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Merge pull request #129 from dyrlund/master
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Fixed various Eclipse warnings
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@tomas-pluskal
tomas-pluskal committed Mar 22, 2016
2 parents bac11b8 + 4297c99 commit fa50404
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Showing 29 changed files with 160 additions and 111 deletions.
26 changes: 15 additions & 11 deletions src/main/java/io/github/mzmine/modules/alignment/joinaligner/JoinAlignerModule.java
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Original file line number Diff line number Diff line change
Expand Up @@ -64,33 +64,37 @@ public void runModule(@Nonnull MZmineProject project,
@Nonnull ParameterSet parameters,
@Nonnull Collection<Task<?>> tasks) {

// Parameter values
final FeatureTablesSelection featureTables = parameters
.getParameter(JoinAlignerParameters.featureTables).getValue();

final MZTolerance mzTolerance = parameters
.getParameter(JoinAlignerParameters.mzTolerance).getValue();

final RTTolerance rtTolerance = parameters
.getParameter(JoinAlignerParameters.rtTolerance).getValue();

final Integer mzWeight = parameters
Integer mzWeight = parameters
.getParameter(JoinAlignerParameters.mzWeight).getValue();

final Integer rtWeight = parameters
Integer rtWeight = parameters
.getParameter(JoinAlignerParameters.rtWeight).getValue();

final Boolean requireSameAnnotation = parameters
Boolean requireSameAnnotation = parameters
.getParameter(JoinAlignerParameters.requireSameAnnotation)
.getValue();

final Boolean requireSameCharge = parameters
Boolean requireSameCharge = parameters
.getParameter(JoinAlignerParameters.requireSameCharge)
.getValue();

final String featureTableName = parameters
.getParameter(JoinAlignerParameters.featureTableName)
.getValue();

// Default values
if (mzWeight == null)
mzWeight = 1;
if (rtWeight == null)
rtWeight = 1;
if (requireSameAnnotation == null)
requireSameAnnotation = false;
if (requireSameCharge == null)
requireSameCharge = false;

final Boolean removeOldTable = parameters
.getParameter(JoinAlignerParameters.removeOldTable).getValue();

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11 changes: 6 additions & 5 deletions ...github/mzmine/modules/featuredetection/chromatogrambuilder/ChromatogramBuilderModule.java
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Original file line number Diff line number Diff line change
Expand Up @@ -68,9 +68,9 @@ public void runModule(@Nonnull MZmineProject project,
final MZTolerance mzTolerance = parameters
.getParameter(ChromatogramBuilderParameters.mzTolerance)
.getValue();
final Float noiseLevel = parameters
final Double noiseLevel = parameters
.getParameter(ChromatogramBuilderParameters.noiseLevel)
.getValue().floatValue();
.getValue();
final Double minDuration = parameters
.getParameter(ChromatogramBuilderParameters.minDuration)
.getValue();
Expand All @@ -81,7 +81,8 @@ public void runModule(@Nonnull MZmineProject project,
.getParameter(ChromatogramBuilderParameters.nameSuffix)
.getValue();

if (rawDataFiles.getMatchingRawDataFiles().isEmpty()) {
if (rawDataFiles == null
|| rawDataFiles.getMatchingRawDataFiles().isEmpty()) {
logger.warn(
"Chromatogram builder module started with no raw data files selected");
return;
Expand All @@ -99,8 +100,8 @@ public void runModule(@Nonnull MZmineProject project,
// 2. ChromatogramToFeatureTableMethod
ChromatogramBuilderTask newTask = new ChromatogramBuilderTask(
"Chromatogram builder", rawDataFile.getName(), rawDataFile,
dataStore, mzTolerance, noiseLevel, minDuration, minHeight,
nameSuffix);
dataStore, mzTolerance, noiseLevel,
minDuration, minHeight, nameSuffix);

// Add the feature table to the project
newTask.setOnSucceeded(e -> {
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6 changes: 3 additions & 3 deletions ...o/github/mzmine/modules/featuredetection/chromatogrambuilder/ChromatogramBuilderTask.java
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Original file line number Diff line number Diff line change
Expand Up @@ -54,12 +54,12 @@ public class ChromatogramBuilderTask extends Task<Object>
private String title, message;
private FeatureTable featureTable;

private MSDKMethod<?> chromatogramBuilderMethod;
private MSDKMethod<?> chromatogramToFeatureTableMethod;
private MSDKMethod<List<Chromatogram>> chromatogramBuilderMethod;
private MSDKMethod<FeatureTable> chromatogramToFeatureTableMethod;

public ChromatogramBuilderTask(String title, @Nullable String message,
@Nonnull RawDataFile rawDataFile, @Nonnull DataPointStore dataStore,
@Nonnull MZTolerance mzTolerance, @Nonnull Float noiseLevel,
@Nonnull MZTolerance mzTolerance, @Nonnull Double noiseLevel,
@Nonnull Double minDuration, @Nonnull Double minHeight,
@Nullable String nameSuffix) {
this.rawDataFile = rawDataFile;
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7 changes: 2 additions & 5 deletions src/main/java/io/github/mzmine/modules/featuredetection/srmdetection/SrmDetectionModule.java
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Original file line number Diff line number Diff line change
Expand Up @@ -30,13 +30,10 @@
import io.github.msdk.datamodel.datastore.DataPointStoreFactory;
import io.github.msdk.datamodel.featuretables.FeatureTable;
import io.github.msdk.datamodel.rawdata.RawDataFile;
import io.github.msdk.featdet.srmdetection.SrmDetectionMethod;
import io.github.mzmine.modules.MZmineProcessingModule;
import io.github.mzmine.modules.featuredetection.chromatogrambuilder.ChromatogramBuilderTask;
import io.github.mzmine.parameters.ParameterSet;
import io.github.mzmine.parameters.parametertypes.selectors.RawDataFilesSelection;
import io.github.mzmine.project.MZmineProject;
import io.github.mzmine.taskcontrol.MSDKTask;
import javafx.concurrent.Task;

/**
Expand Down Expand Up @@ -88,8 +85,8 @@ public void runModule(@Nonnull MZmineProject project,
// 1. SrmDetectionMethod
// 2. ChromatogramToFeatureTableMethod
SrmDetectionTask newTask = new SrmDetectionTask(
"SRM feature detection", rawDataFile.getName(), rawDataFile, dataStore,
nameSuffix);
"SRM feature detection", rawDataFile.getName(), rawDataFile,
dataStore, nameSuffix);

// Add the feature table to the project
newTask.setOnSucceeded(e -> {
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4 changes: 2 additions & 2 deletions src/main/java/io/github/mzmine/modules/featuredetection/srmdetection/SrmDetectionTask.java
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Original file line number Diff line number Diff line change
Expand Up @@ -52,8 +52,8 @@ public class SrmDetectionTask extends Task<Object> implements MZmineTask {
private String title, message;
private FeatureTable featureTable;

private MSDKMethod<?> srmDetectionMethod;
private MSDKMethod<?> chromatogramToFeatureTableMethod;
private MSDKMethod<List<Chromatogram>> srmDetectionMethod;
private MSDKMethod<FeatureTable> chromatogramToFeatureTableMethod;

public SrmDetectionTask(String title, @Nullable String message,
@Nonnull RawDataFile rawDataFile, @Nonnull DataPointStore dataStore,
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4 changes: 2 additions & 2 deletions src/main/java/io/github/mzmine/modules/featuretable/FeatureTableMenu.java
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Original file line number Diff line number Diff line change
Expand Up @@ -175,7 +175,7 @@ public void handle(MouseEvent event) {
cm.getItems().add(new SeparatorMenuItem());

// Sample specific columns
for (TreeTableColumn col : tableColumn.getColumns()) {
for (TreeTableColumn<?, ?> col : tableColumn.getColumns()) {
cb = new CheckBox("Sample: " + col.getText());

// Bind to all equal sample specific columns
Expand All @@ -184,7 +184,7 @@ public void handle(MouseEvent event) {
int childrenColumns2 = tableColumn2.getColumns().size();
if (childrenColumns2 != 0) {

for (TreeTableColumn col2 : tableColumn2
for (TreeTableColumn<?, ?> col2 : tableColumn2
.getColumns()) {
if (col.getText().equals(col2.getText())) {
cb.selectedProperty().bindBidirectional(
Expand Down
20 changes: 10 additions & 10 deletions src/main/java/io/github/mzmine/modules/featuretable/FeatureTableModule.java
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Original file line number Diff line number Diff line change
Expand Up @@ -103,9 +103,9 @@ public void runModule(@Nonnull MZmineProject project,
TreeItem<FeatureTableRow> treeItem;

// Group rows
FeatureTableColumn groupColoumn = featureTable
FeatureTableColumn<Integer> groupColoumn = featureTable
.getColumn(ColumnName.GROUPID, null);
FeatureTableColumn idColoumn = featureTable.getColumn(ColumnName.ID,
FeatureTableColumn<Integer> idColoumn = featureTable.getColumn(ColumnName.ID,
null);
for (FeatureTableRow row : rows) {
// No group column
Expand All @@ -118,18 +118,18 @@ else if (row.getData(groupColoumn) == null) {
treeItem = new TreeItem<>(row);
treeItem.setExpanded(true);
root.getChildren().add(treeItem);
rowMap.put((int) row.getData(idColoumn), treeItem);
rowMap.put(row.getData(idColoumn), treeItem);
}
// The row has a group id
else {
Integer groupID = (int) row.getData(groupColoumn);
Integer groupID = row.getData(groupColoumn);
TreeItem<FeatureTableRow> parentTreeItem = rowMap.get(groupID);
if (parentTreeItem == null) {
parentTreeItem = root;
}
treeItem = new TreeItem<>(row);
parentTreeItem.getChildren().add(treeItem);
rowMap.put((int) row.getData(idColoumn), treeItem);
rowMap.put(row.getData(idColoumn), treeItem);
}
}

Expand Down Expand Up @@ -172,7 +172,7 @@ public ObservableValue<Object> call(
});

// Set column renderer
Class renderClass = ColumnRenderers
Class<?> renderClass = ColumnRenderers
.getRenderClass(column.getName());
Callback<TreeTableColumn<FeatureTableRow, Object>, TreeTableCell<FeatureTableRow, Object>> rendeder = null;
try {
Expand Down Expand Up @@ -228,7 +228,7 @@ public ObservableValue<Object> call(
});

// Set column renderer
Class renderClass = ColumnRenderers
Class<?> renderClass = ColumnRenderers
.getRenderClass(column.getName());
Callback<TreeTableColumn<FeatureTableRow, Object>, TreeTableCell<FeatureTableRow, Object>> rendeder = null;
try {
Expand Down Expand Up @@ -267,11 +267,11 @@ public void handle(MouseEvent event) {
if (event.isPrimaryButtonDown() && event.getClickCount() == 2) {
// Find feature table row
Node node = ((Node) event.getTarget()).getParent();
TreeTableRow row;
TreeTableRow<?> row;
while (!(node instanceof TreeTableRow)) {
node = node.getParent();
}
row = (TreeTableRow) node;
row = (TreeTableRow<?>) node;
FeatureTableRow featureTableRow = (FeatureTableRow) row
.getItem();

Expand All @@ -281,7 +281,7 @@ public void handle(MouseEvent event) {
.getSelectionModel().getSelectedCells();
for (TreeTablePosition<FeatureTableRow, ?> cell : cells) {
if (cell.getTableColumn().getParentColumn() != null) {
TreeTableColumn parentColumn = (TreeTableColumn) cell
TreeTableColumn<?,?> parentColumn = (TreeTableColumn) cell
.getTableColumn().getParentColumn();
List<Sample> samples = featureTable.getSamples();
for (Sample s : samples) {
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3 changes: 2 additions & 1 deletion src/main/java/io/github/mzmine/modules/featuretableimport/FeatureTableImportModule.java
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Original file line number Diff line number Diff line change
Expand Up @@ -102,6 +102,7 @@ public void runModule(@Nonnull MZmineProject project,
.getExtension(fileName.getAbsolutePath());
MSDKMethod<?> method = null;
switch (fileExtension.toUpperCase()) {
default:
case "CSV":
method = new CsvFileImportMethod(fileName, dataStore);
break;
Expand All @@ -122,7 +123,7 @@ public void runModule(@Nonnull MZmineProject project,
// Remove common prefix
if (!Strings.isNullOrEmpty(removePrefix)) {
String name = featureTable.getName();
if (name.startsWith(removePrefix))
if (removePrefix != null && name.startsWith(removePrefix))
name = name.substring(removePrefix.length());
featureTable.setName(name);
}
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42 changes: 23 additions & 19 deletions src/main/java/io/github/mzmine/modules/featuretableimport/FeatureTableImportParameters.java
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Original file line number Diff line number Diff line change
Expand Up @@ -66,14 +66,16 @@ public class FeatureTableImportParameters extends ParameterSet {
src = src.getParent();

}
for (PropertySheet.Item item : sheet.getItems()) {
if (item instanceof FileNamesParameter) {
List<File> fileNames = (List<File>) item.getValue();
if (fileNames == null)
return;
String commonPrefix = FileNameUtil
.findCommonPrefix(fileNames);
editor.setValue(commonPrefix);
if (sheet != null && editor != null) {
for (PropertySheet.Item item : sheet.getItems()) {
if (item instanceof FileNamesParameter) {
List<File> fileNames = (List<File>) item.getValue();
if (fileNames == null)
return;
String commonPrefix = FileNameUtil
.findCommonPrefix(fileNames);
editor.setValue(commonPrefix);
}
}
}
});
Expand All @@ -95,17 +97,19 @@ public class FeatureTableImportParameters extends ParameterSet {
src = src.getParent();

}
for (PropertySheet.Item item : sheet.getItems()) {
if (item instanceof FileNamesParameter) {
List<File> fileNames = (List<File>) item.getValue();
if (fileNames == null)
continue;
String commonSuffix = FileNameUtil
.findCommonSuffix(fileNames);
// If no common suffix then remove file extension
if (Strings.isNullOrEmpty(commonSuffix))
commonSuffix = ".*";
editor.setValue(commonSuffix);
if (sheet != null && editor != null) {
for (PropertySheet.Item item : sheet.getItems()) {
if (item instanceof FileNamesParameter) {
List<File> fileNames = (List<File>) item.getValue();
if (fileNames == null)
continue;
String commonSuffix = FileNameUtil
.findCommonSuffix(fileNames);
// If no common suffix then remove file extension
if (Strings.isNullOrEmpty(commonSuffix))
commonSuffix = ".*";
editor.setValue(commonSuffix);
}
}
}
});
Expand Down
30 changes: 23 additions & 7 deletions src/main/java/io/github/mzmine/modules/filtering/featurefilter/FeatureFilterModule.java
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Original file line number Diff line number Diff line change
Expand Up @@ -66,22 +66,38 @@ public void runModule(@Nonnull MZmineProject project,
@Nonnull Collection<Task<?>> tasks) {

// Boolean values
final Boolean filterByDuration = parameters
Boolean filterByDuration = parameters
.getParameter(FeatureFilterParameters.duration).getValue();
final Boolean filterByArea = parameters
Boolean filterByArea = parameters
.getParameter(FeatureFilterParameters.area).getValue();
final Boolean filterByHeight = parameters
Boolean filterByHeight = parameters
.getParameter(FeatureFilterParameters.height).getValue();
final Boolean filterByDataPoints = parameters
Boolean filterByDataPoints = parameters
.getParameter(FeatureFilterParameters.dataPoints).getValue();
final Boolean filterByFWHM = parameters
Boolean filterByFWHM = parameters
.getParameter(FeatureFilterParameters.fwhm).getValue();
final Boolean filterByTailingFactor = parameters
Boolean filterByTailingFactor = parameters
.getParameter(FeatureFilterParameters.tailingFactor).getValue();
final Boolean filterByAsymmetryFactor = parameters
Boolean filterByAsymmetryFactor = parameters
.getParameter(FeatureFilterParameters.asymmetryFactor)
.getValue();

// Default values
if (filterByDuration == null)
filterByDuration = false;
if (filterByArea == null)
filterByArea = false;
if (filterByHeight == null)
filterByHeight = false;
if (filterByDataPoints == null)
filterByDataPoints = false;
if (filterByFWHM == null)
filterByFWHM = false;
if (filterByTailingFactor == null)
filterByTailingFactor = false;
if (filterByAsymmetryFactor == null)
filterByAsymmetryFactor = false;

// Embedded values
final Range<Double> durationRange = parameters
.getParameter(FeatureFilterParameters.duration)
Expand Down
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