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Rserve integration 6 #39

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Rserve integration 6 #39

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c2a587c
Minor - Cleanup.
May 26, 2015
8d2a6f2
Fixed RSessionWrapper + Moved peaklists deconvolution module to use R…
May 27, 2015
61277bd
Fixed RSessionWrapper.
May 27, 2015
e78be63
Moved CAMERA search module to use Rserve.
May 27, 2015
5131e0c
Moved HeatMap analysis module to use Rserve.
May 28, 2015
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12 changes: 8 additions & 4 deletions src/main/java/net/sf/mzmine/modules/peaklistmethods/dataanalysis/heatmaps/HeatMapModule.java
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Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,6 @@

import net.sf.mzmine.datamodel.MZmineProject;
import net.sf.mzmine.datamodel.PeakList;
import net.sf.mzmine.main.MZmineCore;
import net.sf.mzmine.modules.MZmineModuleCategory;
import net.sf.mzmine.modules.MZmineRunnableModule;
import net.sf.mzmine.parameters.ParameterSet;
Expand All @@ -51,11 +50,16 @@ public class HeatMapModule implements MZmineRunnableModule {
@Nonnull
public ExitCode runModule(@Nonnull MZmineProject project,
@Nonnull ParameterSet parameters, @Nonnull Collection<Task> tasks) {
PeakList[] selectedDatasets = MZmineCore.getDesktop()
.getSelectedPeakLists();
HeatMapTask heatMapTask = new HeatMapTask(project, selectedDatasets[0],

PeakList selectedDataset = parameters
.getParameter(HeatMapParameters.peakLists).getValue()
.getMatchingPeakLists()[0];

HeatMapTask heatMapTask = new HeatMapTask(project, selectedDataset,
parameters);

tasks.add(heatMapTask);

return ExitCode.OK;

}
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13 changes: 9 additions & 4 deletions ...n/java/net/sf/mzmine/modules/peaklistmethods/dataanalysis/heatmaps/HeatMapParameters.java
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Expand Up @@ -31,11 +31,16 @@
import net.sf.mzmine.parameters.parametertypes.ComboParameter;
import net.sf.mzmine.parameters.parametertypes.FileNameParameter;
import net.sf.mzmine.parameters.parametertypes.IntegerParameter;
import net.sf.mzmine.parameters.parametertypes.PeakListsParameter;
import net.sf.mzmine.util.ExitCode;

public class HeatMapParameters extends SimpleParameterSet {

public static final String[] fileTypes = { "pdf", "svg", "png", "fig" };

public static final PeakListsParameter peakLists = new PeakListsParameter(
1, 1);

public static final FileNameParameter fileName = new FileNameParameter(
"Output name", "Select the path and name of the output file.");
public static final ComboParameter<String> fileTypeSelection = new ComboParameter<String>(
Expand Down Expand Up @@ -83,10 +88,10 @@ public class HeatMapParameters extends SimpleParameterSet {
"Row margin", "Row margin of the heat map", 10);

public HeatMapParameters() {
super(new Parameter[] { fileName, fileTypeSelection, selectionData,
referenceGroup, useIdenfiedRows, usePeakArea, scale, log,
showControlSamples, plegend, star, height, width, columnMargin,
rowMargin });
super(new Parameter[] { peakLists, fileName, fileTypeSelection,
selectionData, referenceGroup, useIdenfiedRows, usePeakArea,
scale, log, showControlSamples, plegend, star, height, width,
columnMargin, rowMargin });
}

@Override
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