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eselmeistereselmeister
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Merge pull request #2314 from lorenzgerber/pca_refactor
PCA, add type to EvaluationPCA to remove wildcard types downstream
2 parents 4b4953c + 31f570b commit 0c726c4

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24 files changed

+111
-99
lines changed

24 files changed

+111
-99
lines changed

‎chemclipse/plugins/org.eclipse.chemclipse.model/src/org/eclipse/chemclipse/model/statistics/SampleData.java‎

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@@ -20,12 +20,14 @@ public class SampleData<T> implements ISampleData<T> {
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private double normalizedData;
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public SampleData() {
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this.data = Double.NaN;
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this.normalizedData = Double.NaN;
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this.dataObject = null;
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}
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public SampleData(double data, T data2) {
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this();
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this.data = data;
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this.dataObject = data2;

‎chemclipse/plugins/org.eclipse.chemclipse.xxd.process.supplier.pca.ui/src/org/eclipse/chemclipse/xxd/process/supplier/pca/ui/chart2d/ErrorResidueChart.java‎

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@@ -15,6 +15,8 @@
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import java.util.ArrayList;
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import java.util.List;
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import org.eclipse.chemclipse.model.statistics.ISample;
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import org.eclipse.chemclipse.model.statistics.IVariable;
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import org.eclipse.chemclipse.support.text.ValueFormat;
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import org.eclipse.chemclipse.support.ui.workbench.DisplayUtils;
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import org.eclipse.chemclipse.support.ui.workbench.PreferencesSupport;
@@ -49,10 +51,10 @@ public ErrorResidueChart(Composite parent, int style) {
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createControl();
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}
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public void setInput(EvaluationPCA evaluationPCA) {
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public void setInput(EvaluationPCA<IVariable, ISample, IResultPCA> evaluationPCA) {
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if(evaluationPCA != null) {
55-
IResultsPCA<?, ?> resultsPCA = evaluationPCA.getResults();
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IResultsPCA<IResultPCA, ?> resultsPCA = evaluationPCA.getResults();
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updateChart(resultsPCA);
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} else {
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updateChart(null);
@@ -116,7 +118,7 @@ private void setPrimaryAxisSet(IChartSettings chartSettings) {
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}
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}
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private void updateChart(IResultsPCA<?, ?> pcaResults) {
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private void updateChart(IResultsPCA<IResultPCA, ?> pcaResults) {
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deleteSeries();
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if(pcaResults != null) {
@@ -140,9 +142,9 @@ private void updateChart(IResultsPCA<?, ?> pcaResults) {
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}
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}
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143-
private String[] getCategories(IResultsPCA<? extends IResultPCA, ?> pcaResults) {
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private String[] getCategories(IResultsPCA<IResultPCA, ?> pcaResults) {
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145-
List<? extends IResultPCA> pcaResultList = pcaResults.getPcaResultList();
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List<IResultPCA> pcaResultList = pcaResults.getPcaResultList();
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int size = pcaResultList.size();
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String[] categories = new String[size];
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//
@@ -154,9 +156,9 @@ private String[] getCategories(IResultsPCA<? extends IResultPCA, ?> pcaResults)
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return categories;
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}
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157-
private ISeriesData getSeries(IResultsPCA<? extends IResultPCA, ?> pcaResults) {
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private ISeriesData getSeries(IResultsPCA<IResultPCA, ?> pcaResults) {
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159-
List<? extends IResultPCA> pcaResultList = pcaResults.getPcaResultList();
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List<IResultPCA> pcaResultList = pcaResults.getPcaResultList();
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int size = pcaResultList.size();
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double[] xSeries = new double[size];
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double[] ySeries = new double[size];

‎chemclipse/plugins/org.eclipse.chemclipse.xxd.process.supplier.pca.ui/src/org/eclipse/chemclipse/xxd/process/supplier/pca/ui/chart2d/LoadingsPlot.java‎

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@@ -16,6 +16,7 @@
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import java.util.List;
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import org.eclipse.chemclipse.model.statistics.ISample;
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import org.eclipse.chemclipse.model.statistics.IVariable;
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import org.eclipse.chemclipse.xxd.process.supplier.pca.model.EvaluationPCA;
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import org.eclipse.chemclipse.xxd.process.supplier.pca.model.IResultPCA;
@@ -48,11 +49,11 @@ public void setLabelsType(int labelsType) {
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}
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}
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51-
public void setInput(EvaluationPCA evaluationPCA, int pcX, int pcY) {
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public void setInput(EvaluationPCA<IVariable, ISample, IResultPCA> evaluationPCA, int pcX, int pcY) {
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deleteSeries();
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if(evaluationPCA != null) {
55-
IResultsPCA<? extends IResultPCA, ? extends IVariable> resultsPCA = evaluationPCA.getResults();
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IResultsPCA<IResultPCA, IVariable> resultsPCA = evaluationPCA.getResults();
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List<IScatterSeriesData> series;
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if(labelType == LABEL_RETENTION_TIME_MINUTES) {
5859
series = SeriesConverter.basisVectorsToSeries(resultsPCA, evaluationPCA.getHighlightedVariables(), pcX, pcY);

‎chemclipse/plugins/org.eclipse.chemclipse.xxd.process.supplier.pca.ui/src/org/eclipse/chemclipse/xxd/process/supplier/pca/ui/chart2d/ScorePlot.java‎

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@@ -19,6 +19,7 @@
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import java.util.Map;
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import org.eclipse.chemclipse.model.statistics.ISample;
22+
import org.eclipse.chemclipse.model.statistics.IVariable;
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import org.eclipse.chemclipse.xxd.process.supplier.pca.model.EvaluationPCA;
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import org.eclipse.chemclipse.xxd.process.supplier.pca.model.IResultPCA;
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import org.eclipse.chemclipse.xxd.process.supplier.pca.model.IResultsPCA;
@@ -34,11 +35,11 @@ public ScorePlot(Composite parent, int style) {
3435
super(parent, style, "Score Plot");
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}
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37-
public void setInput(EvaluationPCA evaluationPCA, int pcX, int pcY) {
38+
public void setInput(EvaluationPCA<IVariable, ISample, IResultPCA> evaluationPCA, int pcX, int pcY) {
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deleteSeries();
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if(evaluationPCA != null) {
41-
IResultsPCA<? extends IResultPCA, ?> resultsPCA = evaluationPCA.getResults();
42+
IResultsPCA<IResultPCA, ?> resultsPCA = evaluationPCA.getResults();
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List<ISample> highlightedSamples = evaluationPCA.getHighlightedSamples();
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addSeriesData(SeriesConverter.sampleToSeries(resultsPCA, highlightedSamples, pcX, pcY, extractedResults));
4445
}

‎chemclipse/plugins/org.eclipse.chemclipse.xxd.process.supplier.pca.ui/src/org/eclipse/chemclipse/xxd/process/supplier/pca/ui/chart2d/VarianceChart.java‎

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@@ -15,11 +15,14 @@
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import java.util.ArrayList;
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import java.util.List;
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import org.eclipse.chemclipse.model.statistics.ISample;
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import org.eclipse.chemclipse.model.statistics.IVariable;
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import org.eclipse.chemclipse.support.text.ValueFormat;
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import org.eclipse.chemclipse.support.ui.workbench.DisplayUtils;
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import org.eclipse.chemclipse.support.ui.workbench.PreferencesSupport;
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import org.eclipse.chemclipse.swt.ui.support.Colors;
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import org.eclipse.chemclipse.xxd.process.supplier.pca.model.EvaluationPCA;
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import org.eclipse.chemclipse.xxd.process.supplier.pca.model.IResultPCA;
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import org.eclipse.chemclipse.xxd.process.supplier.pca.model.IResultsPCA;
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import org.eclipse.chemclipse.xxd.process.supplier.pca.model.Variance;
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import org.eclipse.swt.SWT;
@@ -41,7 +44,7 @@
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public class VarianceChart extends BarChart {
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private Variance variance = Variance.EXPLAINED;
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private EvaluationPCA evaluationPCA;
47+
private EvaluationPCA<IVariable, ISample, IResultPCA> evaluationPCA;
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public VarianceChart() {
4750

@@ -61,7 +64,7 @@ public void setVariance(Variance variance) {
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updateChart();
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}
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64-
public void setInput(EvaluationPCA evaluationPCA) {
67+
public void setInput(EvaluationPCA<IVariable, ISample, IResultPCA> evaluationPCA) {
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this.evaluationPCA = evaluationPCA;
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updateChart();

‎chemclipse/plugins/org.eclipse.chemclipse.xxd.process.supplier.pca.ui/src/org/eclipse/chemclipse/xxd/process/supplier/pca/ui/internal/runnable/CalculationExecutor.java‎

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@@ -22,6 +22,7 @@
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import org.eclipse.chemclipse.xxd.process.supplier.pca.model.Algorithm;
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import org.eclipse.chemclipse.xxd.process.supplier.pca.model.EvaluationPCA;
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import org.eclipse.chemclipse.xxd.process.supplier.pca.model.IAnalysisSettings;
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import org.eclipse.chemclipse.xxd.process.supplier.pca.model.IResultPCA;
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import org.eclipse.chemclipse.xxd.process.supplier.pca.model.ISamplesPCA;
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import org.eclipse.core.runtime.IProgressMonitor;
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import org.eclipse.jface.operation.IRunnableWithProgress;
@@ -30,18 +31,18 @@ public class CalculationExecutor implements IRunnableWithProgress {
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private static final Logger logger = Logger.getLogger(CalculationExecutor.class);
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//
33-
private ISamplesPCA<? extends IVariable, ? extends ISample> samples = null;
34-
private EvaluationPCA masterEvaluationPCA = null;
34+
private ISamplesPCA<IVariable, ISample> samples = null;
35+
private EvaluationPCA<IVariable, ISample, IResultPCA> masterEvaluationPCA = null;
3536
//
36-
private EvaluationPCA evaluationPCA = null;
37+
private EvaluationPCA<IVariable, ISample, IResultPCA> evaluationPCA = null;
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38-
public CalculationExecutor(ISamplesPCA<? extends IVariable, ? extends ISample> samples, EvaluationPCA masterEvaluationPCA) {
39+
public CalculationExecutor(ISamplesPCA<IVariable, ISample> samples, EvaluationPCA<IVariable, ISample, IResultPCA> masterEvaluationPCA) {
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4041
this.samples = samples;
4142
this.masterEvaluationPCA = masterEvaluationPCA;
4243
}
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44-
public EvaluationPCA getEvaluationPCA() {
45+
public EvaluationPCA<IVariable, ISample, IResultPCA> getEvaluationPCA() {
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4647
return evaluationPCA;
4748
}

‎chemclipse/plugins/org.eclipse.chemclipse.xxd.process.supplier.pca.ui/src/org/eclipse/chemclipse/xxd/process/supplier/pca/ui/parts/ErrorResiduePart.java‎

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@@ -15,13 +15,13 @@
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import java.util.List;
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import jakarta.inject.Inject;
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import org.eclipse.chemclipse.xxd.process.supplier.pca.model.EvaluationPCA;
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import org.eclipse.chemclipse.xxd.process.supplier.pca.ui.chart2d.ErrorResidueChart;
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import org.eclipse.swt.SWT;
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import org.eclipse.swt.widgets.Composite;
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import jakarta.inject.Inject;
24+
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public class ErrorResiduePart extends AbstractPartPCA<ErrorResidueChart> {
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@Inject
@@ -36,6 +36,7 @@ protected ErrorResidueChart createControl(Composite parent) {
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return new ErrorResidueChart(parent, SWT.NONE);
3737
}
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39+
@SuppressWarnings("unchecked")
3940
@Override
4041
protected boolean updateData(List<Object> objects, String topic) {
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‎chemclipse/plugins/org.eclipse.chemclipse.xxd.process.supplier.pca.ui/src/org/eclipse/chemclipse/xxd/process/supplier/pca/ui/parts/FeatureTablePart.java‎

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@@ -37,6 +37,7 @@ protected ExtendedFeatureListUI createControl(Composite parent) {
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return new ExtendedFeatureListUI(parent, SWT.NONE);
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}
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40+
@SuppressWarnings("unchecked")
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@Override
4142
protected boolean updateData(List<Object> objects, String topic) {
4243

‎chemclipse/plugins/org.eclipse.chemclipse.xxd.process.supplier.pca.ui/src/org/eclipse/chemclipse/xxd/process/supplier/pca/ui/parts/LoadingsPlotPart.java‎

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@@ -14,13 +14,13 @@
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import java.util.List;
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import jakarta.inject.Inject;
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import org.eclipse.chemclipse.xxd.process.supplier.pca.model.EvaluationPCA;
2018
import org.eclipse.chemclipse.xxd.process.supplier.pca.ui.swt.ExtendedLoadingsPlot;
2119
import org.eclipse.swt.SWT;
2220
import org.eclipse.swt.widgets.Composite;
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22+
import jakarta.inject.Inject;
23+
2424
public class LoadingsPlotPart extends AbstractPartPCA<ExtendedLoadingsPlot> {
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2626
@Inject
@@ -35,6 +35,7 @@ protected ExtendedLoadingsPlot createControl(Composite parent) {
3535
return new ExtendedLoadingsPlot(parent, SWT.NONE);
3636
}
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38+
@SuppressWarnings("unchecked")
3839
@Override
3940
protected boolean updateData(List<Object> objects, String topic) {
4041

‎chemclipse/plugins/org.eclipse.chemclipse.xxd.process.supplier.pca.ui/src/org/eclipse/chemclipse/xxd/process/supplier/pca/ui/parts/ScorePlot2DPart.java‎

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@@ -35,6 +35,7 @@ protected ExtendedScorePlot2D createControl(Composite parent) {
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return new ExtendedScorePlot2D(parent, SWT.NONE);
3636
}
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38+
@SuppressWarnings("unchecked")
3839
@Override
3940
protected boolean updateData(List<Object> objects, String topic) {
4041

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