/peaklistmethods/identification/formulapredictionpeaklist/FormulaPredictionPeakListTask.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/peaklistmethods/identification/formulapredictionpeaklist/FormulaPredictionPeakListTask.java (working copy) @@ -18,11 +18,23 @@ */ package net.sf.mzmine.modules.peaklistmethods.identification.formulapredictionpeaklist; -import java.util.*; +import java.util.ArrayList; +import java.util.HashSet; +import java.util.List; +import java.util.Map; +import java.util.Set; import java.util.logging.Level; import java.util.logging.Logger; -import net.sf.mzmine.datamodel.*; +import net.sf.mzmine.datamodel.DataPoint; +import net.sf.mzmine.datamodel.Feature; +import net.sf.mzmine.datamodel.IonizationType; +import net.sf.mzmine.datamodel.IsotopePattern; +import net.sf.mzmine.datamodel.MassList; +import net.sf.mzmine.datamodel.PeakList; +import net.sf.mzmine.datamodel.PeakListRow; +import net.sf.mzmine.datamodel.RawDataFile; +import net.sf.mzmine.datamodel.Scan; import net.sf.mzmine.datamodel.impl.SimplePeakIdentity; import net.sf.mzmine.main.MZmineCore; import net.sf.mzmine.modules.peaklistmethods.identification.formulaprediction.FormulaGenerator; Index: src/main/java/net/sf/mzmine/modules/peaklistmethods/identification/fragmentsearch/FragmentSearchParameters.java =================================================================== --- src/main/java/net/sf/mzmine/modules/peaklistmethods/identification/fragmentsearch/FragmentSearchParameters.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/peaklistmethods/identification/fragmentsearch/FragmentSearchParameters.java (working copy) @@ -22,8 +22,8 @@ import net.sf.mzmine.main.MZmineCore; import net.sf.mzmine.parameters.Parameter; import net.sf.mzmine.parameters.impl.SimpleParameterSet; +import net.sf.mzmine.parameters.parametertypes.DoubleParameter; import net.sf.mzmine.parameters.parametertypes.MZToleranceParameter; -import net.sf.mzmine.parameters.parametertypes.DoubleParameter; import net.sf.mzmine.parameters.parametertypes.PeakListsParameter; import net.sf.mzmine.parameters.parametertypes.PercentParameter; import net.sf.mzmine.parameters.parametertypes.RTToleranceParameter; Index: src/main/java/net/sf/mzmine/modules/peaklistmethods/identification/nist/NistMsSearchParameters.java =================================================================== --- src/main/java/net/sf/mzmine/modules/peaklistmethods/identification/nist/NistMsSearchParameters.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/peaklistmethods/identification/nist/NistMsSearchParameters.java (working copy) @@ -23,14 +23,19 @@ package net.sf.mzmine.modules.peaklistmethods.identification.nist; +import java.io.File; +import java.util.Collection; + import net.sf.mzmine.datamodel.IonizationType; import net.sf.mzmine.parameters.Parameter; import net.sf.mzmine.parameters.impl.SimpleParameterSet; -import net.sf.mzmine.parameters.parametertypes.*; +import net.sf.mzmine.parameters.parametertypes.BooleanParameter; +import net.sf.mzmine.parameters.parametertypes.ComboParameter; +import net.sf.mzmine.parameters.parametertypes.DirectoryParameter; +import net.sf.mzmine.parameters.parametertypes.IntegerParameter; +import net.sf.mzmine.parameters.parametertypes.PeakListsParameter; +import net.sf.mzmine.parameters.parametertypes.RTToleranceParameter; -import java.io.File; -import java.util.Collection; - /** * Holds NIST MS Search parameters. * Index: src/main/java/net/sf/mzmine/modules/peaklistmethods/identification/nist/NistMsSearchTask.java =================================================================== --- src/main/java/net/sf/mzmine/modules/peaklistmethods/identification/nist/NistMsSearchTask.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/peaklistmethods/identification/nist/NistMsSearchTask.java (working copy) @@ -23,23 +23,47 @@ package net.sf.mzmine.modules.peaklistmethods.identification.nist; -import net.sf.mzmine.datamodel.*; -import net.sf.mzmine.datamodel.impl.SimplePeakIdentity; -import net.sf.mzmine.main.MZmineCore; -import net.sf.mzmine.parameters.ParameterSet; -import net.sf.mzmine.parameters.parametertypes.RTTolerance; -import net.sf.mzmine.taskcontrol.AbstractTask; -import net.sf.mzmine.taskcontrol.TaskStatus; +import static net.sf.mzmine.modules.peaklistmethods.identification.nist.NistMsSearchParameters.IONIZATION_METHOD; +import static net.sf.mzmine.modules.peaklistmethods.identification.nist.NistMsSearchParameters.MAX_NUM_PEAKS; +import static net.sf.mzmine.modules.peaklistmethods.identification.nist.NistMsSearchParameters.MIN_MATCH_FACTOR; +import static net.sf.mzmine.modules.peaklistmethods.identification.nist.NistMsSearchParameters.MIN_REVERSE_MATCH_FACTOR; +import static net.sf.mzmine.modules.peaklistmethods.identification.nist.NistMsSearchParameters.NIST_MS_SEARCH_DIR; +import static net.sf.mzmine.modules.peaklistmethods.identification.nist.NistMsSearchParameters.SAME_IDENTITIES; +import static net.sf.mzmine.modules.peaklistmethods.identification.nist.NistMsSearchParameters.SPECTRUM_RT_WIDTH; -import java.io.*; -import java.util.*; +import java.io.BufferedReader; +import java.io.BufferedWriter; +import java.io.File; +import java.io.FileReader; +import java.io.FileWriter; +import java.io.IOException; +import java.util.ArrayList; +import java.util.Collection; +import java.util.Collections; +import java.util.Comparator; +import java.util.HashMap; +import java.util.HashSet; +import java.util.Hashtable; +import java.util.List; +import java.util.Map; import java.util.Map.Entry; +import java.util.Set; import java.util.logging.Level; import java.util.logging.Logger; import java.util.regex.Matcher; import java.util.regex.Pattern; -import static net.sf.mzmine.modules.peaklistmethods.identification.nist.NistMsSearchParameters.*; +import net.sf.mzmine.datamodel.Feature; +import net.sf.mzmine.datamodel.IonizationType; +import net.sf.mzmine.datamodel.PeakIdentity; +import net.sf.mzmine.datamodel.PeakList; +import net.sf.mzmine.datamodel.PeakListRow; +import net.sf.mzmine.datamodel.impl.SimplePeakIdentity; +import net.sf.mzmine.main.MZmineCore; +import net.sf.mzmine.parameters.ParameterSet; +import net.sf.mzmine.parameters.parametertypes.RTTolerance; +import net.sf.mzmine.taskcontrol.AbstractTask; +import net.sf.mzmine.taskcontrol.TaskStatus; /** * Performs NIST MS Search. Index: src/main/java/net/sf/mzmine/modules/peaklistmethods/io/csvexport/CSVExportTask.java =================================================================== --- src/main/java/net/sf/mzmine/modules/peaklistmethods/io/csvexport/CSVExportTask.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/peaklistmethods/io/csvexport/CSVExportTask.java (working copy) @@ -23,11 +23,11 @@ import java.io.FileWriter; import net.sf.mzmine.datamodel.Feature; +import net.sf.mzmine.datamodel.Feature.FeatureStatus; import net.sf.mzmine.datamodel.PeakIdentity; import net.sf.mzmine.datamodel.PeakList; import net.sf.mzmine.datamodel.PeakListRow; import net.sf.mzmine.datamodel.RawDataFile; -import net.sf.mzmine.datamodel.Feature.FeatureStatus; import net.sf.mzmine.parameters.ParameterSet; import net.sf.mzmine.taskcontrol.AbstractTask; import net.sf.mzmine.taskcontrol.TaskStatus; Index: src/main/java/net/sf/mzmine/modules/peaklistmethods/isotopes/deisotoper/IsotopeGrouperTask.java =================================================================== --- src/main/java/net/sf/mzmine/modules/peaklistmethods/isotopes/deisotoper/IsotopeGrouperTask.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/peaklistmethods/isotopes/deisotoper/IsotopeGrouperTask.java (working copy) @@ -25,12 +25,12 @@ import net.sf.mzmine.datamodel.DataPoint; import net.sf.mzmine.datamodel.Feature; +import net.sf.mzmine.datamodel.IsotopePattern.IsotopePatternStatus; import net.sf.mzmine.datamodel.MZmineProject; import net.sf.mzmine.datamodel.PeakList; +import net.sf.mzmine.datamodel.PeakList.PeakListAppliedMethod; import net.sf.mzmine.datamodel.PeakListRow; import net.sf.mzmine.datamodel.RawDataFile; -import net.sf.mzmine.datamodel.IsotopePattern.IsotopePatternStatus; -import net.sf.mzmine.datamodel.PeakList.PeakListAppliedMethod; import net.sf.mzmine.datamodel.impl.SimpleDataPoint; import net.sf.mzmine.datamodel.impl.SimpleFeature; import net.sf.mzmine.datamodel.impl.SimpleIsotopePattern; Index: src/main/java/net/sf/mzmine/modules/peaklistmethods/isotopes/isotopeprediction/IsotopePatternCalculator.java =================================================================== --- src/main/java/net/sf/mzmine/modules/peaklistmethods/isotopes/isotopeprediction/IsotopePatternCalculator.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/peaklistmethods/isotopes/isotopeprediction/IsotopePatternCalculator.java (working copy) @@ -25,8 +25,8 @@ import net.sf.mzmine.datamodel.DataPoint; import net.sf.mzmine.datamodel.IsotopePattern; +import net.sf.mzmine.datamodel.IsotopePattern.IsotopePatternStatus; import net.sf.mzmine.datamodel.Polarity; -import net.sf.mzmine.datamodel.IsotopePattern.IsotopePatternStatus; import net.sf.mzmine.datamodel.impl.SimpleDataPoint; import net.sf.mzmine.datamodel.impl.SimpleIsotopePattern; import net.sf.mzmine.main.MZmineCore; Index: src/main/java/net/sf/mzmine/modules/peaklistmethods/normalization/linear/LinearNormalizerTask.java =================================================================== --- src/main/java/net/sf/mzmine/modules/peaklistmethods/normalization/linear/LinearNormalizerTask.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/peaklistmethods/normalization/linear/LinearNormalizerTask.java (working copy) @@ -25,10 +25,10 @@ import net.sf.mzmine.datamodel.Feature; import net.sf.mzmine.datamodel.MZmineProject; import net.sf.mzmine.datamodel.PeakList; +import net.sf.mzmine.datamodel.PeakList.PeakListAppliedMethod; import net.sf.mzmine.datamodel.PeakListRow; import net.sf.mzmine.datamodel.RawDataFile; import net.sf.mzmine.datamodel.Scan; -import net.sf.mzmine.datamodel.PeakList.PeakListAppliedMethod; import net.sf.mzmine.datamodel.impl.SimpleFeature; import net.sf.mzmine.datamodel.impl.SimplePeakList; import net.sf.mzmine.datamodel.impl.SimplePeakListAppliedMethod; Index: src/main/java/net/sf/mzmine/modules/peaklistmethods/normalization/rtnormalizer/RTNormalizerTask.java =================================================================== --- src/main/java/net/sf/mzmine/modules/peaklistmethods/normalization/rtnormalizer/RTNormalizerTask.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/peaklistmethods/normalization/rtnormalizer/RTNormalizerTask.java (working copy) @@ -26,9 +26,9 @@ import net.sf.mzmine.datamodel.MZmineProject; import net.sf.mzmine.datamodel.PeakIdentity; import net.sf.mzmine.datamodel.PeakList; +import net.sf.mzmine.datamodel.PeakList.PeakListAppliedMethod; import net.sf.mzmine.datamodel.PeakListRow; import net.sf.mzmine.datamodel.RawDataFile; -import net.sf.mzmine.datamodel.PeakList.PeakListAppliedMethod; import net.sf.mzmine.datamodel.impl.SimpleFeature; import net.sf.mzmine.datamodel.impl.SimplePeakList; import net.sf.mzmine.datamodel.impl.SimplePeakListAppliedMethod; Index: src/main/java/net/sf/mzmine/modules/peaklistmethods/normalization/standardcompound/StandardCompoundNormalizerTask.java =================================================================== --- src/main/java/net/sf/mzmine/modules/peaklistmethods/normalization/standardcompound/StandardCompoundNormalizerTask.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/peaklistmethods/normalization/standardcompound/StandardCompoundNormalizerTask.java (working copy) @@ -24,9 +24,9 @@ import net.sf.mzmine.datamodel.Feature; import net.sf.mzmine.datamodel.MZmineProject; import net.sf.mzmine.datamodel.PeakList; +import net.sf.mzmine.datamodel.PeakList.PeakListAppliedMethod; import net.sf.mzmine.datamodel.PeakListRow; import net.sf.mzmine.datamodel.RawDataFile; -import net.sf.mzmine.datamodel.PeakList.PeakListAppliedMethod; import net.sf.mzmine.datamodel.impl.SimpleFeature; import net.sf.mzmine.datamodel.impl.SimplePeakList; import net.sf.mzmine.datamodel.impl.SimplePeakListAppliedMethod; Index: src/main/java/net/sf/mzmine/modules/peaklistmethods/peakpicking/deconvolution/DeconvolutionTask.java =================================================================== --- src/main/java/net/sf/mzmine/modules/peaklistmethods/peakpicking/deconvolution/DeconvolutionTask.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/peaklistmethods/peakpicking/deconvolution/DeconvolutionTask.java (working copy) @@ -30,9 +30,9 @@ import net.sf.mzmine.datamodel.Feature; import net.sf.mzmine.datamodel.MZmineProject; import net.sf.mzmine.datamodel.PeakList; +import net.sf.mzmine.datamodel.PeakList.PeakListAppliedMethod; import net.sf.mzmine.datamodel.PeakListRow; import net.sf.mzmine.datamodel.RawDataFile; -import net.sf.mzmine.datamodel.PeakList.PeakListAppliedMethod; import net.sf.mzmine.datamodel.impl.SimplePeakList; import net.sf.mzmine.datamodel.impl.SimplePeakListAppliedMethod; import net.sf.mzmine.datamodel.impl.SimplePeakListRow; Index: src/main/java/net/sf/mzmine/modules/peaklistmethods/peakpicking/deconvolution/PeakResolverSetupDialog.java =================================================================== --- src/main/java/net/sf/mzmine/modules/peaklistmethods/peakpicking/deconvolution/PeakResolverSetupDialog.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/peaklistmethods/peakpicking/deconvolution/PeakResolverSetupDialog.java (working copy) @@ -19,7 +19,30 @@ package net.sf.mzmine.modules.peaklistmethods.peakpicking.deconvolution; -import net.sf.mzmine.datamodel.*; +import java.awt.BorderLayout; +import java.awt.Color; +import java.awt.Dimension; +import java.awt.Font; +import java.awt.GridBagConstraints; +import java.awt.event.ActionEvent; +import java.util.ArrayList; +import java.util.logging.Level; +import java.util.logging.Logger; + +import javax.swing.Box; +import javax.swing.JCheckBox; +import javax.swing.JComboBox; +import javax.swing.JComponent; +import javax.swing.JLabel; +import javax.swing.JPanel; +import javax.swing.JSeparator; +import javax.swing.SwingConstants; + +import net.sf.mzmine.datamodel.DataPoint; +import net.sf.mzmine.datamodel.Feature; +import net.sf.mzmine.datamodel.PeakList; +import net.sf.mzmine.datamodel.PeakListRow; +import net.sf.mzmine.datamodel.RawDataFile; import net.sf.mzmine.main.MZmineCore; import net.sf.mzmine.modules.visualization.tic.PeakDataSet; import net.sf.mzmine.modules.visualization.tic.TICPlot; @@ -30,14 +53,6 @@ import org.jfree.data.xy.XYDataset; -import javax.swing.*; - -import java.awt.*; -import java.awt.event.ActionEvent; -import java.util.ArrayList; -import java.util.logging.Level; -import java.util.logging.Logger; - /** * This class extends ParameterSetupDialog class. */ Index: src/main/java/net/sf/mzmine/modules/peaklistmethods/peakpicking/deconvolution/centwave/CentWaveDetector.java =================================================================== --- src/main/java/net/sf/mzmine/modules/peaklistmethods/peakpicking/deconvolution/centwave/CentWaveDetector.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/peaklistmethods/peakpicking/deconvolution/centwave/CentWaveDetector.java (working copy) @@ -23,9 +23,22 @@ package net.sf.mzmine.modules.peaklistmethods.peakpicking.deconvolution.centwave; +import static net.sf.mzmine.modules.peaklistmethods.peakpicking.deconvolution.centwave.CentWaveDetectorParameters.INTEGRATION_METHOD; +import static net.sf.mzmine.modules.peaklistmethods.peakpicking.deconvolution.centwave.CentWaveDetectorParameters.PEAK_DURATION; +import static net.sf.mzmine.modules.peaklistmethods.peakpicking.deconvolution.centwave.CentWaveDetectorParameters.PEAK_SCALES; +import static net.sf.mzmine.modules.peaklistmethods.peakpicking.deconvolution.centwave.CentWaveDetectorParameters.SN_THRESHOLD; + +import java.util.ArrayList; +import java.util.Arrays; +import java.util.List; +import java.util.logging.Logger; + +import javax.annotation.Nonnull; + import net.sf.mzmine.datamodel.Feature; import net.sf.mzmine.modules.peaklistmethods.peakpicking.deconvolution.PeakResolver; import net.sf.mzmine.modules.peaklistmethods.peakpicking.deconvolution.ResolvedPeak; +import net.sf.mzmine.modules.peaklistmethods.peakpicking.deconvolution.centwave.CentWaveDetectorParameters.PeakIntegrationMethod; import net.sf.mzmine.parameters.ParameterSet; import net.sf.mzmine.util.RUtilities; import net.sf.mzmine.util.Range; @@ -33,15 +46,6 @@ import org.rosuda.JRI.REXP; import org.rosuda.JRI.Rengine; -import javax.annotation.Nonnull; - -import java.util.ArrayList; -import java.util.Arrays; -import java.util.List; -import java.util.logging.Logger; - -import static net.sf.mzmine.modules.peaklistmethods.peakpicking.deconvolution.centwave.CentWaveDetectorParameters.*; - /** * Use XCMS findPeaks.centWave to identify peaks. * Index: src/main/java/net/sf/mzmine/modules/peaklistmethods/peakpicking/deconvolution/centwave/CentWaveDetectorParameters.java =================================================================== --- src/main/java/net/sf/mzmine/modules/peaklistmethods/peakpicking/deconvolution/centwave/CentWaveDetectorParameters.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/peaklistmethods/peakpicking/deconvolution/centwave/CentWaveDetectorParameters.java (working copy) @@ -23,6 +23,8 @@ package net.sf.mzmine.modules.peaklistmethods.peakpicking.deconvolution.centwave; +import java.text.NumberFormat; + import net.sf.mzmine.main.MZmineCore; import net.sf.mzmine.modules.peaklistmethods.peakpicking.deconvolution.PeakResolverSetupDialog; import net.sf.mzmine.parameters.Parameter; @@ -33,8 +35,6 @@ import net.sf.mzmine.util.ExitCode; import net.sf.mzmine.util.Range; -import java.text.NumberFormat; - /** * Parameters used by CentWaveDetector. * Index: src/main/java/net/sf/mzmine/modules/peaklistmethods/peakpicking/deconvolution/noiseamplitude/NoiseAmplitudePeakDetector.java =================================================================== --- src/main/java/net/sf/mzmine/modules/peaklistmethods/peakpicking/deconvolution/noiseamplitude/NoiseAmplitudePeakDetector.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/peaklistmethods/peakpicking/deconvolution/noiseamplitude/NoiseAmplitudePeakDetector.java (working copy) @@ -19,11 +19,9 @@ package net.sf.mzmine.modules.peaklistmethods.peakpicking.deconvolution.noiseamplitude; -import net.sf.mzmine.datamodel.Feature; -import net.sf.mzmine.modules.peaklistmethods.peakpicking.deconvolution.PeakResolver; -import net.sf.mzmine.modules.peaklistmethods.peakpicking.deconvolution.ResolvedPeak; -import net.sf.mzmine.parameters.ParameterSet; -import net.sf.mzmine.util.Range; +import static net.sf.mzmine.modules.peaklistmethods.peakpicking.deconvolution.noiseamplitude.NoiseAmplitudePeakDetectorParameters.MIN_PEAK_HEIGHT; +import static net.sf.mzmine.modules.peaklistmethods.peakpicking.deconvolution.noiseamplitude.NoiseAmplitudePeakDetectorParameters.NOISE_AMPLITUDE; +import static net.sf.mzmine.modules.peaklistmethods.peakpicking.deconvolution.noiseamplitude.NoiseAmplitudePeakDetectorParameters.PEAK_DURATION; import java.util.ArrayList; import java.util.List; @@ -31,7 +29,11 @@ import javax.annotation.Nonnull; -import static net.sf.mzmine.modules.peaklistmethods.peakpicking.deconvolution.noiseamplitude.NoiseAmplitudePeakDetectorParameters.*; +import net.sf.mzmine.datamodel.Feature; +import net.sf.mzmine.modules.peaklistmethods.peakpicking.deconvolution.PeakResolver; +import net.sf.mzmine.modules.peaklistmethods.peakpicking.deconvolution.ResolvedPeak; +import net.sf.mzmine.parameters.ParameterSet; +import net.sf.mzmine.util.Range; /** * Index: src/main/java/net/sf/mzmine/modules/peaklistmethods/peakpicking/peakextender/ExtendedPeak.java =================================================================== --- src/main/java/net/sf/mzmine/modules/peaklistmethods/peakpicking/peakextender/ExtendedPeak.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/peaklistmethods/peakpicking/peakextender/ExtendedPeak.java (working copy) @@ -14,9 +14,9 @@ import net.sf.mzmine.main.MZmineCore; import net.sf.mzmine.util.CollectionUtils; import net.sf.mzmine.util.MathUtils; +import net.sf.mzmine.util.PeakUtils; import net.sf.mzmine.util.Range; import net.sf.mzmine.util.ScanUtils; -import net.sf.mzmine.util.PeakUtils; public class ExtendedPeak implements Feature { Index: src/main/java/net/sf/mzmine/modules/peaklistmethods/peakpicking/peakextender/PeakExtenderParameters.java =================================================================== --- src/main/java/net/sf/mzmine/modules/peaklistmethods/peakpicking/peakextender/PeakExtenderParameters.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/peaklistmethods/peakpicking/peakextender/PeakExtenderParameters.java (working copy) @@ -23,8 +23,8 @@ import net.sf.mzmine.parameters.Parameter; import net.sf.mzmine.parameters.impl.SimpleParameterSet; import net.sf.mzmine.parameters.parametertypes.BooleanParameter; +import net.sf.mzmine.parameters.parametertypes.DoubleParameter; import net.sf.mzmine.parameters.parametertypes.MZToleranceParameter; -import net.sf.mzmine.parameters.parametertypes.DoubleParameter; import net.sf.mzmine.parameters.parametertypes.PeakListsParameter; import net.sf.mzmine.parameters.parametertypes.StringParameter; Index: src/main/java/net/sf/mzmine/modules/peaklistmethods/peakpicking/peakextender/PeakExtenderTask.java =================================================================== --- src/main/java/net/sf/mzmine/modules/peaklistmethods/peakpicking/peakextender/PeakExtenderTask.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/peaklistmethods/peakpicking/peakextender/PeakExtenderTask.java (working copy) @@ -26,10 +26,10 @@ import net.sf.mzmine.datamodel.Feature; import net.sf.mzmine.datamodel.MZmineProject; import net.sf.mzmine.datamodel.PeakList; +import net.sf.mzmine.datamodel.PeakList.PeakListAppliedMethod; import net.sf.mzmine.datamodel.PeakListRow; import net.sf.mzmine.datamodel.RawDataFile; import net.sf.mzmine.datamodel.Scan; -import net.sf.mzmine.datamodel.PeakList.PeakListAppliedMethod; import net.sf.mzmine.datamodel.impl.SimplePeakList; import net.sf.mzmine.datamodel.impl.SimplePeakListAppliedMethod; import net.sf.mzmine.datamodel.impl.SimplePeakListRow; Index: src/main/java/net/sf/mzmine/modules/peaklistmethods/peakpicking/shapemodeler/ShapeModelerTask.java =================================================================== --- src/main/java/net/sf/mzmine/modules/peaklistmethods/peakpicking/shapemodeler/ShapeModelerTask.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/peaklistmethods/peakpicking/shapemodeler/ShapeModelerTask.java (working copy) @@ -26,9 +26,9 @@ import net.sf.mzmine.datamodel.Feature; import net.sf.mzmine.datamodel.MZmineProject; import net.sf.mzmine.datamodel.PeakList; +import net.sf.mzmine.datamodel.PeakList.PeakListAppliedMethod; import net.sf.mzmine.datamodel.PeakListRow; import net.sf.mzmine.datamodel.RawDataFile; -import net.sf.mzmine.datamodel.PeakList.PeakListAppliedMethod; import net.sf.mzmine.datamodel.impl.SimplePeakList; import net.sf.mzmine.datamodel.impl.SimplePeakListAppliedMethod; import net.sf.mzmine.datamodel.impl.SimplePeakListRow; Index: src/main/java/net/sf/mzmine/modules/peaklistmethods/peakpicking/smoothing/SmoothingTask.java =================================================================== --- src/main/java/net/sf/mzmine/modules/peaklistmethods/peakpicking/smoothing/SmoothingTask.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/peaklistmethods/peakpicking/smoothing/SmoothingTask.java (working copy) @@ -30,9 +30,9 @@ import net.sf.mzmine.datamodel.Feature; import net.sf.mzmine.datamodel.MZmineProject; import net.sf.mzmine.datamodel.PeakList; +import net.sf.mzmine.datamodel.PeakList.PeakListAppliedMethod; import net.sf.mzmine.datamodel.PeakListRow; import net.sf.mzmine.datamodel.RawDataFile; -import net.sf.mzmine.datamodel.PeakList.PeakListAppliedMethod; import net.sf.mzmine.datamodel.impl.SimpleDataPoint; import net.sf.mzmine.datamodel.impl.SimpleFeature; import net.sf.mzmine.datamodel.impl.SimplePeakList; Index: src/main/java/net/sf/mzmine/modules/projectmethods/projectload/version_2_0/PeakListOpenHandler_2_0.java =================================================================== --- src/main/java/net/sf/mzmine/modules/projectmethods/projectload/version_2_0/PeakListOpenHandler_2_0.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/projectmethods/projectload/version_2_0/PeakListOpenHandler_2_0.java (working copy) @@ -32,13 +32,13 @@ import javax.xml.parsers.SAXParserFactory; import net.sf.mzmine.datamodel.DataPoint; +import net.sf.mzmine.datamodel.Feature.FeatureStatus; +import net.sf.mzmine.datamodel.IsotopePattern.IsotopePatternStatus; import net.sf.mzmine.datamodel.PeakIdentity; import net.sf.mzmine.datamodel.PeakList; +import net.sf.mzmine.datamodel.PeakList.PeakListAppliedMethod; import net.sf.mzmine.datamodel.RawDataFile; import net.sf.mzmine.datamodel.Scan; -import net.sf.mzmine.datamodel.Feature.FeatureStatus; -import net.sf.mzmine.datamodel.IsotopePattern.IsotopePatternStatus; -import net.sf.mzmine.datamodel.PeakList.PeakListAppliedMethod; import net.sf.mzmine.datamodel.impl.SimpleDataPoint; import net.sf.mzmine.datamodel.impl.SimpleFeature; import net.sf.mzmine.datamodel.impl.SimpleIsotopePattern; Index: src/main/java/net/sf/mzmine/modules/projectmethods/projectload/version_2_3/PeakListOpenHandler_2_3.java =================================================================== --- src/main/java/net/sf/mzmine/modules/projectmethods/projectload/version_2_3/PeakListOpenHandler_2_3.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/projectmethods/projectload/version_2_3/PeakListOpenHandler_2_3.java (working copy) @@ -32,12 +32,12 @@ import javax.xml.parsers.SAXParserFactory; import net.sf.mzmine.datamodel.DataPoint; +import net.sf.mzmine.datamodel.Feature.FeatureStatus; +import net.sf.mzmine.datamodel.IsotopePattern.IsotopePatternStatus; import net.sf.mzmine.datamodel.PeakList; +import net.sf.mzmine.datamodel.PeakList.PeakListAppliedMethod; import net.sf.mzmine.datamodel.RawDataFile; import net.sf.mzmine.datamodel.Scan; -import net.sf.mzmine.datamodel.Feature.FeatureStatus; -import net.sf.mzmine.datamodel.IsotopePattern.IsotopePatternStatus; -import net.sf.mzmine.datamodel.PeakList.PeakListAppliedMethod; import net.sf.mzmine.datamodel.impl.SimpleDataPoint; import net.sf.mzmine.datamodel.impl.SimpleFeature; import net.sf.mzmine.datamodel.impl.SimpleIsotopePattern; Index: src/main/java/net/sf/mzmine/modules/projectmethods/projectload/version_2_5/PeakListOpenHandler_2_5.java =================================================================== --- src/main/java/net/sf/mzmine/modules/projectmethods/projectload/version_2_5/PeakListOpenHandler_2_5.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/projectmethods/projectload/version_2_5/PeakListOpenHandler_2_5.java (working copy) @@ -32,12 +32,12 @@ import javax.xml.parsers.SAXParserFactory; import net.sf.mzmine.datamodel.DataPoint; +import net.sf.mzmine.datamodel.Feature.FeatureStatus; +import net.sf.mzmine.datamodel.IsotopePattern.IsotopePatternStatus; import net.sf.mzmine.datamodel.PeakList; +import net.sf.mzmine.datamodel.PeakList.PeakListAppliedMethod; import net.sf.mzmine.datamodel.RawDataFile; import net.sf.mzmine.datamodel.Scan; -import net.sf.mzmine.datamodel.Feature.FeatureStatus; -import net.sf.mzmine.datamodel.IsotopePattern.IsotopePatternStatus; -import net.sf.mzmine.datamodel.PeakList.PeakListAppliedMethod; import net.sf.mzmine.datamodel.impl.SimpleDataPoint; import net.sf.mzmine.datamodel.impl.SimpleFeature; import net.sf.mzmine.datamodel.impl.SimpleIsotopePattern; Index: src/main/java/net/sf/mzmine/modules/projectmethods/projectsave/PeakListSaveHandler.java =================================================================== --- src/main/java/net/sf/mzmine/modules/projectmethods/projectsave/PeakListSaveHandler.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/projectmethods/projectsave/PeakListSaveHandler.java (working copy) @@ -42,9 +42,9 @@ import net.sf.mzmine.datamodel.IsotopePattern; import net.sf.mzmine.datamodel.PeakIdentity; import net.sf.mzmine.datamodel.PeakList; +import net.sf.mzmine.datamodel.PeakList.PeakListAppliedMethod; import net.sf.mzmine.datamodel.PeakListRow; import net.sf.mzmine.datamodel.RawDataFile; -import net.sf.mzmine.datamodel.PeakList.PeakListAppliedMethod; import net.sf.mzmine.datamodel.impl.SimplePeakList; import org.xml.sax.SAXException; Index: src/main/java/net/sf/mzmine/modules/rawdatamethods/filtering/baselinecorrection/BaselineCorrectionParameters.java =================================================================== --- src/main/java/net/sf/mzmine/modules/rawdatamethods/filtering/baselinecorrection/BaselineCorrectionParameters.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/rawdatamethods/filtering/baselinecorrection/BaselineCorrectionParameters.java (working copy) @@ -30,8 +30,8 @@ import net.sf.mzmine.parameters.impl.SimpleParameterSet; import net.sf.mzmine.parameters.parametertypes.BooleanParameter; import net.sf.mzmine.parameters.parametertypes.ComboParameter; +import net.sf.mzmine.parameters.parametertypes.DoubleParameter; import net.sf.mzmine.parameters.parametertypes.MSLevelParameter; -import net.sf.mzmine.parameters.parametertypes.DoubleParameter; import net.sf.mzmine.parameters.parametertypes.RawDataFilesParameter; import net.sf.mzmine.parameters.parametertypes.StringParameter; Index: src/main/java/net/sf/mzmine/modules/rawdatamethods/filtering/baselinecorrection/BaselineCorrectionTask.java =================================================================== --- src/main/java/net/sf/mzmine/modules/rawdatamethods/filtering/baselinecorrection/BaselineCorrectionTask.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/rawdatamethods/filtering/baselinecorrection/BaselineCorrectionTask.java (working copy) @@ -23,6 +23,10 @@ package net.sf.mzmine.modules.rawdatamethods.filtering.baselinecorrection; +import java.io.IOException; +import java.util.logging.Level; +import java.util.logging.Logger; + import net.sf.mzmine.datamodel.DataPoint; import net.sf.mzmine.datamodel.MZmineProject; import net.sf.mzmine.datamodel.RawDataFile; @@ -39,10 +43,6 @@ import org.rosuda.JRI.Rengine; -import java.io.IOException; -import java.util.logging.Level; -import java.util.logging.Logger; - /** * Task that performs baseline correction. * Index: src/main/java/net/sf/mzmine/modules/rawdatamethods/peakpicking/msms/MsMsPeakPickingTask.java =================================================================== --- src/main/java/net/sf/mzmine/modules/rawdatamethods/peakpicking/msms/MsMsPeakPickingTask.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/rawdatamethods/peakpicking/msms/MsMsPeakPickingTask.java (working copy) @@ -22,11 +22,11 @@ import java.util.logging.Logger; import net.sf.mzmine.datamodel.DataPoint; +import net.sf.mzmine.datamodel.Feature.FeatureStatus; import net.sf.mzmine.datamodel.MZmineProject; import net.sf.mzmine.datamodel.PeakListRow; import net.sf.mzmine.datamodel.RawDataFile; import net.sf.mzmine.datamodel.Scan; -import net.sf.mzmine.datamodel.Feature.FeatureStatus; import net.sf.mzmine.datamodel.impl.SimpleFeature; import net.sf.mzmine.datamodel.impl.SimplePeakList; import net.sf.mzmine.datamodel.impl.SimplePeakListRow; Index: src/main/java/net/sf/mzmine/modules/rawdatamethods/targetedpeakdetection/Gap.java =================================================================== --- src/main/java/net/sf/mzmine/modules/rawdatamethods/targetedpeakdetection/Gap.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/rawdatamethods/targetedpeakdetection/Gap.java (working copy) @@ -22,10 +22,10 @@ import java.util.Vector; import net.sf.mzmine.datamodel.DataPoint; +import net.sf.mzmine.datamodel.Feature.FeatureStatus; import net.sf.mzmine.datamodel.PeakListRow; import net.sf.mzmine.datamodel.RawDataFile; import net.sf.mzmine.datamodel.Scan; -import net.sf.mzmine.datamodel.Feature.FeatureStatus; import net.sf.mzmine.datamodel.impl.SimpleDataPoint; import net.sf.mzmine.datamodel.impl.SimpleFeature; import net.sf.mzmine.util.Range; Index: src/main/java/net/sf/mzmine/modules/rawdatamethods/targetedpeakdetection/TargetedPeakDetectionModuleTask.java =================================================================== --- src/main/java/net/sf/mzmine/modules/rawdatamethods/targetedpeakdetection/TargetedPeakDetectionModuleTask.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/rawdatamethods/targetedpeakdetection/TargetedPeakDetectionModuleTask.java (working copy) @@ -18,8 +18,6 @@ */ package net.sf.mzmine.modules.rawdatamethods.targetedpeakdetection; -import com.Ostermiller.util.CSVParser; - import java.io.File; import java.io.FileReader; import java.util.ArrayList; @@ -44,6 +42,8 @@ import net.sf.mzmine.taskcontrol.TaskStatus; import net.sf.mzmine.util.Range; +import com.Ostermiller.util.CSVParser; + class TargetedPeakDetectionModuleTask extends AbstractTask { private Logger logger = Logger.getLogger(this.getClass().getName()); Index: src/main/java/net/sf/mzmine/modules/visualization/histogram/HistogramVisualizerModule.java =================================================================== --- src/main/java/net/sf/mzmine/modules/visualization/histogram/HistogramVisualizerModule.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/visualization/histogram/HistogramVisualizerModule.java (working copy) @@ -23,7 +23,6 @@ import javax.annotation.Nonnull; -import net.sf.mzmine.main.MZmineCore; import net.sf.mzmine.modules.MZmineModuleCategory; import net.sf.mzmine.modules.MZmineProcessingModule; import net.sf.mzmine.parameters.ParameterSet; Index: src/main/java/net/sf/mzmine/modules/visualization/neutralloss/NeutralLossSetHighlightDialog.java =================================================================== --- src/main/java/net/sf/mzmine/modules/visualization/neutralloss/NeutralLossSetHighlightDialog.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/visualization/neutralloss/NeutralLossSetHighlightDialog.java (working copy) @@ -35,13 +35,13 @@ import javax.swing.JFormattedTextField; import javax.swing.JPanel; -import org.jfree.data.general.DatasetChangeEvent; - import net.sf.mzmine.desktop.Desktop; import net.sf.mzmine.main.MZmineCore; import net.sf.mzmine.util.GUIUtils; import net.sf.mzmine.util.Range; +import org.jfree.data.general.DatasetChangeEvent; + /** * Dialog for selection of highlighted precursor m/z range */ Index: src/main/java/net/sf/mzmine/modules/visualization/neutralloss/NeutralLossVisualizerModule.java =================================================================== --- src/main/java/net/sf/mzmine/modules/visualization/neutralloss/NeutralLossVisualizerModule.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/visualization/neutralloss/NeutralLossVisualizerModule.java (working copy) @@ -24,7 +24,6 @@ import javax.annotation.Nonnull; import net.sf.mzmine.datamodel.RawDataFile; -import net.sf.mzmine.main.MZmineCore; import net.sf.mzmine.modules.MZmineModuleCategory; import net.sf.mzmine.modules.MZmineProcessingModule; import net.sf.mzmine.parameters.ParameterSet; Index: src/main/java/net/sf/mzmine/modules/visualization/peaklist/PeakListTablePopupMenu.java =================================================================== --- src/main/java/net/sf/mzmine/modules/visualization/peaklist/PeakListTablePopupMenu.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/visualization/peaklist/PeakListTablePopupMenu.java (working copy) @@ -19,7 +19,26 @@ package net.sf.mzmine.modules.visualization.peaklist; -import net.sf.mzmine.datamodel.*; +import java.awt.Component; +import java.awt.Point; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.HashMap; +import java.util.List; +import java.util.Map; + +import javax.swing.JMenu; +import javax.swing.JMenuItem; +import javax.swing.JPopupMenu; +import javax.swing.table.AbstractTableModel; + +import net.sf.mzmine.datamodel.Feature; +import net.sf.mzmine.datamodel.PeakIdentity; +import net.sf.mzmine.datamodel.PeakList; +import net.sf.mzmine.datamodel.PeakListRow; +import net.sf.mzmine.datamodel.RawDataFile; import net.sf.mzmine.datamodel.impl.SimplePeakListRow; import net.sf.mzmine.main.MZmineCore; import net.sf.mzmine.modules.peaklistmethods.identification.dbsearch.OnlineDBSearchModule; @@ -29,7 +48,11 @@ import net.sf.mzmine.modules.visualization.intensityplot.IntensityPlotModule; import net.sf.mzmine.modules.visualization.peaklist.export.IsotopePatternExportModule; import net.sf.mzmine.modules.visualization.peaklist.export.MSMSExportModule; -import net.sf.mzmine.modules.visualization.peaklist.table.*; +import net.sf.mzmine.modules.visualization.peaklist.table.CommonColumnType; +import net.sf.mzmine.modules.visualization.peaklist.table.DataFileColumnType; +import net.sf.mzmine.modules.visualization.peaklist.table.PeakListTable; +import net.sf.mzmine.modules.visualization.peaklist.table.PeakListTableColumnModel; +import net.sf.mzmine.modules.visualization.peaklist.table.PeakListTableModel; import net.sf.mzmine.modules.visualization.peaksummary.PeakSummaryVisualizerModule; import net.sf.mzmine.modules.visualization.spectra.SpectraVisualizerModule; import net.sf.mzmine.modules.visualization.threed.ThreeDVisualizerModule; @@ -39,15 +62,6 @@ import net.sf.mzmine.util.GUIUtils; import net.sf.mzmine.util.Range; -import javax.swing.*; -import javax.swing.table.AbstractTableModel; - -import java.awt.*; -import java.awt.event.ActionEvent; -import java.awt.event.ActionListener; -import java.util.*; -import java.util.List; - /** * Peak-list table pop-up menu. */ Index: src/main/java/net/sf/mzmine/modules/visualization/peaklist/table/PeakListTable.java =================================================================== --- src/main/java/net/sf/mzmine/modules/visualization/peaklist/table/PeakListTable.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/visualization/peaklist/table/PeakListTable.java (working copy) @@ -19,6 +19,24 @@ package net.sf.mzmine.modules.visualization.peaklist.table; +import java.awt.Font; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.MouseEvent; + +import javax.swing.BorderFactory; +import javax.swing.DefaultCellEditor; +import javax.swing.DefaultComboBoxModel; +import javax.swing.JComboBox; +import javax.swing.JComponent; +import javax.swing.JLabel; +import javax.swing.JPanel; +import javax.swing.JTable; +import javax.swing.UIManager; +import javax.swing.event.RowSorterEvent; +import javax.swing.table.TableCellEditor; +import javax.swing.table.TableRowSorter; + import net.sf.mzmine.datamodel.PeakIdentity; import net.sf.mzmine.datamodel.PeakList; import net.sf.mzmine.datamodel.PeakListRow; @@ -26,19 +44,13 @@ import net.sf.mzmine.modules.visualization.peaklist.PeakListTablePopupMenu; import net.sf.mzmine.modules.visualization.peaklist.PeakListTableWindow; import net.sf.mzmine.parameters.ParameterSet; -import net.sf.mzmine.util.components.*; +import net.sf.mzmine.util.components.ComponentToolTipManager; +import net.sf.mzmine.util.components.ComponentToolTipProvider; +import net.sf.mzmine.util.components.GroupableTableHeader; +import net.sf.mzmine.util.components.PeakSummaryComponent; +import net.sf.mzmine.util.components.PopupListener; import net.sf.mzmine.util.dialogs.PeakIdentitySetupDialog; -import javax.swing.*; -import javax.swing.event.RowSorterEvent; -import javax.swing.table.TableCellEditor; -import javax.swing.table.TableRowSorter; - -import java.awt.*; -import java.awt.event.ActionEvent; -import java.awt.event.ActionListener; -import java.awt.event.MouseEvent; - public class PeakListTable extends JTable implements ComponentToolTipProvider { static final String EDIT_IDENTITY = "Edit"; Index: src/main/java/net/sf/mzmine/modules/visualization/peaklist/table/PeakListTableModel.java =================================================================== --- src/main/java/net/sf/mzmine/modules/visualization/peaklist/table/PeakListTableModel.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/visualization/peaklist/table/PeakListTableModel.java (working copy) @@ -22,11 +22,11 @@ import javax.swing.table.AbstractTableModel; import net.sf.mzmine.datamodel.Feature; +import net.sf.mzmine.datamodel.Feature.FeatureStatus; import net.sf.mzmine.datamodel.PeakIdentity; import net.sf.mzmine.datamodel.PeakList; import net.sf.mzmine.datamodel.PeakListRow; import net.sf.mzmine.datamodel.RawDataFile; -import net.sf.mzmine.datamodel.Feature.FeatureStatus; public class PeakListTableModel extends AbstractTableModel { Index: src/main/java/net/sf/mzmine/modules/visualization/scatterplot/scatterplotchart/ScatterPlotChart.java =================================================================== --- src/main/java/net/sf/mzmine/modules/visualization/scatterplot/scatterplotchart/ScatterPlotChart.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/visualization/scatterplot/scatterplotchart/ScatterPlotChart.java (working copy) @@ -19,6 +19,16 @@ package net.sf.mzmine.modules.visualization.scatterplot.scatterplotchart; +import java.awt.BasicStroke; +import java.awt.Color; +import java.awt.event.ActionEvent; +import java.awt.event.MouseEvent; +import java.util.HashMap; +import java.util.Map; + +import javax.swing.JComponent; +import javax.swing.JPopupMenu; + import net.sf.mzmine.datamodel.Feature; import net.sf.mzmine.datamodel.PeakIdentity; import net.sf.mzmine.datamodel.PeakList; @@ -47,14 +57,6 @@ import org.jfree.chart.plot.XYPlot; import org.jfree.ui.RectangleInsets; -import javax.swing.*; - -import java.awt.*; -import java.awt.event.ActionEvent; -import java.awt.event.MouseEvent; -import java.util.HashMap; -import java.util.Map; - public class ScatterPlotChart extends ChartPanel implements ComponentToolTipProvider { Index: src/main/java/net/sf/mzmine/modules/visualization/spectra/SpectraVisualizerWindow.java =================================================================== --- src/main/java/net/sf/mzmine/modules/visualization/spectra/SpectraVisualizerWindow.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/visualization/spectra/SpectraVisualizerWindow.java (working copy) @@ -36,10 +36,10 @@ import net.sf.mzmine.datamodel.DataPoint; import net.sf.mzmine.datamodel.Feature; import net.sf.mzmine.datamodel.IsotopePattern; +import net.sf.mzmine.datamodel.IsotopePattern.IsotopePatternStatus; import net.sf.mzmine.datamodel.PeakList; import net.sf.mzmine.datamodel.RawDataFile; import net.sf.mzmine.datamodel.Scan; -import net.sf.mzmine.datamodel.IsotopePattern.IsotopePatternStatus; import net.sf.mzmine.main.MZmineCore; import net.sf.mzmine.modules.peaklistmethods.isotopes.isotopeprediction.IsotopePatternCalculator; import net.sf.mzmine.modules.visualization.spectra.datasets.IsotopesDataSet; Index: src/main/java/net/sf/mzmine/modules/visualization/threed/TextControlDialog.java =================================================================== --- src/main/java/net/sf/mzmine/modules/visualization/threed/TextControlDialog.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/visualization/threed/TextControlDialog.java (working copy) @@ -19,16 +19,21 @@ package net.sf.mzmine.modules.visualization.threed; +import java.awt.Component; +import java.awt.Container; +import java.awt.Window; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.rmi.RemoteException; + +import javax.swing.BoxLayout; +import javax.swing.JButton; +import javax.swing.JDialog; + import visad.TextControl; import visad.VisADException; import visad.util.TextControlWidget; -import javax.swing.*; -import java.awt.*; -import java.awt.event.ActionEvent; -import java.awt.event.ActionListener; -import java.rmi.RemoteException; - /** * A dialog that holds a VisAD TextControlWidget. * Index: src/main/java/net/sf/mzmine/modules/visualization/threed/ThreeDDisplay.java =================================================================== --- src/main/java/net/sf/mzmine/modules/visualization/threed/ThreeDDisplay.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/visualization/threed/ThreeDDisplay.java (working copy) @@ -19,11 +19,49 @@ package net.sf.mzmine.modules.visualization.threed; +import java.awt.Color; +import java.awt.Font; +import java.awt.event.KeyEvent; +import java.rmi.RemoteException; +import java.text.NumberFormat; +import java.util.Hashtable; +import java.util.Iterator; + import net.sf.mzmine.datamodel.Feature; import net.sf.mzmine.datamodel.PeakIdentity; import net.sf.mzmine.datamodel.PeakList; import net.sf.mzmine.main.MZmineCore; -import visad.*; +import visad.AxisScale; +import visad.BaseColorControl; +import visad.CommonUnit; +import visad.ConstantMap; +import visad.Data; +import visad.DataReference; +import visad.DataReferenceImpl; +import visad.Display; +import visad.FieldImpl; +import visad.FlatField; +import visad.FunctionType; +import visad.GraphicsModeControl; +import visad.Gridded2DSet; +import visad.KeyboardBehavior; +import visad.LogCoordinateSystem; +import visad.MathType; +import visad.MouseHelper; +import visad.ProjectionControl; +import visad.RealTuple; +import visad.RealTupleType; +import visad.RealType; +import visad.ReferenceException; +import visad.SI; +import visad.ScalarMap; +import visad.Set; +import visad.Text; +import visad.TextControl; +import visad.TextType; +import visad.Tuple; +import visad.TupleType; +import visad.VisADException; import visad.bom.PickManipulationRendererJ3D; import visad.java3d.DisplayImplJ3D; import visad.java3d.DisplayRendererJ3D; @@ -30,13 +68,6 @@ import visad.java3d.KeyboardBehaviorJ3D; import visad.java3d.MouseBehaviorJ3D; -import java.awt.*; -import java.awt.event.KeyEvent; -import java.rmi.RemoteException; -import java.text.NumberFormat; -import java.util.Hashtable; -import java.util.Iterator; - /** * VisAD's DisplayImplJ3D modified for our purposes. */ Index: src/main/java/net/sf/mzmine/modules/visualization/threed/ThreeDPropertiesDialog.java =================================================================== --- src/main/java/net/sf/mzmine/modules/visualization/threed/ThreeDPropertiesDialog.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/visualization/threed/ThreeDPropertiesDialog.java (working copy) @@ -19,16 +19,17 @@ package net.sf.mzmine.modules.visualization.threed; -import net.sf.mzmine.main.MZmineCore; -import net.sf.mzmine.util.GUIUtils; -import visad.*; -import visad.util.ColorMapWidget; -import visad.util.GMCWidget; +import static java.awt.GridBagConstraints.CENTER; +import static java.awt.GridBagConstraints.EAST; +import static java.awt.GridBagConstraints.HORIZONTAL; +import static java.awt.GridBagConstraints.NONE; +import static java.awt.GridBagConstraints.WEST; -import javax.swing.*; -import javax.swing.event.ChangeEvent; -import javax.swing.event.ChangeListener; -import java.awt.*; +import java.awt.Color; +import java.awt.Component; +import java.awt.GridBagConstraints; +import java.awt.GridBagLayout; +import java.awt.Insets; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.beans.PropertyChangeEvent; @@ -38,8 +39,29 @@ import java.util.logging.Level; import java.util.logging.Logger; -import static java.awt.GridBagConstraints.*; +import javax.swing.BorderFactory; +import javax.swing.BoxLayout; +import javax.swing.JButton; +import javax.swing.JCheckBox; +import javax.swing.JColorChooser; +import javax.swing.JDialog; +import javax.swing.JFormattedTextField; +import javax.swing.JLabel; +import javax.swing.JPanel; +import javax.swing.JSlider; +import javax.swing.event.ChangeEvent; +import javax.swing.event.ChangeListener; +import net.sf.mzmine.main.MZmineCore; +import net.sf.mzmine.util.GUIUtils; +import visad.Display; +import visad.DisplayRealType; +import visad.ScalarMap; +import visad.TextControl; +import visad.VisADException; +import visad.util.ColorMapWidget; +import visad.util.GMCWidget; + /** * 3D visualizer properties dialog */ Index: src/main/java/net/sf/mzmine/modules/visualization/threed/ThreeDVisualizerWindow.java =================================================================== --- src/main/java/net/sf/mzmine/modules/visualization/threed/ThreeDVisualizerWindow.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/visualization/threed/ThreeDVisualizerWindow.java (working copy) @@ -19,6 +19,26 @@ package net.sf.mzmine.modules.visualization.threed; +import java.awt.BorderLayout; +import java.awt.Color; +import java.awt.Component; +import java.awt.Dimension; +import java.awt.Font; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.MouseWheelEvent; +import java.awt.event.MouseWheelListener; +import java.rmi.RemoteException; +import java.util.logging.Level; +import java.util.logging.Logger; + +import javax.swing.BorderFactory; +import javax.swing.JDialog; +import javax.swing.JFrame; +import javax.swing.JLabel; +import javax.swing.SwingConstants; +import javax.swing.WindowConstants; + import net.sf.mzmine.datamodel.PeakList; import net.sf.mzmine.datamodel.RawDataFile; import net.sf.mzmine.main.MZmineCore; @@ -28,17 +48,6 @@ import visad.VisADException; import visad.java3d.MouseBehaviorJ3D; -import javax.swing.*; - -import java.awt.*; -import java.awt.event.ActionEvent; -import java.awt.event.ActionListener; -import java.awt.event.MouseWheelEvent; -import java.awt.event.MouseWheelListener; -import java.rmi.RemoteException; -import java.util.logging.Level; -import java.util.logging.Logger; - /** * 3D visualizer frame. */ Index: src/main/java/net/sf/mzmine/modules/visualization/tic/ExportChromatogramTask.java =================================================================== --- src/main/java/net/sf/mzmine/modules/visualization/tic/ExportChromatogramTask.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/visualization/tic/ExportChromatogramTask.java (working copy) @@ -23,9 +23,6 @@ package net.sf.mzmine.modules.visualization.tic; -import net.sf.mzmine.taskcontrol.AbstractTask; -import net.sf.mzmine.taskcontrol.TaskStatus; - import java.io.BufferedWriter; import java.io.File; import java.io.FileWriter; @@ -33,6 +30,9 @@ import java.util.logging.Level; import java.util.logging.Logger; +import net.sf.mzmine.taskcontrol.AbstractTask; +import net.sf.mzmine.taskcontrol.TaskStatus; + /** * Exports a chromatogram to a CSV file. * Index: src/main/java/net/sf/mzmine/modules/visualization/tic/ExportPopUpMenu.java =================================================================== --- src/main/java/net/sf/mzmine/modules/visualization/tic/ExportPopUpMenu.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/visualization/tic/ExportPopUpMenu.java (working copy) @@ -23,14 +23,15 @@ package net.sf.mzmine.modules.visualization.tic; -import net.sf.mzmine.datamodel.RawDataFile; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; -import javax.swing.*; +import javax.swing.JMenu; +import javax.swing.JMenuItem; import javax.swing.event.MenuEvent; import javax.swing.event.MenuListener; -import java.awt.event.ActionEvent; -import java.awt.event.ActionListener; +import net.sf.mzmine.datamodel.RawDataFile; /** * A pop-up menu to select chromatograms for export. Index: src/main/java/net/sf/mzmine/modules/visualization/tic/PeakTICPlotRenderer.java =================================================================== --- src/main/java/net/sf/mzmine/modules/visualization/tic/PeakTICPlotRenderer.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/visualization/tic/PeakTICPlotRenderer.java (working copy) @@ -19,6 +19,11 @@ package net.sf.mzmine.modules.visualization.tic; +import java.awt.AlphaComposite; +import java.awt.Composite; +import java.awt.Graphics2D; +import java.awt.geom.Rectangle2D; + import org.jfree.chart.axis.ValueAxis; import org.jfree.chart.plot.CrosshairState; import org.jfree.chart.plot.PlotRenderingInfo; @@ -27,9 +32,6 @@ import org.jfree.chart.renderer.xy.XYItemRendererState; import org.jfree.data.xy.XYDataset; -import java.awt.*; -import java.awt.geom.Rectangle2D; - public class PeakTICPlotRenderer extends XYAreaRenderer { private static final float OPACITY = 0.6f; Index: src/main/java/net/sf/mzmine/modules/visualization/tic/TICDataSet.java =================================================================== --- src/main/java/net/sf/mzmine/modules/visualization/tic/TICDataSet.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/visualization/tic/TICDataSet.java (working copy) @@ -19,11 +19,30 @@ package net.sf.mzmine.modules.visualization.tic; +import static net.sf.mzmine.taskcontrol.TaskStatus.CANCELED; +import static net.sf.mzmine.taskcontrol.TaskStatus.ERROR; +import static net.sf.mzmine.taskcontrol.TaskStatus.FINISHED; +import static net.sf.mzmine.taskcontrol.TaskStatus.PROCESSING; +import static net.sf.mzmine.taskcontrol.TaskStatus.WAITING; + +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Collection; +import java.util.LinkedList; +import java.util.logging.Level; +import java.util.logging.Logger; + +import javax.swing.SwingUtilities; + import net.sf.mzmine.datamodel.DataPoint; import net.sf.mzmine.datamodel.RawDataFile; import net.sf.mzmine.datamodel.Scan; import net.sf.mzmine.main.MZmineCore; -import net.sf.mzmine.taskcontrol.*; +import net.sf.mzmine.taskcontrol.Task; +import net.sf.mzmine.taskcontrol.TaskEvent; +import net.sf.mzmine.taskcontrol.TaskListener; +import net.sf.mzmine.taskcontrol.TaskPriority; +import net.sf.mzmine.taskcontrol.TaskStatus; import net.sf.mzmine.util.CollectionUtils; import net.sf.mzmine.util.Range; import net.sf.mzmine.util.ScanUtils; @@ -30,17 +49,6 @@ import org.jfree.data.xy.AbstractXYZDataset; -import javax.swing.*; - -import java.util.ArrayList; -import java.util.Arrays; -import java.util.Collection; -import java.util.LinkedList; -import java.util.logging.Level; -import java.util.logging.Logger; - -import static net.sf.mzmine.taskcontrol.TaskStatus.*; - /** * TIC visualizer data set. One data set is created per file shown in this visualizer. We need to create separate * data set for each file because the user may add/remove files later. Index: src/main/java/net/sf/mzmine/modules/visualization/tic/TICPlot.java =================================================================== --- src/main/java/net/sf/mzmine/modules/visualization/tic/TICPlot.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/visualization/tic/TICPlot.java (working copy) @@ -19,9 +19,28 @@ package net.sf.mzmine.modules.visualization.tic; +import java.awt.BasicStroke; +import java.awt.Color; +import java.awt.Cursor; +import java.awt.Font; +import java.awt.Shape; +import java.awt.Stroke; +import java.awt.Window; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.MouseEvent; +import java.awt.geom.Ellipse2D; +import java.util.logging.Level; +import java.util.logging.Logger; + +import javax.swing.JFrame; +import javax.swing.JPopupMenu; +import javax.swing.KeyStroke; + import net.sf.mzmine.main.MZmineCore; import net.sf.mzmine.util.GUIUtils; import net.sf.mzmine.util.dialogs.AxesSetupDialog; + import org.jfree.chart.ChartFactory; import org.jfree.chart.ChartPanel; import org.jfree.chart.JFreeChart; @@ -40,15 +59,6 @@ import org.jfree.data.xy.XYDataset; import org.jfree.ui.RectangleInsets; -import javax.swing.*; -import java.awt.*; -import java.awt.event.ActionEvent; -import java.awt.event.ActionListener; -import java.awt.event.MouseEvent; -import java.awt.geom.Ellipse2D; -import java.util.logging.Level; -import java.util.logging.Logger; - /** * TIC plot. */ Index: src/main/java/net/sf/mzmine/modules/visualization/tic/TICToolBar.java =================================================================== --- src/main/java/net/sf/mzmine/modules/visualization/tic/TICToolBar.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/visualization/tic/TICToolBar.java (working copy) @@ -19,12 +19,17 @@ package net.sf.mzmine.modules.visualization.tic; +import java.awt.Color; +import java.awt.Insets; +import java.awt.event.ActionListener; + +import javax.swing.Icon; +import javax.swing.ImageIcon; +import javax.swing.JToolBar; +import javax.swing.SwingConstants; + import net.sf.mzmine.util.GUIUtils; -import javax.swing.*; -import java.awt.*; -import java.awt.event.ActionListener; - /** * TIC visualizer's toolbar. */ Index: src/main/java/net/sf/mzmine/modules/visualization/tic/TICToolTipGenerator.java =================================================================== --- src/main/java/net/sf/mzmine/modules/visualization/tic/TICToolTipGenerator.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/visualization/tic/TICToolTipGenerator.java (working copy) @@ -19,12 +19,13 @@ package net.sf.mzmine.modules.visualization.tic; +import java.text.NumberFormat; + import net.sf.mzmine.main.MZmineCore; + import org.jfree.chart.labels.XYToolTipGenerator; import org.jfree.data.xy.XYDataset; -import java.text.NumberFormat; - /** * Tooltip generator for TIC visualizer */ Index: src/main/java/net/sf/mzmine/modules/visualization/twod/TwoDDataSet.java =================================================================== --- src/main/java/net/sf/mzmine/modules/visualization/twod/TwoDDataSet.java (revision 3347) +++ src/main/java/net/sf/mzmine/modules/visualization/twod/TwoDDataSet.java (working copy) @@ -29,10 +29,10 @@ import net.sf.mzmine.datamodel.impl.SimpleDataPoint; import net.sf.mzmine.main.MZmineCore; import net.sf.mzmine.taskcontrol.Task; +import net.sf.mzmine.taskcontrol.TaskEvent; +import net.sf.mzmine.taskcontrol.TaskListener; import net.sf.mzmine.taskcontrol.TaskPriority; import net.sf.mzmine.taskcontrol.TaskStatus; -import net.sf.mzmine.taskcontrol.TaskListener; -import net.sf.mzmine.taskcontrol.TaskEvent; import net.sf.mzmine.util.DataPointSorter; import net.sf.mzmine.util.Range; import net.sf.mzmine.util.SortingDirection; Index: src/main/java/net/sf/mzmine/parameters/parametertypes/AdductsComponent.java =================================================================== --- src/main/java/net/sf/mzmine/parameters/parametertypes/AdductsComponent.java (revision 3347) +++ src/main/java/net/sf/mzmine/parameters/parametertypes/AdductsComponent.java (working copy) @@ -23,9 +23,13 @@ package net.sf.mzmine.parameters.parametertypes; -import net.sf.mzmine.modules.peaklistmethods.identification.adductsearch.*; +import javax.swing.JButton; -import javax.swing.*; +import net.sf.mzmine.modules.peaklistmethods.identification.adductsearch.AddAdductsAction; +import net.sf.mzmine.modules.peaklistmethods.identification.adductsearch.AdductType; +import net.sf.mzmine.modules.peaklistmethods.identification.adductsearch.DefaultAdductsAction; +import net.sf.mzmine.modules.peaklistmethods.identification.adductsearch.ExportAdductsAction; +import net.sf.mzmine.modules.peaklistmethods.identification.adductsearch.ImportAdductsAction; /** * A component for selecting adducts. Index: src/main/java/net/sf/mzmine/parameters/parametertypes/AdductsParameter.java =================================================================== --- src/main/java/net/sf/mzmine/parameters/parametertypes/AdductsParameter.java (revision 3347) +++ src/main/java/net/sf/mzmine/parameters/parametertypes/AdductsParameter.java (working copy) @@ -23,14 +23,19 @@ package net.sf.mzmine.parameters.parametertypes; -import net.sf.mzmine.modules.peaklistmethods.identification.adductsearch.AdductType; -import org.w3c.dom.*; - import java.util.ArrayList; import java.util.Arrays; import java.util.List; import java.util.logging.Logger; +import net.sf.mzmine.modules.peaklistmethods.identification.adductsearch.AdductType; + +import org.w3c.dom.Document; +import org.w3c.dom.Element; +import org.w3c.dom.NamedNodeMap; +import org.w3c.dom.Node; +import org.w3c.dom.NodeList; + /** * Adducts parameter. * Index: src/main/java/net/sf/mzmine/parameters/parametertypes/DirectoryComponent.java =================================================================== --- src/main/java/net/sf/mzmine/parameters/parametertypes/DirectoryComponent.java (revision 3347) +++ src/main/java/net/sf/mzmine/parameters/parametertypes/DirectoryComponent.java (working copy) @@ -22,14 +22,18 @@ */ package net.sf.mzmine.parameters.parametertypes; -import net.sf.mzmine.main.MZmineCore; - -import javax.swing.*; -import java.awt.*; +import java.awt.Font; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.io.File; +import javax.swing.JButton; +import javax.swing.JFileChooser; +import javax.swing.JPanel; +import javax.swing.JTextField; + +import net.sf.mzmine.main.MZmineCore; + /** */ public class DirectoryComponent extends JPanel implements ActionListener { Index: src/main/java/net/sf/mzmine/parameters/parametertypes/DirectoryParameter.java =================================================================== --- src/main/java/net/sf/mzmine/parameters/parametertypes/DirectoryParameter.java (revision 3347) +++ src/main/java/net/sf/mzmine/parameters/parametertypes/DirectoryParameter.java (working copy) @@ -22,12 +22,13 @@ */ package net.sf.mzmine.parameters.parametertypes; +import java.io.File; +import java.util.Collection; + import net.sf.mzmine.parameters.UserParameter; + import org.w3c.dom.Element; -import java.io.File; -import java.util.Collection; - /** * A parameter that represents a file system directory. */ Index: src/main/java/net/sf/mzmine/parameters/parametertypes/DoubleParameter.java =================================================================== --- src/main/java/net/sf/mzmine/parameters/parametertypes/DoubleParameter.java (revision 3347) +++ src/main/java/net/sf/mzmine/parameters/parametertypes/DoubleParameter.java (working copy) @@ -19,16 +19,21 @@ package net.sf.mzmine.parameters.parametertypes; -import net.sf.mzmine.parameters.UserParameter; -import org.w3c.dom.Element; - -import javax.swing.*; -import javax.swing.text.JTextComponent; -import java.awt.*; +import java.awt.Dimension; +import java.awt.Toolkit; import java.text.NumberFormat; import java.text.ParseException; import java.util.Collection; +import javax.swing.InputVerifier; +import javax.swing.JComponent; +import javax.swing.JTextField; +import javax.swing.text.JTextComponent; + +import net.sf.mzmine.parameters.UserParameter; + +import org.w3c.dom.Element; + /** * Number parameter. Note that we prefer to use JTextField rather than * JFormattedTextField, because JFormattedTextField sometimes has odd behavior. Index: src/main/java/net/sf/mzmine/parameters/parametertypes/FileNameParameter.java =================================================================== --- src/main/java/net/sf/mzmine/parameters/parametertypes/FileNameParameter.java (revision 3347) +++ src/main/java/net/sf/mzmine/parameters/parametertypes/FileNameParameter.java (working copy) @@ -22,10 +22,10 @@ import java.io.File; import java.util.Collection; +import net.sf.mzmine.parameters.UserParameter; + import org.w3c.dom.Element; -import net.sf.mzmine.parameters.UserParameter; - /** * Simple Parameter implementation * Index: src/main/java/net/sf/mzmine/parameters/parametertypes/IntegerParameter.java =================================================================== --- src/main/java/net/sf/mzmine/parameters/parametertypes/IntegerParameter.java (revision 3347) +++ src/main/java/net/sf/mzmine/parameters/parametertypes/IntegerParameter.java (working copy) @@ -19,14 +19,19 @@ package net.sf.mzmine.parameters.parametertypes; +import java.awt.Dimension; +import java.awt.Toolkit; +import java.util.Collection; + +import javax.swing.InputVerifier; +import javax.swing.JComponent; +import javax.swing.JTextField; +import javax.swing.text.JTextComponent; + import net.sf.mzmine.parameters.UserParameter; + import org.w3c.dom.Element; -import javax.swing.*; -import javax.swing.text.JTextComponent; -import java.awt.*; -import java.util.Collection; - /** * Integer parameter. Note that we prefer to use JTextField rather than * JFormattedTextField, because JFormattedTextField sometimes has odd behavior. Index: src/main/java/net/sf/mzmine/parameters/parametertypes/MZToleranceParameter.java =================================================================== --- src/main/java/net/sf/mzmine/parameters/parametertypes/MZToleranceParameter.java (revision 3347) +++ src/main/java/net/sf/mzmine/parameters/parametertypes/MZToleranceParameter.java (working copy) @@ -21,12 +21,12 @@ import java.util.Collection; +import net.sf.mzmine.parameters.UserParameter; + import org.w3c.dom.Document; import org.w3c.dom.Element; import org.w3c.dom.NodeList; -import net.sf.mzmine.parameters.UserParameter; - public class MZToleranceParameter implements UserParameter { Index: src/main/java/net/sf/mzmine/parameters/parametertypes/MultiChoiceComponent.java =================================================================== --- src/main/java/net/sf/mzmine/parameters/parametertypes/MultiChoiceComponent.java (revision 3347) +++ src/main/java/net/sf/mzmine/parameters/parametertypes/MultiChoiceComponent.java (working copy) @@ -19,8 +19,11 @@ package net.sf.mzmine.parameters.parametertypes; -import javax.swing.*; -import java.awt.*; +import java.awt.BorderLayout; +import java.awt.Color; +import java.awt.Dimension; +import java.awt.Font; +import java.awt.Rectangle; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.util.ArrayList; @@ -27,6 +30,17 @@ import java.util.Collection; import java.util.TreeSet; +import javax.swing.Box; +import javax.swing.BoxLayout; +import javax.swing.JButton; +import javax.swing.JCheckBox; +import javax.swing.JPanel; +import javax.swing.JScrollPane; +import javax.swing.ScrollPaneConstants; +import javax.swing.Scrollable; +import javax.swing.SwingConstants; +import javax.swing.ToolTipManager; + /** */ public class MultiChoiceComponent extends JPanel implements ActionListener { Index: src/main/java/net/sf/mzmine/parameters/parametertypes/OptionalModuleParameter.java =================================================================== --- src/main/java/net/sf/mzmine/parameters/parametertypes/OptionalModuleParameter.java (revision 3347) +++ src/main/java/net/sf/mzmine/parameters/parametertypes/OptionalModuleParameter.java (working copy) @@ -22,8 +22,8 @@ import java.util.Collection; import net.sf.mzmine.parameters.Parameter; +import net.sf.mzmine.parameters.ParameterSet; import net.sf.mzmine.parameters.UserParameter; -import net.sf.mzmine.parameters.ParameterSet; import org.w3c.dom.Element; Index: src/main/java/net/sf/mzmine/project/impl/MZmineProjectImpl.java =================================================================== --- src/main/java/net/sf/mzmine/project/impl/MZmineProjectImpl.java (revision 3347) +++ src/main/java/net/sf/mzmine/project/impl/MZmineProjectImpl.java (working copy) @@ -24,8 +24,6 @@ import java.util.Vector; import javax.swing.SwingUtilities; -import javax.swing.tree.TreeNode; -import javax.swing.tree.TreePath; import net.sf.mzmine.datamodel.MZmineProject; import net.sf.mzmine.datamodel.PeakList; Index: src/main/java/net/sf/mzmine/taskcontrol/AbstractTask.java =================================================================== --- src/main/java/net/sf/mzmine/taskcontrol/AbstractTask.java (revision 3347) +++ src/main/java/net/sf/mzmine/taskcontrol/AbstractTask.java (working copy) @@ -21,9 +21,6 @@ import java.util.LinkedList; -import net.sf.mzmine.taskcontrol.Task; -import net.sf.mzmine.taskcontrol.TaskStatus; - /** * An abstract implementation of task which defines common methods to make Task * implementation easier Index: src/main/java/net/sf/mzmine/util/components/DragOrderedJList.java =================================================================== --- src/main/java/net/sf/mzmine/util/components/DragOrderedJList.java (revision 3347) +++ src/main/java/net/sf/mzmine/util/components/DragOrderedJList.java (working copy) @@ -19,8 +19,6 @@ package net.sf.mzmine.util.components; -import javax.swing.*; - import java.awt.Component; import java.awt.event.MouseAdapter; import java.awt.event.MouseEvent; @@ -27,6 +25,10 @@ import java.awt.event.MouseMotionAdapter; import java.util.Vector; +import javax.swing.DefaultListModel; +import javax.swing.JList; +import javax.swing.ListModel; + /** * A modified JList that can reorder items in the DefaultListModel by dragging with the mouse. */ Index: src/main/java/net/sf/mzmine/util/components/PeakSummaryComponent.java =================================================================== --- src/main/java/net/sf/mzmine/util/components/PeakSummaryComponent.java (revision 3347) +++ src/main/java/net/sf/mzmine/util/components/PeakSummaryComponent.java (working copy) @@ -19,7 +19,40 @@ package net.sf.mzmine.util.components; -import net.sf.mzmine.datamodel.*; +import java.awt.BorderLayout; +import java.awt.Color; +import java.awt.Component; +import java.awt.Dimension; +import java.awt.Font; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.text.DecimalFormat; +import java.text.Format; +import java.util.HashMap; +import java.util.Map; + +import javax.swing.BorderFactory; +import javax.swing.Box; +import javax.swing.BoxLayout; +import javax.swing.JButton; +import javax.swing.JComboBox; +import javax.swing.JLabel; +import javax.swing.JPanel; +import javax.swing.JScrollPane; +import javax.swing.JTable; +import javax.swing.ListSelectionModel; +import javax.swing.SwingUtilities; +import javax.swing.border.Border; +import javax.swing.border.EtchedBorder; +import javax.swing.table.TableCellRenderer; +import javax.swing.table.TableColumn; +import javax.swing.table.TableModel; + +import net.sf.mzmine.datamodel.Feature; +import net.sf.mzmine.datamodel.IsotopePattern; +import net.sf.mzmine.datamodel.PeakIdentity; +import net.sf.mzmine.datamodel.PeakListRow; +import net.sf.mzmine.datamodel.RawDataFile; import net.sf.mzmine.main.MZmineCore; import net.sf.mzmine.modules.rawdatamethods.peakpicking.manual.ManualPeakPickerModule; import net.sf.mzmine.modules.visualization.spectra.SpectraVisualizerModule; @@ -29,21 +62,6 @@ import net.sf.mzmine.modules.visualization.twod.TwoDVisualizerModule; import net.sf.mzmine.util.Range; -import javax.swing.*; -import javax.swing.border.Border; -import javax.swing.border.EtchedBorder; -import javax.swing.table.TableCellRenderer; -import javax.swing.table.TableColumn; -import javax.swing.table.TableModel; - -import java.awt.*; -import java.awt.event.ActionEvent; -import java.awt.event.ActionListener; -import java.text.DecimalFormat; -import java.text.Format; -import java.util.HashMap; -import java.util.Map; - public class PeakSummaryComponent extends JPanel implements ActionListener { private static final DecimalFormat formatter = new DecimalFormat("###.#"); Index: src/main/java/net/sf/mzmine/util/dialogs/LoadSaveFileChooser.java =================================================================== --- src/main/java/net/sf/mzmine/util/dialogs/LoadSaveFileChooser.java (revision 3347) +++ src/main/java/net/sf/mzmine/util/dialogs/LoadSaveFileChooser.java (working copy) @@ -23,10 +23,12 @@ package net.sf.mzmine.util.dialogs; -import javax.swing.*; -import java.awt.*; +import java.awt.Component; import java.io.File; +import javax.swing.JFileChooser; +import javax.swing.JOptionPane; + /** * A JFileChooser with convenience functions for loading and saving files. * Index: src/main/java/net/sf/mzmine/util/interpolatinglookuppaintscale/InterpolatingLookupPaintScale.java =================================================================== --- src/main/java/net/sf/mzmine/util/interpolatinglookuppaintscale/InterpolatingLookupPaintScale.java (revision 3347) +++ src/main/java/net/sf/mzmine/util/interpolatinglookuppaintscale/InterpolatingLookupPaintScale.java (working copy) @@ -23,8 +23,8 @@ import java.awt.Paint; import java.io.Serializable; import java.util.Map; +import java.util.Map.Entry; import java.util.TreeMap; -import java.util.Map.Entry; import org.jfree.chart.renderer.PaintScale; import org.jfree.util.PublicCloneable; Index: src/main/java/net/sf/mzmine/util/interpolatinglookuppaintscale/InterpolatingLookupPaintScaleSetupDialogTableCellRenderer.java =================================================================== --- src/main/java/net/sf/mzmine/util/interpolatinglookuppaintscale/InterpolatingLookupPaintScaleSetupDialogTableCellRenderer.java (revision 3347) +++ src/main/java/net/sf/mzmine/util/interpolatinglookuppaintscale/InterpolatingLookupPaintScaleSetupDialogTableCellRenderer.java (working copy) @@ -22,6 +22,7 @@ import java.awt.Color; import java.awt.Component; import java.util.TreeMap; + import javax.swing.JTable; import javax.swing.table.DefaultTableCellRenderer; Index: src/main/java/net/sf/mzmine/util/interpolatinglookuppaintscale/InterpolatingLookupPaintScaleSetupDialogTableModel.java =================================================================== --- src/main/java/net/sf/mzmine/util/interpolatinglookuppaintscale/InterpolatingLookupPaintScaleSetupDialogTableModel.java (revision 3347) +++ src/main/java/net/sf/mzmine/util/interpolatinglookuppaintscale/InterpolatingLookupPaintScaleSetupDialogTableModel.java (working copy) @@ -21,6 +21,7 @@ import java.awt.Color; import java.util.TreeMap; + import javax.swing.table.AbstractTableModel; public class InterpolatingLookupPaintScaleSetupDialogTableModel extends AbstractTableModel {