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This repository was archived by the owner on May 5, 2024. It is now read-only.

Commit 2a83d3a

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tomas-pluskaltomas-pluskal
committed
Renamed "Order.." to "Sort.."
1 parent 277b261 commit 2a83d3a

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6 files changed

+32
-32
lines changed

6 files changed

+32
-32
lines changed

‎src/main/java/net/sf/mzmine/desktop/impl/projecttree/ProjectTreeMouseHandler.java

Lines changed: 10 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -35,12 +35,12 @@
3535
import net.sf.mzmine.datamodel.RawDataFile;
3636
import net.sf.mzmine.datamodel.Scan;
3737
import net.sf.mzmine.main.MZmineCore;
38-
import net.sf.mzmine.modules.peaklistmethods.orderpeaklists.OrderPeakListsModule;
39-
import net.sf.mzmine.modules.peaklistmethods.orderpeaklists.OrderPeakListsParameters;
38+
import net.sf.mzmine.modules.peaklistmethods.sortpeaklists.SortPeakListsModule;
39+
import net.sf.mzmine.modules.peaklistmethods.sortpeaklists.SortPeakListsParameters;
4040
import net.sf.mzmine.modules.rawdatamethods.exportscans.ExportScansModule;
41-
import net.sf.mzmine.modules.rawdatamethods.orderdatafiles.OrderDataFilesModule;
42-
import net.sf.mzmine.modules.rawdatamethods.orderdatafiles.OrderDataFilesParameters;
4341
import net.sf.mzmine.modules.rawdatamethods.rawdataexport.RawDataExportModule;
42+
import net.sf.mzmine.modules.rawdatamethods.sortdatafiles.SortDataFilesModule;
43+
import net.sf.mzmine.modules.rawdatamethods.sortdatafiles.SortDataFilesParameters;
4444
import net.sf.mzmine.modules.visualization.infovisualizer.InfoVisualizerModule;
4545
import net.sf.mzmine.modules.visualization.peaklisttable.PeakListTableModule;
4646
import net.sf.mzmine.modules.visualization.peaksummary.PeakSummaryVisualizerModule;
@@ -169,10 +169,10 @@ public void actionPerformed(ActionEvent e) {
169169
// save current selection
170170
TreePath savedSelection[] = tree.getSelectionPaths();
171171
RawDataFile selectedFiles[] = tree.getSelectedObjects(RawDataFile.class);
172-
OrderDataFilesModule module = MZmineCore.getModuleInstance(OrderDataFilesModule.class);
172+
SortDataFilesModule module = MZmineCore.getModuleInstance(SortDataFilesModule.class);
173173
ParameterSet params =
174-
MZmineCore.getConfiguration().getModuleParameters(OrderDataFilesModule.class);
175-
params.getParameter(OrderDataFilesParameters.dataFiles)
174+
MZmineCore.getConfiguration().getModuleParameters(SortDataFilesModule.class);
175+
params.getParameter(SortDataFilesParameters.dataFiles)
176176
.setValue(RawDataFilesSelectionType.SPECIFIC_FILES, selectedFiles);
177177
module.runModule(MZmineCore.getProjectManager().getCurrentProject(), params,
178178
new ArrayList<Task>());
@@ -304,10 +304,10 @@ public void actionPerformed(ActionEvent e) {
304304
// save current selection
305305
TreePath savedSelection[] = tree.getSelectionPaths();
306306
PeakList selectedPeakLists[] = tree.getSelectedObjects(PeakList.class);
307-
OrderPeakListsModule module = MZmineCore.getModuleInstance(OrderPeakListsModule.class);
307+
SortPeakListsModule module = MZmineCore.getModuleInstance(SortPeakListsModule.class);
308308
ParameterSet params =
309-
MZmineCore.getConfiguration().getModuleParameters(OrderPeakListsModule.class);
310-
params.getParameter(OrderPeakListsParameters.peakLists)
309+
MZmineCore.getConfiguration().getModuleParameters(SortPeakListsModule.class);
310+
params.getParameter(SortPeakListsParameters.peakLists)
311311
.setValue(PeakListsSelectionType.SPECIFIC_PEAKLISTS, selectedPeakLists);
312312
module.runModule(MZmineCore.getProjectManager().getCurrentProject(), params,
313313
new ArrayList<Task>());

‎src/main/java/net/sf/mzmine/main/MZmineModulesList.java

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -77,13 +77,13 @@
7777
import net.sf.mzmine.modules.peaklistmethods.normalization.linear.LinearNormalizerModule;
7878
import net.sf.mzmine.modules.peaklistmethods.normalization.rtnormalizer.RTNormalizerModule;
7979
import net.sf.mzmine.modules.peaklistmethods.normalization.standardcompound.StandardCompoundNormalizerModule;
80-
import net.sf.mzmine.modules.peaklistmethods.orderpeaklists.OrderPeakListsModule;
8180
import net.sf.mzmine.modules.peaklistmethods.peakpicking.adap3decompositionV1_5.ADAP3DecompositionV1_5Module;
8281
import net.sf.mzmine.modules.peaklistmethods.peakpicking.adap3decompositionV2.ADAP3DecompositionV2Module;
8382
import net.sf.mzmine.modules.peaklistmethods.peakpicking.deconvolution.DeconvolutionModule;
8483
import net.sf.mzmine.modules.peaklistmethods.peakpicking.peakextender.PeakExtenderModule;
8584
import net.sf.mzmine.modules.peaklistmethods.peakpicking.shapemodeler.ShapeModelerModule;
8685
import net.sf.mzmine.modules.peaklistmethods.peakpicking.smoothing.SmoothingModule;
86+
import net.sf.mzmine.modules.peaklistmethods.sortpeaklists.SortPeakListsModule;
8787
import net.sf.mzmine.modules.projectmethods.projectclose.ProjectCloseModule;
8888
import net.sf.mzmine.modules.projectmethods.projectload.ProjectLoadModule;
8989
import net.sf.mzmine.modules.projectmethods.projectsave.ProjectSaveAsModule;
@@ -97,14 +97,14 @@
9797
import net.sf.mzmine.modules.rawdatamethods.filtering.scanfilters.ScanFiltersModule;
9898
import net.sf.mzmine.modules.rawdatamethods.filtering.scansmoothing.ScanSmoothingModule;
9999
import net.sf.mzmine.modules.rawdatamethods.merge.RawFileMergeModule;
100-
import net.sf.mzmine.modules.rawdatamethods.orderdatafiles.OrderDataFilesModule;
101100
import net.sf.mzmine.modules.rawdatamethods.peakpicking.gridmass.GridMassModule;
102101
import net.sf.mzmine.modules.rawdatamethods.peakpicking.manual.ManualPeakPickerModule;
103102
import net.sf.mzmine.modules.rawdatamethods.peakpicking.massdetection.MassDetectionModule;
104103
import net.sf.mzmine.modules.rawdatamethods.peakpicking.msms.MsMsPeakPickerModule;
105104
import net.sf.mzmine.modules.rawdatamethods.peakpicking.targetedpeakdetection.TargetedPeakDetectionModule;
106105
import net.sf.mzmine.modules.rawdatamethods.rawdataexport.RawDataExportModule;
107106
import net.sf.mzmine.modules.rawdatamethods.rawdataimport.RawDataImportModule;
107+
import net.sf.mzmine.modules.rawdatamethods.sortdatafiles.SortDataFilesModule;
108108
import net.sf.mzmine.modules.tools.isotopepatternpreview.IsotopePatternPreviewModule;
109109
import net.sf.mzmine.modules.tools.msmsspectramerge.MsMsSpectraMergeModule;
110110
import net.sf.mzmine.modules.tools.mzrangecalculator.MzRangeFormulaCalculatorModule;
@@ -158,10 +158,10 @@ public class MZmineModulesList {
158158
// Not ready for prime time: ADAP3DModule.class,
159159
GridMassModule.class, ManualPeakPickerModule.class, MsMsPeakPickerModule.class,
160160
ScanFiltersModule.class, CropFilterModule.class, BaselineCorrectionModule.class,
161-
AlignScansModule.class, ScanSmoothingModule.class, OrderDataFilesModule.class,
161+
AlignScansModule.class, ScanSmoothingModule.class, SortDataFilesModule.class,
162162

163163
// Alignment
164-
OrderPeakListsModule.class, JoinAlignerModule.class, HierarAlignerGcModule.class,
164+
SortPeakListsModule.class, JoinAlignerModule.class, HierarAlignerGcModule.class,
165165

166166
RansacAlignerModule.class, ADAP3AlignerModule.class,
167167
// PathAlignerModule.class,

‎src/main/java/net/sf/mzmine/modules/peaklistmethods/orderpeaklists/OrderPeakListsModule.java renamed to ‎src/main/java/net/sf/mzmine/modules/peaklistmethods/sortpeaklists/SortPeakListsModule.java

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -16,7 +16,7 @@
1616
* USA
1717
*/
1818

19-
package net.sf.mzmine.modules.peaklistmethods.orderpeaklists;
19+
package net.sf.mzmine.modules.peaklistmethods.sortpeaklists;
2020

2121
import java.util.ArrayList;
2222
import java.util.Arrays;
@@ -45,12 +45,12 @@
4545
* This is a very simple module which reorders feature lists alphabetically
4646
*
4747
*/
48-
public class OrderPeakListsModule implements MZmineProcessingModule {
48+
public class SortPeakListsModule implements MZmineProcessingModule {
4949

5050
private Logger logger = Logger.getLogger(this.getClass().getName());
5151

52-
private static final String MODULE_NAME = "Order feature lists";
53-
private static final String MODULE_DESCRIPTION = "Order selected feature lists alphabetically";
52+
private static final String MODULE_NAME = "Sort feature lists";
53+
private static final String MODULE_DESCRIPTION = "Sort selected feature lists alphabetically";
5454

5555
@Override
5656
public @Nonnull String getName() {
@@ -68,7 +68,7 @@ public ExitCode runModule(@Nonnull MZmineProject project, @Nonnull ParameterSet
6868
@Nonnull Collection<Task> tasks) {
6969

7070
List<PeakList> peakLists = Arrays.asList(parameters
71-
.getParameter(OrderPeakListsParameters.peakLists).getValue().getMatchingPeakLists());
71+
.getParameter(SortPeakListsParameters.peakLists).getValue().getMatchingPeakLists());
7272

7373

7474
PeakListTreeModel model = null;
@@ -133,7 +133,7 @@ public int compare(DefaultMutableTreeNode o1, DefaultMutableTreeNode o2) {
133133

134134
@Override
135135
public @Nonnull Class<? extends ParameterSet> getParameterSetClass() {
136-
return OrderPeakListsParameters.class;
136+
return SortPeakListsParameters.class;
137137
}
138138

139139
}

‎src/main/java/net/sf/mzmine/modules/peaklistmethods/orderpeaklists/OrderPeakListsParameters.java renamed to ‎src/main/java/net/sf/mzmine/modules/peaklistmethods/sortpeaklists/SortPeakListsParameters.java

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -16,17 +16,17 @@
1616
* USA
1717
*/
1818

19-
package net.sf.mzmine.modules.peaklistmethods.orderpeaklists;
19+
package net.sf.mzmine.modules.peaklistmethods.sortpeaklists;
2020

2121
import net.sf.mzmine.parameters.Parameter;
2222
import net.sf.mzmine.parameters.impl.SimpleParameterSet;
2323
import net.sf.mzmine.parameters.parametertypes.selectors.PeakListsParameter;
2424

25-
public class OrderPeakListsParameters extends SimpleParameterSet {
25+
public class SortPeakListsParameters extends SimpleParameterSet {
2626

2727
public static final PeakListsParameter peakLists = new PeakListsParameter();
2828

29-
public OrderPeakListsParameters() {
29+
public SortPeakListsParameters() {
3030
super(new Parameter[] {peakLists});
3131
}
3232

‎src/main/java/net/sf/mzmine/modules/rawdatamethods/orderdatafiles/OrderDataFilesModule.java renamed to ‎src/main/java/net/sf/mzmine/modules/rawdatamethods/sortdatafiles/SortDataFilesModule.java

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -16,7 +16,7 @@
1616
* USA
1717
*/
1818

19-
package net.sf.mzmine.modules.rawdatamethods.orderdatafiles;
19+
package net.sf.mzmine.modules.rawdatamethods.sortdatafiles;
2020

2121
import java.util.ArrayList;
2222
import java.util.Arrays;
@@ -43,10 +43,10 @@
4343
/**
4444
* This is a very simple module which reorders data files alphabetically
4545
*/
46-
public class OrderDataFilesModule implements MZmineProcessingModule {
46+
public class SortDataFilesModule implements MZmineProcessingModule {
4747

48-
private static final String MODULE_NAME = "Order raw data files";
49-
private static final String MODULE_DESCRIPTION = "Order selected raw data files alphabetically";
48+
private static final String MODULE_NAME = "Sort raw data files";
49+
private static final String MODULE_DESCRIPTION = "Sort selected raw data files alphabetically";
5050

5151
@Override
5252
public @Nonnull String getName() {
@@ -64,7 +64,7 @@ public ExitCode runModule(@Nonnull MZmineProject project, @Nonnull ParameterSet
6464
@Nonnull Collection<Task> tasks) {
6565

6666
List<RawDataFile> dataFiles = Arrays.asList(parameters
67-
.getParameter(OrderDataFilesParameters.dataFiles).getValue().getMatchingRawDataFiles());
67+
.getParameter(SortDataFilesParameters.dataFiles).getValue().getMatchingRawDataFiles());
6868

6969

7070
RawDataTreeModel model = null;
@@ -128,7 +128,7 @@ public int compare(DefaultMutableTreeNode o1, DefaultMutableTreeNode o2) {
128128

129129
@Override
130130
public @Nonnull Class<? extends ParameterSet> getParameterSetClass() {
131-
return OrderDataFilesParameters.class;
131+
return SortDataFilesParameters.class;
132132
}
133133

134134
}

‎src/main/java/net/sf/mzmine/modules/rawdatamethods/orderdatafiles/OrderDataFilesParameters.java renamed to ‎src/main/java/net/sf/mzmine/modules/rawdatamethods/sortdatafiles/SortDataFilesParameters.java

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -16,17 +16,17 @@
1616
* USA
1717
*/
1818

19-
package net.sf.mzmine.modules.rawdatamethods.orderdatafiles;
19+
package net.sf.mzmine.modules.rawdatamethods.sortdatafiles;
2020

2121
import net.sf.mzmine.parameters.Parameter;
2222
import net.sf.mzmine.parameters.impl.SimpleParameterSet;
2323
import net.sf.mzmine.parameters.parametertypes.selectors.RawDataFilesParameter;
2424

25-
public class OrderDataFilesParameters extends SimpleParameterSet {
25+
public class SortDataFilesParameters extends SimpleParameterSet {
2626

2727
public static final RawDataFilesParameter dataFiles = new RawDataFilesParameter();
2828

29-
public OrderDataFilesParameters() {
29+
public SortDataFilesParameters() {
3030
super(new Parameter[] {dataFiles});
3131
}
3232

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