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package jalview.gui; |
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import java.awt.BorderLayout; |
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import java.awt.Color; |
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import java.awt.Dimension; |
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import java.awt.Graphics; |
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import java.awt.event.ActionEvent; |
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import java.awt.event.ActionListener; |
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import java.awt.print.PageFormat; |
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import java.awt.print.Printable; |
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import java.awt.print.PrinterException; |
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import java.awt.print.PrinterJob; |
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import javax.swing.ButtonGroup; |
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import javax.swing.JLabel; |
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import javax.swing.JMenuItem; |
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import javax.swing.JProgressBar; |
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import javax.swing.JRadioButtonMenuItem; |
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import javax.swing.SwingConstants; |
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import javax.swing.event.InternalFrameAdapter; |
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import javax.swing.event.InternalFrameEvent; |
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import jalview.analysis.scoremodels.ScoreModels; |
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import jalview.api.AlignViewportI; |
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import jalview.api.analysis.ScoreModelI; |
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import jalview.api.analysis.SimilarityParamsI; |
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import jalview.bin.Console; |
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import jalview.datamodel.Alignment; |
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import jalview.datamodel.AlignmentI; |
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import jalview.datamodel.AlignmentView; |
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import jalview.datamodel.HiddenColumns; |
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import jalview.datamodel.SequenceI; |
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import jalview.gui.ImageExporter.ImageWriterI; |
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import jalview.gui.JalviewColourChooser.ColourChooserListener; |
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import jalview.io.exceptions.ImageOutputException; |
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import jalview.jbgui.GPCAPanel; |
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import jalview.math.RotatableMatrix.Axis; |
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import jalview.util.ImageMaker; |
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import jalview.util.MessageManager; |
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import jalview.viewmodel.AlignmentViewport; |
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import jalview.viewmodel.PCAModel; |
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| 41.7% |
Uncovered Elements: 148 (254) |
Complexity: 67 |
Complexity Density: 0.36 |
|
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public class PCAPanel extends GPCAPanel |
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implements Runnable, IProgressIndicator |
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{ |
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private static final int MIN_WIDTH = 470; |
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private static final int MIN_HEIGHT = 250; |
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private RotatableCanvas rc; |
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|
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AlignmentPanel ap; |
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AlignmentViewport av; |
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private PCAModel pcaModel; |
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private int top = 0; |
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private IProgressIndicator progressBar; |
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private boolean working; |
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String newPcaTitle = null; |
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@param |
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@param |
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@param |
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| 82.1% |
Uncovered Elements: 5 (28) |
Complexity: 3 |
Complexity Density: 0.12 |
|
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2 |
public PCAPanel(AlignmentPanel alignPanel, String modelName,... |
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SimilarityParamsI params) |
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{ |
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super(); |
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this.setFrameIcon(null); |
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this.av = alignPanel.av; |
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this.ap = alignPanel; |
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boolean nucleotide = av.getAlignment().isNucleotide(); |
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|
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progressBar = new ProgressBar(statusPanel, statusBar); |
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|
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addInternalFrameListener(new InternalFrameAdapter() |
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{ |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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2 |
@Override... |
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public void internalFrameClosed(InternalFrameEvent e) |
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{ |
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close_actionPerformed(); |
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} |
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}); |
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|
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boolean selected = av.getSelectionGroup() != null |
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&& av.getSelectionGroup().getSize() > 0; |
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AlignmentView seqstrings = av.getAlignmentView(selected); |
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SequenceI[] seqs; |
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if (!selected) |
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{ |
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seqs = av.getAlignment().getSequencesArray(); |
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} |
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else |
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{ |
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seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment()); |
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} |
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|
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ScoreModelI scoreModel = ScoreModels.getInstance() |
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.getScoreModel(modelName, ap); |
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setPcaModel( |
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new PCAModel(seqstrings, seqs, nucleotide, scoreModel, params)); |
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|
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newPcaTitle = alignPanel.alignFrame.formCalculationTitle( |
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MessageManager.formatMessage("label.calc_title", "PCA", |
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getPcaModel().getScoreModelName()), |
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selected, ap.alignFrame.getTitle()); |
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|
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PaintRefresher.Register(this, av.getSequenceSetId()); |
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|
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setRotatableCanvas(new RotatableCanvas(alignPanel)); |
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|
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if (params.getSecondaryStructureSource() != null) |
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{ |
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|
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JLabel subtitleLabel = new JLabel( |
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" Secondary Structure Provider : " |
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+ params.getSecondaryStructureSource(), |
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SwingConstants.LEFT); |
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this.getContentPane().add(subtitleLabel, BorderLayout.NORTH); |
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} |
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this.getContentPane().add(getRotatableCanvas(), BorderLayout.CENTER); |
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|
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addKeyListener(getRotatableCanvas()); |
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validate(); |
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} |
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| 85.7% |
Uncovered Elements: 1 (7) |
Complexity: 2 |
Complexity Density: 0.4 |
|
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protected void close_actionPerformed()... |
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{ |
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setPcaModel(null); |
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if (this.rc != null) |
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{ |
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this.rc.sequencePoints = null; |
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this.rc.setAxisEndPoints(null); |
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this.rc = null; |
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} |
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} |
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| 0% |
Uncovered Elements: 3 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
|
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@Override... |
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protected void bgcolour_actionPerformed() |
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{ |
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String ttl = MessageManager.getString("label.select_background_colour"); |
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ColourChooserListener listener = new ColourChooserListener() |
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{ |
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| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
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0 |
@Override... |
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public void colourSelected(Color c) |
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{ |
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rc.setBgColour(c); |
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rc.repaint(); |
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} |
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}; |
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JalviewColourChooser.showColourChooser(this, ttl, rc.getBgColour(), |
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listener); |
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} |
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|
193 |
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| 82.1% |
Uncovered Elements: 5 (28) |
Complexity: 4 |
Complexity Density: 0.17 |
|
194 |
1 |
@Override... |
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public void run() |
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{ |
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working = true; |
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long progId = System.currentTimeMillis(); |
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1 |
IProgressIndicator progress = this; |
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String message = MessageManager.getString("label.pca_recalculating"); |
201 |
1 |
if (getParent() == null) |
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{ |
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progress = ap.alignFrame; |
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message = MessageManager.getString("label.pca_calculating"); |
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} |
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1 |
progress.setProgressBar(message, progId); |
207 |
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try |
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{ |
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1 |
getPcaModel().calculate(); |
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|
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1 |
xCombobox.setSelectedIndex(0); |
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1 |
yCombobox.setSelectedIndex(1); |
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1 |
zCombobox.setSelectedIndex(2); |
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|
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1 |
getPcaModel().updateRc(getRotatableCanvas()); |
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|
217 |
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setTop(getPcaModel().getTop()); |
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|
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} catch (OutOfMemoryError er) |
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{ |
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new OOMWarning("calculating PCA", er); |
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0 |
working = false; |
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0 |
return; |
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} finally |
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{ |
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1 |
progress.setProgressBar("", progId); |
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} |
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|
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1 |
repaint(); |
230 |
1 |
if (getParent() == null) |
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{ |
232 |
1 |
Desktop.addInternalFrame(this, newPcaTitle, |
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475, 450); |
234 |
1 |
this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT)); |
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} |
236 |
1 |
working = false; |
237 |
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} |
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|
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|
240 |
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|
241 |
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|
242 |
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| 33.3% |
Uncovered Elements: 6 (9) |
Complexity: 2 |
Complexity Density: 0.29 |
|
243 |
12 |
@Override... |
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protected void doDimensionChange() |
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{ |
246 |
12 |
if (getTop() == 0) |
247 |
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{ |
248 |
12 |
return; |
249 |
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} |
250 |
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|
251 |
0 |
int dim1 = getTop() - xCombobox.getSelectedIndex(); |
252 |
0 |
int dim2 = getTop() - yCombobox.getSelectedIndex(); |
253 |
0 |
int dim3 = getTop() - zCombobox.getSelectedIndex(); |
254 |
0 |
getPcaModel().updateRcView(dim1, dim2, dim3); |
255 |
0 |
getRotatableCanvas().resetView(); |
256 |
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} |
257 |
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258 |
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259 |
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|
260 |
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|
261 |
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|
262 |
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@param |
263 |
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@param |
264 |
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|
|
|
| 90.9% |
Uncovered Elements: 1 (11) |
Complexity: 4 |
Complexity Density: 0.36 |
|
265 |
3 |
public void setSelectedDimensionIndex(int index, Axis axis)... |
266 |
|
{ |
267 |
3 |
switch (axis) |
268 |
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{ |
269 |
1 |
case X: |
270 |
1 |
xCombobox.setSelectedIndex(index); |
271 |
1 |
break; |
272 |
1 |
case Y: |
273 |
1 |
yCombobox.setSelectedIndex(index); |
274 |
1 |
break; |
275 |
1 |
case Z: |
276 |
1 |
zCombobox.setSelectedIndex(index); |
277 |
1 |
break; |
278 |
0 |
default: |
279 |
|
} |
280 |
|
} |
281 |
|
|
|
|
| 0% |
Uncovered Elements: 6 (6) |
Complexity: 2 |
Complexity Density: 0.33 |
|
282 |
0 |
@Override... |
283 |
|
protected void outputValues_actionPerformed() |
284 |
|
{ |
285 |
0 |
CutAndPasteTransfer cap = new CutAndPasteTransfer(); |
286 |
0 |
try |
287 |
|
{ |
288 |
0 |
cap.setText(getPcaModel().getDetails()); |
289 |
0 |
Desktop.addInternalFrame(cap, |
290 |
|
MessageManager.getString("label.pca_details"), 500, 500); |
291 |
|
} catch (OutOfMemoryError oom) |
292 |
|
{ |
293 |
0 |
new OOMWarning("opening PCA details", oom); |
294 |
0 |
cap.dispose(); |
295 |
|
} |
296 |
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} |
297 |
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|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
298 |
0 |
@Override... |
299 |
|
protected void showLabels_actionPerformed() |
300 |
|
{ |
301 |
0 |
getRotatableCanvas().showLabels(showLabels.getState()); |
302 |
|
} |
303 |
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|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
304 |
0 |
@Override... |
305 |
|
protected void print_actionPerformed() |
306 |
|
{ |
307 |
0 |
PCAPrinter printer = new PCAPrinter(); |
308 |
0 |
printer.start(); |
309 |
|
} |
310 |
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|
311 |
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|
312 |
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|
313 |
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|
314 |
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| 0% |
Uncovered Elements: 23 (23) |
Complexity: 8 |
Complexity Density: 0.53 |
|
315 |
0 |
@Override... |
316 |
|
public void originalSeqData_actionPerformed() |
317 |
|
{ |
318 |
|
|
319 |
0 |
if (getPcaModel().getInputData() == null) |
320 |
|
{ |
321 |
0 |
Console.info( |
322 |
|
"Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action."); |
323 |
0 |
return; |
324 |
|
} |
325 |
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|
326 |
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|
327 |
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|
328 |
|
|
329 |
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|
330 |
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|
331 |
0 |
char gc = '-'; |
332 |
0 |
try |
333 |
|
{ |
334 |
|
|
335 |
|
|
336 |
0 |
gc = av.getGapCharacter(); |
337 |
|
} catch (Exception ex) |
338 |
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{ |
339 |
|
} |
340 |
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|
341 |
0 |
Object[] alAndColsel = getPcaModel().getInputData() |
342 |
|
.getAlignmentAndHiddenColumns(gc); |
343 |
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|
344 |
0 |
if (alAndColsel != null && alAndColsel[0] != null) |
345 |
|
{ |
346 |
|
|
347 |
|
|
348 |
0 |
AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]); |
349 |
0 |
AlignmentI dataset = (av != null && av.getAlignment() != null) |
350 |
|
? av.getAlignment().getDataset() |
351 |
|
: null; |
352 |
0 |
if (dataset != null) |
353 |
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{ |
354 |
0 |
al.setDataset(dataset); |
355 |
|
} |
356 |
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|
357 |
0 |
if (true) |
358 |
|
{ |
359 |
|
|
360 |
0 |
AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1], |
361 |
|
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); |
362 |
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|
363 |
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|
364 |
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|
365 |
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|
366 |
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|
367 |
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|
368 |
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|
369 |
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|
370 |
0 |
Desktop.addInternalFrame(af, MessageManager.formatMessage( |
371 |
|
"label.original_data_for_params", new String[] |
372 |
|
{ this.title }), AlignFrame.DEFAULT_WIDTH, |
373 |
|
AlignFrame.DEFAULT_HEIGHT); |
374 |
|
} |
375 |
|
} |
376 |
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|
377 |
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|
378 |
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|
379 |
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|
380 |
|
|
381 |
|
|
382 |
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|
383 |
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|
384 |
|
} |
385 |
|
|
|
|
| 0% |
Uncovered Elements: 28 (28) |
Complexity: 7 |
Complexity Density: 0.39 |
|
386 |
|
class PCAPrinter extends Thread implements Printable |
387 |
|
{ |
|
|
| 0% |
Uncovered Elements: 14 (14) |
Complexity: 4 |
Complexity Density: 0.4 |
|
388 |
0 |
@Override... |
389 |
|
public void run() |
390 |
|
{ |
391 |
0 |
PrinterJob printJob = PrinterJob.getPrinterJob(); |
392 |
0 |
PageFormat defaultPage = printJob.defaultPage(); |
393 |
0 |
PageFormat pf = printJob.pageDialog(defaultPage); |
394 |
|
|
395 |
0 |
if (defaultPage == pf) |
396 |
|
{ |
397 |
|
|
398 |
|
|
399 |
|
|
400 |
0 |
return; |
401 |
|
} |
402 |
|
|
403 |
0 |
printJob.setPrintable(this, pf); |
404 |
|
|
405 |
0 |
if (printJob.printDialog()) |
406 |
|
{ |
407 |
0 |
try |
408 |
|
{ |
409 |
0 |
printJob.print(); |
410 |
|
} catch (Exception PrintException) |
411 |
|
{ |
412 |
0 |
PrintException.printStackTrace(); |
413 |
|
} |
414 |
|
} |
415 |
|
} |
416 |
|
|
|
|
| 0% |
Uncovered Elements: 12 (12) |
Complexity: 3 |
Complexity Density: 0.38 |
|
417 |
0 |
@Override... |
418 |
|
public int print(Graphics pg, PageFormat pf, int pi) |
419 |
|
throws PrinterException |
420 |
|
{ |
421 |
0 |
pg.translate((int) pf.getImageableX(), (int) pf.getImageableY()); |
422 |
|
|
423 |
0 |
getRotatableCanvas().drawBackground(pg); |
424 |
0 |
getRotatableCanvas().drawScene(pg); |
425 |
0 |
if (getRotatableCanvas().drawAxes) |
426 |
|
{ |
427 |
0 |
getRotatableCanvas().drawAxes(pg); |
428 |
|
} |
429 |
|
|
430 |
0 |
if (pi == 0) |
431 |
|
{ |
432 |
0 |
return Printable.PAGE_EXISTS; |
433 |
|
} |
434 |
|
else |
435 |
|
{ |
436 |
0 |
return Printable.NO_SUCH_PAGE; |
437 |
|
} |
438 |
|
} |
439 |
|
} |
440 |
|
|
|
|
| 0% |
Uncovered Elements: 8 (8) |
Complexity: 2 |
Complexity Density: 0.25 |
|
441 |
0 |
public void makePCAImage(ImageMaker.TYPE type)... |
442 |
|
{ |
443 |
0 |
int width = getRotatableCanvas().getWidth(); |
444 |
0 |
int height = getRotatableCanvas().getHeight(); |
445 |
0 |
ImageWriterI writer = new ImageWriterI() |
446 |
|
{ |
|
|
| 0% |
Uncovered Elements: 7 (7) |
Complexity: 2 |
Complexity Density: 0.4 |
|
447 |
0 |
@Override... |
448 |
|
public void exportImage(Graphics g) throws Exception |
449 |
|
{ |
450 |
0 |
RotatableCanvas canvas = getRotatableCanvas(); |
451 |
0 |
canvas.drawBackground(g); |
452 |
0 |
canvas.drawScene(g); |
453 |
0 |
if (canvas.drawAxes) |
454 |
|
{ |
455 |
0 |
canvas.drawAxes(g); |
456 |
|
} |
457 |
|
} |
458 |
|
}; |
459 |
0 |
String pca = MessageManager.getString("label.pca"); |
460 |
0 |
ImageExporter exporter = new ImageExporter(writer, null, type, pca); |
461 |
0 |
try |
462 |
|
{ |
463 |
0 |
exporter.doExport(null, this, width, height, pca); |
464 |
|
} catch (ImageOutputException ioex) |
465 |
|
{ |
466 |
0 |
Console.error("Unexpected error whilst writing " + type.toString(), |
467 |
|
ioex); |
468 |
|
} |
469 |
|
} |
470 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
471 |
0 |
@Override... |
472 |
|
protected void viewMenu_menuSelected() |
473 |
|
{ |
474 |
0 |
buildAssociatedViewMenu(); |
475 |
|
} |
476 |
|
|
477 |
|
|
478 |
|
|
479 |
|
|
480 |
|
|
|
|
| 0% |
Uncovered Elements: 28 (28) |
Complexity: 5 |
Complexity Density: 0.23 |
|
481 |
0 |
void buildAssociatedViewMenu()... |
482 |
|
{ |
483 |
0 |
AlignmentPanel[] aps = PaintRefresher |
484 |
|
.getAssociatedPanels(av.getSequenceSetId()); |
485 |
0 |
if (aps.length == 1 && getRotatableCanvas().av == aps[0].av) |
486 |
|
{ |
487 |
0 |
associateViewsMenu.setVisible(false); |
488 |
0 |
return; |
489 |
|
} |
490 |
|
|
491 |
0 |
associateViewsMenu.setVisible(true); |
492 |
|
|
493 |
0 |
if ((viewMenu |
494 |
|
.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem)) |
495 |
|
{ |
496 |
0 |
viewMenu.insertSeparator(viewMenu.getItemCount() - 1); |
497 |
|
} |
498 |
|
|
499 |
0 |
associateViewsMenu.removeAll(); |
500 |
|
|
501 |
0 |
JRadioButtonMenuItem item; |
502 |
0 |
ButtonGroup buttonGroup = new ButtonGroup(); |
503 |
0 |
int iSize = aps.length; |
504 |
|
|
505 |
0 |
for (int i = 0; i < iSize; i++) |
506 |
|
{ |
507 |
0 |
final AlignmentPanel panel = aps[i]; |
508 |
0 |
item = new JRadioButtonMenuItem(panel.av.getViewName(), |
509 |
|
panel.av == getRotatableCanvas().av); |
510 |
0 |
buttonGroup.add(item); |
511 |
0 |
item.addActionListener(new ActionListener() |
512 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
513 |
0 |
@Override... |
514 |
|
public void actionPerformed(ActionEvent evt) |
515 |
|
{ |
516 |
0 |
selectAssociatedView(panel); |
517 |
|
} |
518 |
|
}); |
519 |
|
|
520 |
0 |
associateViewsMenu.add(item); |
521 |
|
} |
522 |
|
|
523 |
0 |
final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem( |
524 |
|
"All Views"); |
525 |
|
|
526 |
0 |
buttonGroup.add(itemf); |
527 |
|
|
528 |
0 |
itemf.setSelected(getRotatableCanvas().isApplyToAllViews()); |
529 |
0 |
itemf.addActionListener(new ActionListener() |
530 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
531 |
0 |
@Override... |
532 |
|
public void actionPerformed(ActionEvent evt) |
533 |
|
{ |
534 |
0 |
getRotatableCanvas().setApplyToAllViews(itemf.isSelected()); |
535 |
|
} |
536 |
|
}); |
537 |
0 |
associateViewsMenu.add(itemf); |
538 |
|
|
539 |
|
} |
540 |
|
|
541 |
|
|
542 |
|
|
543 |
|
|
544 |
|
@see |
545 |
|
|
546 |
|
|
547 |
|
|
|
|
| 0% |
Uncovered Elements: 6 (6) |
Complexity: 2 |
Complexity Density: 0.33 |
|
548 |
0 |
@Override... |
549 |
|
protected void outputPoints_actionPerformed() |
550 |
|
{ |
551 |
0 |
CutAndPasteTransfer cap = new CutAndPasteTransfer(); |
552 |
0 |
try |
553 |
|
{ |
554 |
0 |
cap.setText(getPcaModel().getPointsasCsv(false, |
555 |
|
xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(), |
556 |
|
zCombobox.getSelectedIndex())); |
557 |
0 |
Desktop.addInternalFrame(cap, MessageManager |
558 |
|
.formatMessage("label.points_for_params", new String[] |
559 |
|
{ this.getTitle() }), 500, 500); |
560 |
|
} catch (OutOfMemoryError oom) |
561 |
|
{ |
562 |
0 |
new OOMWarning("exporting PCA points", oom); |
563 |
0 |
cap.dispose(); |
564 |
|
} |
565 |
|
} |
566 |
|
|
567 |
|
|
568 |
|
|
569 |
|
|
570 |
|
@see |
571 |
|
|
572 |
|
|
573 |
|
|
|
|
| 0% |
Uncovered Elements: 6 (6) |
Complexity: 2 |
Complexity Density: 0.33 |
|
574 |
0 |
@Override... |
575 |
|
protected void outputProjPoints_actionPerformed() |
576 |
|
{ |
577 |
0 |
CutAndPasteTransfer cap = new CutAndPasteTransfer(); |
578 |
0 |
try |
579 |
|
{ |
580 |
0 |
cap.setText(getPcaModel().getPointsasCsv(true, |
581 |
|
xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(), |
582 |
|
zCombobox.getSelectedIndex())); |
583 |
0 |
Desktop.addInternalFrame(cap, MessageManager.formatMessage( |
584 |
|
"label.transformed_points_for_params", new String[] |
585 |
|
{ this.getTitle() }), 500, 500); |
586 |
|
} catch (OutOfMemoryError oom) |
587 |
|
{ |
588 |
0 |
new OOMWarning("exporting transformed PCA points", oom); |
589 |
0 |
cap.dispose(); |
590 |
|
} |
591 |
|
} |
592 |
|
|
593 |
|
|
594 |
|
|
595 |
|
|
596 |
|
@see |
597 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
598 |
0 |
@Override... |
599 |
|
public void setProgressBar(String message, long id) |
600 |
|
{ |
601 |
0 |
progressBar.setProgressBar(message, id); |
602 |
|
|
603 |
|
|
604 |
|
|
605 |
|
|
606 |
|
|
607 |
|
|
608 |
|
|
609 |
|
|
610 |
|
|
611 |
|
|
612 |
|
|
613 |
|
|
614 |
|
|
615 |
|
|
616 |
|
|
617 |
|
|
618 |
|
|
619 |
|
|
620 |
|
|
621 |
|
|
622 |
|
|
623 |
|
|
624 |
|
|
625 |
|
|
626 |
|
|
627 |
|
|
628 |
|
|
629 |
|
|
630 |
|
|
631 |
|
|
632 |
|
|
633 |
|
|
634 |
|
|
635 |
|
|
636 |
|
|
637 |
|
|
638 |
|
|
639 |
|
|
640 |
|
|
641 |
|
|
642 |
|
|
643 |
|
|
644 |
|
|
645 |
|
} |
646 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
647 |
0 |
@Override... |
648 |
|
public void registerHandler(final long id, |
649 |
|
final IProgressIndicatorHandler handler) |
650 |
|
{ |
651 |
0 |
progressBar.registerHandler(id, handler); |
652 |
|
|
653 |
|
|
654 |
|
|
655 |
|
|
656 |
|
|
657 |
|
|
658 |
|
|
659 |
|
|
660 |
|
|
661 |
|
|
662 |
|
|
663 |
|
|
664 |
|
|
665 |
|
|
666 |
|
|
667 |
|
|
668 |
|
|
669 |
|
|
670 |
|
|
671 |
|
|
672 |
|
|
673 |
|
|
674 |
|
|
675 |
|
|
676 |
|
|
677 |
|
|
678 |
|
} |
679 |
|
|
680 |
|
|
681 |
|
|
682 |
|
@return |
683 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
684 |
0 |
@Override... |
685 |
|
public boolean operationInProgress() |
686 |
|
{ |
687 |
0 |
return progressBar.operationInProgress(); |
688 |
|
} |
689 |
|
|
|
|
| 0% |
Uncovered Elements: 6 (6) |
Complexity: 1 |
Complexity Density: 0.17 |
|
690 |
0 |
@Override... |
691 |
|
protected void resetButton_actionPerformed() |
692 |
|
{ |
693 |
0 |
int t = getTop(); |
694 |
0 |
setTop(0); |
695 |
0 |
xCombobox.setSelectedIndex(0); |
696 |
0 |
yCombobox.setSelectedIndex(1); |
697 |
0 |
setTop(t); |
698 |
0 |
zCombobox.setSelectedIndex(2); |
699 |
|
} |
700 |
|
|
701 |
|
|
702 |
|
|
703 |
|
|
704 |
|
@return |
705 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
706 |
0 |
public boolean isWorking()... |
707 |
|
{ |
708 |
0 |
return working; |
709 |
|
} |
710 |
|
|
711 |
|
|
712 |
|
|
713 |
|
|
714 |
|
|
715 |
|
@param |
716 |
|
@return |
717 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (7) |
Complexity: 3 |
Complexity Density: 0.43 |
|
718 |
3 |
public int getSelectedDimensionIndex(Axis axis)... |
719 |
|
{ |
720 |
3 |
switch (axis) |
721 |
|
{ |
722 |
1 |
case X: |
723 |
1 |
return xCombobox.getSelectedIndex(); |
724 |
1 |
case Y: |
725 |
1 |
return yCombobox.getSelectedIndex(); |
726 |
1 |
default: |
727 |
1 |
return zCombobox.getSelectedIndex(); |
728 |
|
} |
729 |
|
} |
730 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
731 |
1 |
public void setShowLabels(boolean show)... |
732 |
|
{ |
733 |
1 |
showLabels.setSelected(show); |
734 |
|
} |
735 |
|
|
736 |
|
|
737 |
|
|
738 |
|
|
739 |
|
|
740 |
|
|
741 |
|
@param |
742 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
743 |
1 |
public void setInputData(AlignmentView data)... |
744 |
|
{ |
745 |
1 |
getPcaModel().setInputData(data); |
746 |
1 |
originalSeqData.setVisible(data != null); |
747 |
|
} |
748 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
749 |
10 |
public AlignViewportI getAlignViewport()... |
750 |
|
{ |
751 |
10 |
return av; |
752 |
|
} |
753 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
754 |
10 |
public PCAModel getPcaModel()... |
755 |
|
{ |
756 |
10 |
return pcaModel; |
757 |
|
} |
758 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
759 |
4 |
public void setPcaModel(PCAModel pcaModel)... |
760 |
|
{ |
761 |
4 |
this.pcaModel = pcaModel; |
762 |
|
} |
763 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
764 |
24 |
public RotatableCanvas getRotatableCanvas()... |
765 |
|
{ |
766 |
24 |
return rc; |
767 |
|
} |
768 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
769 |
2 |
public void setRotatableCanvas(RotatableCanvas rc)... |
770 |
|
{ |
771 |
2 |
this.rc = rc; |
772 |
|
} |
773 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
774 |
12 |
public int getTop()... |
775 |
|
{ |
776 |
12 |
return top; |
777 |
|
} |
778 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
779 |
2 |
public void setTop(int top)... |
780 |
|
{ |
781 |
2 |
this.top = top; |
782 |
|
} |
783 |
|
|
784 |
|
|
785 |
|
|
786 |
|
|
787 |
|
@param |
788 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (6) |
Complexity: 1 |
Complexity Density: 0.17 |
|
789 |
1 |
public void selectAssociatedView(AlignmentPanel panel)... |
790 |
|
{ |
791 |
1 |
getRotatableCanvas().setApplyToAllViews(false); |
792 |
|
|
793 |
1 |
ap = panel; |
794 |
1 |
av = panel.av; |
795 |
|
|
796 |
1 |
getRotatableCanvas().av = panel.av; |
797 |
1 |
getRotatableCanvas().ap = panel; |
798 |
1 |
PaintRefresher.Register(PCAPanel.this, panel.av.getSequenceSetId()); |
799 |
|
} |
800 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
801 |
0 |
@Override... |
802 |
|
public JProgressBar getProgressBar(long id) |
803 |
|
{ |
804 |
0 |
return progressBar.getProgressBar(id); |
805 |
|
} |
806 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
807 |
0 |
public String getMessage(long id)... |
808 |
|
{ |
809 |
0 |
return progressBar.getMessage(id); |
810 |
|
} |
811 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
812 |
0 |
public void setProgressBarMessage(long id, String message)... |
813 |
|
{ |
814 |
0 |
progressBar.setProgressBarMessage(id, message); |
815 |
|
} |
816 |
|
} |