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package jalview.gui; |
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import jalview.analysis.AnnotationSorter; |
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import jalview.api.AlignViewportI; |
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import jalview.api.AlignmentViewPanel; |
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import jalview.bin.Cache; |
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import jalview.bin.Jalview; |
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import jalview.datamodel.AlignmentI; |
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import jalview.datamodel.HiddenColumns; |
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import jalview.datamodel.SearchResultsI; |
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import jalview.datamodel.SequenceFeature; |
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import jalview.datamodel.SequenceGroup; |
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import jalview.datamodel.SequenceI; |
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import jalview.gui.ImageExporter.ImageWriterI; |
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import jalview.io.HTMLOutput; |
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import jalview.jbgui.GAlignmentPanel; |
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import jalview.math.AlignmentDimension; |
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import jalview.schemes.ResidueProperties; |
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import jalview.structure.StructureSelectionManager; |
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import jalview.util.Comparison; |
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import jalview.util.ImageMaker; |
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import jalview.util.MessageManager; |
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import jalview.util.Platform; |
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import jalview.viewmodel.ViewportListenerI; |
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import jalview.viewmodel.ViewportRanges; |
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import java.awt.BorderLayout; |
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import java.awt.Color; |
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import java.awt.Container; |
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import java.awt.Dimension; |
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import java.awt.Font; |
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import java.awt.FontMetrics; |
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import java.awt.Graphics; |
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import java.awt.Graphics2D; |
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import java.awt.event.AdjustmentEvent; |
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import java.awt.event.AdjustmentListener; |
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import java.awt.event.ComponentAdapter; |
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import java.awt.event.ComponentEvent; |
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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.beans.PropertyChangeEvent; |
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import java.beans.PropertyChangeListener; |
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import java.io.File; |
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import java.io.FileWriter; |
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import java.io.PrintWriter; |
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import java.util.List; |
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import javax.swing.SwingUtilities; |
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@author |
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@version |
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| 50.2% |
Uncovered Elements: 394 (791) |
Complexity: 184 |
Complexity Density: 0.35 |
|
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public class AlignmentPanel extends GAlignmentPanel implements |
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AdjustmentListener, Printable, AlignmentViewPanel, ViewportListenerI |
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{ |
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public AlignViewport av; |
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OverviewPanel overviewPanel; |
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private SeqPanel seqPanel; |
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private IdPanel idPanel; |
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IdwidthAdjuster idwidthAdjuster; |
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public AlignFrame alignFrame; |
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private ScalePanel scalePanel; |
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private AnnotationPanel annotationPanel; |
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private AnnotationLabels alabels; |
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private int hextent = 0; |
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private int vextent = 0; |
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private boolean scrollComplementaryPanel = true; |
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private PropertyChangeListener propertyChangeListener; |
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private CalculationChooser calculationDialog; |
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@param |
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@param |
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| 100% |
Uncovered Elements: 0 (25) |
Complexity: 1 |
Complexity Density: 0.04 |
|
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public AlignmentPanel(AlignFrame af, final AlignViewport av)... |
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{ |
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alignFrame = af; |
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this.av = av; |
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setSeqPanel(new SeqPanel(av, this)); |
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setIdPanel(new IdPanel(av, this)); |
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setScalePanel(new ScalePanel(av, this)); |
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idPanelHolder.add(getIdPanel(), BorderLayout.CENTER); |
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idwidthAdjuster = new IdwidthAdjuster(this); |
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idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER); |
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setAnnotationPanel(new AnnotationPanel(this)); |
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setAlabels(new AnnotationLabels(this)); |
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annotationScroller.setViewportView(getAnnotationPanel()); |
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annotationSpaceFillerHolder.add(getAlabels(), BorderLayout.CENTER); |
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scalePanelHolder.add(getScalePanel(), BorderLayout.CENTER); |
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seqPanelHolder.add(getSeqPanel(), BorderLayout.CENTER); |
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setScrollValues(0, 0); |
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hscroll.addAdjustmentListener(this); |
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vscroll.addAdjustmentListener(this); |
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addComponentListener(new ComponentAdapter() |
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{ |
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| 100% |
Uncovered Elements: 0 (10) |
Complexity: 2 |
Complexity Density: 0.25 |
|
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@Override... |
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public void componentResized(ComponentEvent evt) |
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{ |
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ViewportRanges ranges = av.getRanges(); |
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if (av.getWrapAlignment()) |
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{ |
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int widthInRes = getSeqPanel().seqCanvas.getWrappedCanvasWidth( |
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getSeqPanel().seqCanvas.getWidth()); |
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ranges.setViewportWidth(widthInRes); |
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} |
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else |
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{ |
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int widthInRes = getSeqPanel().seqCanvas.getWidth() |
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/ av.getCharWidth(); |
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int heightInSeq = getSeqPanel().seqCanvas.getHeight() |
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/ av.getCharHeight(); |
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ranges.setViewportWidth(widthInRes); |
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ranges.setViewportHeight(heightInSeq); |
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} |
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} |
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}); |
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final AlignmentPanel ap = this; |
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propertyChangeListener = new PropertyChangeListener() |
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{ |
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| 80% |
Uncovered Elements: 1 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
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@Override... |
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public void propertyChange(PropertyChangeEvent evt) |
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{ |
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if (evt.getPropertyName().equals("alignment")) |
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{ |
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PaintRefresher.Refresh(ap, av.getSequenceSetId(), true, true); |
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alignmentChanged(); |
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} |
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} |
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}; |
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av.addPropertyChangeListener(propertyChangeListener); |
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av.getRanges().addPropertyChangeListener(this); |
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fontChanged(); |
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adjustAnnotationHeight(); |
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updateLayout(); |
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} |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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@Override... |
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public AlignViewportI getAlignViewport() |
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{ |
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return av; |
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} |
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| 71.4% |
Uncovered Elements: 2 (7) |
Complexity: 2 |
Complexity Density: 0.4 |
|
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public void alignmentChanged()... |
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{ |
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av.alignmentChanged(this); |
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if (getCalculationDialog() != null) |
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{ |
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getCalculationDialog().validateCalcTypes(); |
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} |
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alignFrame.updateEditMenuBar(); |
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paintAlignment(true, true); |
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} |
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| 100% |
Uncovered Elements: 0 (13) |
Complexity: 1 |
Complexity Density: 0.08 |
|
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public void fontChanged()... |
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{ |
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FontMetrics fm = getFontMetrics(av.getFont()); |
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scalePanelHolder.setPreferredSize( |
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new Dimension(10, av.getCharHeight() + fm.getDescent())); |
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idSpaceFillerPanel1.setPreferredSize( |
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new Dimension(10, av.getCharHeight() + fm.getDescent())); |
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idwidthAdjuster.invalidate(); |
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scalePanelHolder.invalidate(); |
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getIdPanel().getIdCanvas().gg = null; |
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getSeqPanel().seqCanvas.img = null; |
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getAnnotationPanel().adjustPanelHeight(); |
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Dimension d = calculateIdWidth(); |
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d.setSize(d.width + 4, d.height); |
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getIdPanel().getIdCanvas().setPreferredSize(d); |
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hscrollFillerPanel.setPreferredSize(d); |
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repaint(); |
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} |
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@return |
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| 92.9% |
Uncovered Elements: 1 (14) |
Complexity: 3 |
Complexity Density: 0.3 |
|
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public Dimension calculateIdWidth()... |
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{ |
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Dimension r = null; |
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if (av.getIdWidth() < 0) |
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{ |
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188 |
int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300); |
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int maxwidth = Math.max(20, Math.min(afwidth - 200, 2 * afwidth / 3)); |
260 |
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r = calculateIdWidth(maxwidth); |
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av.setIdWidth(r.width); |
262 |
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} |
263 |
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else |
264 |
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{ |
265 |
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r = new Dimension(); |
266 |
321 |
r.width = av.getIdWidth(); |
267 |
321 |
r.height = 0; |
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} |
269 |
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return r; |
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} |
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@param |
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@return |
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| 93.9% |
Uncovered Elements: 2 (33) |
Complexity: 8 |
Complexity Density: 0.38 |
|
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188 |
public Dimension calculateIdWidth(int maxwidth)... |
282 |
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{ |
283 |
188 |
Container c = new Container(); |
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285 |
188 |
FontMetrics fm = c.getFontMetrics( |
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new Font(av.font.getName(), Font.ITALIC, av.font.getSize())); |
287 |
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AlignmentI al = av.getAlignment(); |
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188 |
int i = 0; |
290 |
188 |
int idWidth = 0; |
291 |
188 |
String id; |
292 |
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293 |
2135 |
while ((i < al.getHeight()) && (al.getSequenceAt(i) != null)) |
294 |
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{ |
295 |
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SequenceI s = al.getSequenceAt(i); |
296 |
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297 |
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id = s.getDisplayId(av.getShowJVSuffix()); |
298 |
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299 |
1947 |
if (fm.stringWidth(id) > idWidth) |
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{ |
301 |
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idWidth = fm.stringWidth(id); |
302 |
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} |
303 |
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304 |
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i++; |
305 |
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} |
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i = 0; |
309 |
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310 |
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if (al.getAlignmentAnnotation() != null) |
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{ |
312 |
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fm = c.getFontMetrics(getAlabels().getFont()); |
313 |
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314 |
1273 |
while (i < al.getAlignmentAnnotation().length) |
315 |
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{ |
316 |
1085 |
String label = al.getAlignmentAnnotation()[i].label; |
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318 |
1085 |
if (fm.stringWidth(label) > idWidth) |
319 |
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{ |
320 |
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idWidth = fm.stringWidth(label); |
321 |
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} |
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1085 |
i++; |
324 |
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} |
325 |
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} |
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188 |
return new Dimension( |
328 |
188 |
maxwidth < 0 ? idWidth : Math.min(maxwidth, idWidth), 12); |
329 |
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} |
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334 |
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| 0% |
Uncovered Elements: 3 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
|
335 |
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public void highlightSearchResults(SearchResultsI results)... |
336 |
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{ |
337 |
0 |
boolean scrolled = scrollToPosition(results, 0, true, false); |
338 |
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339 |
0 |
boolean fastPaint = !(scrolled && av.getWrapAlignment()); |
340 |
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341 |
0 |
getSeqPanel().seqCanvas.highlightSearchResults(results, fastPaint); |
342 |
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} |
343 |
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345 |
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346 |
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347 |
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348 |
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@param |
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@param |
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@return |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
352 |
3 |
public boolean scrollToPosition(SearchResultsI searchResults,... |
353 |
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boolean redrawOverview) |
354 |
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{ |
355 |
3 |
return scrollToPosition(searchResults, 0, redrawOverview, false); |
356 |
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} |
357 |
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358 |
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359 |
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360 |
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361 |
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362 |
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363 |
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364 |
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@param |
365 |
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@param |
366 |
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367 |
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368 |
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@param |
369 |
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370 |
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@param |
371 |
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372 |
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@return |
373 |
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| 46.5% |
Uncovered Elements: 38 (71) |
Complexity: 18 |
Complexity Density: 0.42 |
|
374 |
3 |
protected boolean scrollToPosition(SearchResultsI results,... |
375 |
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int verticalOffset, boolean redrawOverview, boolean centre) |
376 |
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{ |
377 |
3 |
int startv, endv, starts, ends; |
378 |
3 |
ViewportRanges ranges = av.getRanges(); |
379 |
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|
380 |
3 |
if (results == null || results.isEmpty() || av == null |
381 |
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|| av.getAlignment() == null) |
382 |
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{ |
383 |
0 |
return false; |
384 |
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} |
385 |
3 |
int seqIndex = av.getAlignment().findIndex(results); |
386 |
3 |
if (seqIndex == -1) |
387 |
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{ |
388 |
2 |
return false; |
389 |
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} |
390 |
1 |
SequenceI seq = av.getAlignment().getSequenceAt(seqIndex); |
391 |
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|
392 |
1 |
int[] r = results.getResults(seq, 0, av.getAlignment().getWidth()); |
393 |
1 |
if (r == null) |
394 |
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{ |
395 |
0 |
return false; |
396 |
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} |
397 |
1 |
int start = r[0]; |
398 |
1 |
int end = r[1]; |
399 |
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400 |
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401 |
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402 |
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403 |
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404 |
1 |
if (centre) |
405 |
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{ |
406 |
0 |
int offset = (ranges.getEndRes() - ranges.getStartRes() + 1) / 2 - 1; |
407 |
0 |
start = Math.max(start - offset, 0); |
408 |
0 |
end = end + offset - 1; |
409 |
|
} |
410 |
1 |
if (start < 0) |
411 |
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{ |
412 |
0 |
return false; |
413 |
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} |
414 |
1 |
if (end == seq.getEnd()) |
415 |
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{ |
416 |
0 |
return false; |
417 |
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} |
418 |
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|
419 |
1 |
if (av.hasHiddenColumns()) |
420 |
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{ |
421 |
0 |
HiddenColumns hidden = av.getAlignment().getHiddenColumns(); |
422 |
0 |
start = hidden.absoluteToVisibleColumn(start); |
423 |
0 |
end = hidden.absoluteToVisibleColumn(end); |
424 |
0 |
if (start == end) |
425 |
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{ |
426 |
0 |
if (!hidden.isVisible(r[0])) |
427 |
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{ |
428 |
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429 |
0 |
return false; |
430 |
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} |
431 |
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} |
432 |
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} |
433 |
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434 |
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435 |
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436 |
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|
437 |
1 |
seqIndex = Math.max(0, seqIndex - verticalOffset); |
438 |
1 |
boolean scrollNeeded = true; |
439 |
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|
440 |
1 |
if (!av.getWrapAlignment()) |
441 |
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{ |
442 |
? |
if ((startv = ranges.getStartRes()) >= start) |
443 |
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{ |
444 |
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445 |
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446 |
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|
447 |
0 |
setScrollValues(start, seqIndex); |
448 |
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} |
449 |
? |
else if ((endv = ranges.getEndRes()) <= end) |
450 |
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{ |
451 |
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|
452 |
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|
453 |
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|
454 |
1 |
setScrollValues(startv + end - endv, seqIndex); |
455 |
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} |
456 |
0 |
else if ((starts = ranges.getStartSeq()) > seqIndex) |
457 |
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{ |
458 |
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|
459 |
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|
460 |
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|
461 |
0 |
setScrollValues(ranges.getStartRes(), seqIndex); |
462 |
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} |
463 |
0 |
else if ((ends = ranges.getEndSeq()) <= seqIndex) |
464 |
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{ |
465 |
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|
466 |
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|
467 |
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|
468 |
0 |
setScrollValues(ranges.getStartRes(), starts + seqIndex - ends |
469 |
|
+ 1); |
470 |
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} |
471 |
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|
472 |
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|
473 |
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|
474 |
1 |
scrollNeeded = false; |
475 |
|
} |
476 |
|
else |
477 |
|
{ |
478 |
0 |
scrollNeeded = ranges.scrollToWrappedVisible(start); |
479 |
|
} |
480 |
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|
481 |
1 |
paintAlignment(redrawOverview, false); |
482 |
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|
483 |
1 |
return scrollNeeded; |
484 |
|
} |
485 |
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486 |
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487 |
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488 |
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|
489 |
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@return |
490 |
|
|
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|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
491 |
0 |
public OverviewPanel getOverviewPanel()... |
492 |
|
{ |
493 |
0 |
return overviewPanel; |
494 |
|
} |
495 |
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|
496 |
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|
497 |
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|
498 |
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|
499 |
|
@param |
500 |
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|
501 |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
502 |
0 |
public void setOverviewPanel(OverviewPanel op)... |
503 |
|
{ |
504 |
0 |
overviewPanel = op; |
505 |
|
} |
506 |
|
|
507 |
|
|
508 |
|
|
509 |
|
@param |
510 |
|
|
511 |
|
|
512 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
|
513 |
292 |
public void setAnnotationVisible(boolean b)... |
514 |
|
{ |
515 |
292 |
if (!av.getWrapAlignment()) |
516 |
|
{ |
517 |
278 |
annotationSpaceFillerHolder.setVisible(b); |
518 |
278 |
annotationScroller.setVisible(b); |
519 |
|
} |
520 |
292 |
repaint(); |
521 |
|
} |
522 |
|
|
523 |
|
|
524 |
|
|
525 |
|
|
526 |
|
|
|
|
| 71.4% |
Uncovered Elements: 2 (7) |
Complexity: 2 |
Complexity Density: 0.4 |
|
527 |
411 |
@Override... |
528 |
|
public void adjustAnnotationHeight() |
529 |
|
{ |
530 |
|
|
531 |
|
|
532 |
411 |
if (alignFrame.getHeight() == 0) |
533 |
|
{ |
534 |
0 |
System.out.println("NEEDS FIXING"); |
535 |
|
} |
536 |
411 |
validateAnnotationDimensions(true); |
537 |
411 |
addNotify(); |
538 |
|
|
539 |
|
|
540 |
411 |
paintAlignment(true, false); |
541 |
|
} |
542 |
|
|
543 |
|
|
544 |
|
|
545 |
|
|
546 |
|
|
|
|
| 86.4% |
Uncovered Elements: 3 (22) |
Complexity: 4 |
Complexity Density: 0.25 |
|
547 |
411 |
protected void validateAnnotationDimensions(boolean adjustPanelHeight)... |
548 |
|
{ |
549 |
411 |
int annotationHeight = getAnnotationPanel().adjustPanelHeight(); |
550 |
|
|
551 |
411 |
if (adjustPanelHeight) |
552 |
|
{ |
553 |
411 |
int rowHeight = av.getCharHeight(); |
554 |
411 |
int alignmentHeight = rowHeight * av.getAlignment().getHeight(); |
555 |
|
|
556 |
|
|
557 |
|
|
558 |
|
|
559 |
|
|
560 |
|
|
561 |
411 |
int stuff = Platform.isAMac() ? 120 : 140; |
562 |
411 |
int availableHeight = alignFrame.getHeight() - stuff; |
563 |
|
|
564 |
|
|
565 |
|
|
566 |
|
|
567 |
|
|
568 |
411 |
if (annotationHeight + alignmentHeight > availableHeight) |
569 |
|
{ |
570 |
269 |
annotationHeight = Math.min(annotationHeight, |
571 |
|
availableHeight - 2 * rowHeight); |
572 |
|
} |
573 |
|
} |
574 |
|
else |
575 |
|
{ |
576 |
|
|
577 |
0 |
annotationHeight = annotationScroller.getSize().height; |
578 |
|
} |
579 |
411 |
hscroll.addNotify(); |
580 |
|
|
581 |
411 |
annotationScroller.setPreferredSize( |
582 |
|
new Dimension(annotationScroller.getWidth(), annotationHeight)); |
583 |
|
|
584 |
411 |
Dimension e = idPanel.getSize(); |
585 |
411 |
alabels.setSize(new Dimension(e.width, annotationHeight)); |
586 |
|
|
587 |
411 |
annotationSpaceFillerHolder.setPreferredSize(new Dimension( |
588 |
|
annotationSpaceFillerHolder.getWidth(), annotationHeight)); |
589 |
411 |
annotationScroller.validate(); |
590 |
411 |
annotationScroller.addNotify(); |
591 |
|
} |
592 |
|
|
593 |
|
|
594 |
|
|
595 |
|
|
596 |
|
@param |
597 |
|
|
598 |
|
|
|
|
| 81.8% |
Uncovered Elements: 6 (33) |
Complexity: 5 |
Complexity Density: 0.2 |
|
599 |
292 |
public void updateLayout()... |
600 |
|
{ |
601 |
292 |
fontChanged(); |
602 |
292 |
setAnnotationVisible(av.isShowAnnotation()); |
603 |
292 |
boolean wrap = av.getWrapAlignment(); |
604 |
292 |
ViewportRanges ranges = av.getRanges(); |
605 |
292 |
ranges.setStartSeq(0); |
606 |
292 |
scalePanelHolder.setVisible(!wrap); |
607 |
292 |
hscroll.setVisible(!wrap); |
608 |
292 |
idwidthAdjuster.setVisible(!wrap); |
609 |
|
|
610 |
292 |
if (wrap) |
611 |
|
{ |
612 |
14 |
annotationScroller.setVisible(false); |
613 |
14 |
annotationSpaceFillerHolder.setVisible(false); |
614 |
|
} |
615 |
278 |
else if (av.isShowAnnotation()) |
616 |
|
{ |
617 |
278 |
annotationScroller.setVisible(true); |
618 |
278 |
annotationSpaceFillerHolder.setVisible(true); |
619 |
|
} |
620 |
|
|
621 |
292 |
int canvasWidth = getSeqPanel().seqCanvas.getWidth(); |
622 |
292 |
if (canvasWidth > 0) |
623 |
|
{ |
624 |
2 |
if (wrap) |
625 |
|
{ |
626 |
2 |
int widthInRes = getSeqPanel().seqCanvas |
627 |
|
.getWrappedCanvasWidth(canvasWidth); |
628 |
2 |
ranges.setViewportWidth(widthInRes); |
629 |
|
} |
630 |
|
else |
631 |
|
{ |
632 |
0 |
int widthInRes = (canvasWidth / av.getCharWidth()); |
633 |
0 |
int heightInSeq = (getSeqPanel().seqCanvas.getHeight() |
634 |
|
/ av.getCharHeight()); |
635 |
|
|
636 |
0 |
ranges.setViewportWidth(widthInRes); |
637 |
0 |
ranges.setViewportHeight(heightInSeq); |
638 |
|
} |
639 |
|
} |
640 |
|
|
641 |
292 |
idSpaceFillerPanel1.setVisible(!wrap); |
642 |
|
|
643 |
292 |
repaint(); |
644 |
|
} |
645 |
|
|
646 |
|
|
647 |
|
|
648 |
|
|
649 |
|
@param |
650 |
|
|
651 |
|
@param |
652 |
|
|
653 |
|
|
654 |
|
|
|
|
| 90.9% |
Uncovered Elements: 4 (44) |
Complexity: 11 |
Complexity Density: 0.42 |
|
655 |
1586 |
public void setScrollValues(int xpos, int ypos)... |
656 |
|
{ |
657 |
1586 |
int x = xpos; |
658 |
1586 |
int y = ypos; |
659 |
|
|
660 |
1586 |
if (av == null || av.getAlignment() == null) |
661 |
|
{ |
662 |
0 |
return; |
663 |
|
} |
664 |
|
|
665 |
1586 |
if (av.getWrapAlignment()) |
666 |
|
{ |
667 |
178 |
setScrollingForWrappedPanel(x); |
668 |
|
} |
669 |
|
else |
670 |
|
{ |
671 |
1408 |
int width = av.getAlignment().getWidth(); |
672 |
1408 |
int height = av.getAlignment().getHeight(); |
673 |
|
|
674 |
1408 |
if (av.hasHiddenColumns()) |
675 |
|
{ |
676 |
|
|
677 |
190 |
width = av.getAlignment().getHiddenColumns() |
678 |
|
.absoluteToVisibleColumn(width); |
679 |
|
} |
680 |
|
|
681 |
1408 |
hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth(); |
682 |
1408 |
vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight(); |
683 |
|
|
684 |
1408 |
if (hextent > width) |
685 |
|
{ |
686 |
24 |
hextent = width; |
687 |
|
} |
688 |
|
|
689 |
1408 |
if (vextent > height) |
690 |
|
{ |
691 |
56 |
vextent = height; |
692 |
|
} |
693 |
|
|
694 |
1408 |
if ((hextent + x) > width) |
695 |
|
{ |
696 |
2 |
x = width - hextent; |
697 |
|
} |
698 |
|
|
699 |
1408 |
if ((vextent + y) > height) |
700 |
|
{ |
701 |
8 |
y = height - vextent; |
702 |
|
} |
703 |
|
|
704 |
1408 |
if (y < 0) |
705 |
|
{ |
706 |
0 |
y = 0; |
707 |
|
} |
708 |
|
|
709 |
1408 |
if (x < 0) |
710 |
|
{ |
711 |
1 |
x = 0; |
712 |
|
} |
713 |
|
|
714 |
|
|
715 |
1408 |
hscroll.setValues(x, hextent, 0, width); |
716 |
1408 |
vscroll.setValues(y, vextent, 0, height); |
717 |
|
} |
718 |
|
} |
719 |
|
|
720 |
|
|
721 |
|
|
722 |
|
|
723 |
|
|
724 |
|
@param |
725 |
|
|
726 |
|
|
|
|
| 96.8% |
Uncovered Elements: 1 (31) |
Complexity: 8 |
Complexity Density: 0.38 |
|
727 |
381 |
@Override... |
728 |
|
public void adjustmentValueChanged(AdjustmentEvent evt) |
729 |
|
{ |
730 |
381 |
if (av.getWrapAlignment()) |
731 |
|
{ |
732 |
26 |
adjustScrollingWrapped(evt); |
733 |
26 |
return; |
734 |
|
} |
735 |
|
|
736 |
355 |
ViewportRanges ranges = av.getRanges(); |
737 |
|
|
738 |
355 |
if (evt.getSource() == hscroll) |
739 |
|
{ |
740 |
141 |
int oldX = ranges.getStartRes(); |
741 |
141 |
int oldwidth = ranges.getViewportWidth(); |
742 |
141 |
int x = hscroll.getValue(); |
743 |
141 |
int width = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth(); |
744 |
|
|
745 |
|
|
746 |
|
|
747 |
|
|
748 |
141 |
if ((x == oldX) && (width == oldwidth)) |
749 |
|
{ |
750 |
32 |
return; |
751 |
|
} |
752 |
109 |
ranges.setViewportStartAndWidth(x, width); |
753 |
|
} |
754 |
214 |
else if (evt.getSource() == vscroll) |
755 |
|
{ |
756 |
214 |
int oldY = ranges.getStartSeq(); |
757 |
214 |
int oldheight = ranges.getViewportHeight(); |
758 |
214 |
int y = vscroll.getValue(); |
759 |
214 |
int height = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight(); |
760 |
|
|
761 |
|
|
762 |
|
|
763 |
|
|
764 |
214 |
if ((y == oldY) && (height == oldheight)) |
765 |
|
{ |
766 |
44 |
return; |
767 |
|
} |
768 |
170 |
ranges.setViewportStartAndHeight(y, height); |
769 |
|
} |
770 |
279 |
repaint(); |
771 |
|
} |
772 |
|
|
773 |
|
|
774 |
|
|
775 |
|
|
776 |
|
|
777 |
|
@param |
778 |
|
|
|
|
| 44% |
Uncovered Elements: 14 (25) |
Complexity: 6 |
Complexity Density: 0.4 |
|
779 |
26 |
protected void adjustScrollingWrapped(AdjustmentEvent evt)... |
780 |
|
{ |
781 |
26 |
if (evt.getSource() == hscroll) |
782 |
|
{ |
783 |
0 |
return; |
784 |
|
} |
785 |
26 |
final ViewportRanges ranges = av.getRanges(); |
786 |
|
|
787 |
26 |
if (evt.getSource() == vscroll) |
788 |
|
{ |
789 |
26 |
int newY = vscroll.getValue(); |
790 |
|
|
791 |
|
|
792 |
|
|
793 |
|
|
794 |
|
|
795 |
|
|
796 |
26 |
int oldX = ranges.getStartRes(); |
797 |
26 |
int oldY = ranges.getWrappedScrollPosition(oldX); |
798 |
26 |
if (oldY == newY) |
799 |
|
{ |
800 |
26 |
return; |
801 |
|
} |
802 |
0 |
if (newY > -1) |
803 |
|
{ |
804 |
|
|
805 |
|
|
806 |
|
|
807 |
0 |
int rowSize = ranges.getViewportWidth(); |
808 |
0 |
int newX = newY > oldY ? oldX + rowSize : oldX - rowSize; |
809 |
0 |
ranges.setViewportStartAndWidth(Math.max(0, newX), rowSize); |
810 |
|
} |
811 |
|
} |
812 |
|
else |
813 |
|
{ |
814 |
|
|
815 |
|
|
816 |
|
|
817 |
0 |
SwingUtilities.invokeLater(new Runnable() |
818 |
|
{ |
|
|
| 0% |
Uncovered Elements: 3 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
|
819 |
0 |
@Override... |
820 |
|
public void run() |
821 |
|
{ |
822 |
|
|
823 |
|
|
824 |
|
|
825 |
|
|
826 |
0 |
Cache.log.warn( |
827 |
|
"Unexpected path through code: Wrapped jar file opened with wrap alignment set in preferences"); |
828 |
|
|
829 |
|
|
830 |
0 |
ranges.setStartRes(0); |
831 |
0 |
ranges.setStartSeq(0); |
832 |
|
} |
833 |
|
}); |
834 |
|
} |
835 |
0 |
repaint(); |
836 |
|
} |
837 |
|
|
838 |
|
|
839 |
|
@see |
840 |
|
|
|
|
| 85.7% |
Uncovered Elements: 2 (14) |
Complexity: 4 |
Complexity Density: 0.5 |
|
841 |
1786 |
@Override... |
842 |
|
public void paintAlignment(boolean updateOverview, |
843 |
|
boolean updateStructures) |
844 |
|
{ |
845 |
1786 |
final AnnotationSorter sorter = new AnnotationSorter(getAlignment(), |
846 |
|
av.isShowAutocalculatedAbove()); |
847 |
1786 |
sorter.sort(getAlignment().getAlignmentAnnotation(), |
848 |
|
av.getSortAnnotationsBy()); |
849 |
1786 |
repaint(); |
850 |
|
|
851 |
1786 |
if (updateStructures) |
852 |
|
{ |
853 |
1328 |
av.getStructureSelectionManager().sequenceColoursChanged(this); |
854 |
|
} |
855 |
1786 |
if (updateOverview) |
856 |
|
{ |
857 |
|
|
858 |
1772 |
if (overviewPanel != null) |
859 |
|
{ |
860 |
0 |
overviewPanel.updateOverviewImage(); |
861 |
|
} |
862 |
|
} |
863 |
|
} |
864 |
|
|
865 |
|
|
866 |
|
|
867 |
|
|
868 |
|
@param |
869 |
|
|
870 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (7) |
Complexity: 1 |
Complexity Density: 0.14 |
|
871 |
908 |
@Override... |
872 |
|
public void paintComponent(Graphics g) |
873 |
|
{ |
874 |
908 |
invalidate(); |
875 |
|
|
876 |
908 |
Dimension d = getIdPanel().getIdCanvas().getPreferredSize(); |
877 |
908 |
idPanelHolder.setPreferredSize(d); |
878 |
908 |
hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12)); |
879 |
|
|
880 |
908 |
validate(); |
881 |
|
|
882 |
|
|
883 |
|
|
884 |
|
|
885 |
|
|
886 |
908 |
ViewportRanges ranges = av.getRanges(); |
887 |
908 |
setScrollValues(ranges.getStartRes(), ranges.getStartSeq()); |
888 |
|
} |
889 |
|
|
890 |
|
|
891 |
|
|
892 |
|
|
893 |
|
|
894 |
|
@param |
895 |
|
|
896 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (5) |
Complexity: 1 |
Complexity Density: 0.2 |
|
897 |
178 |
private void setScrollingForWrappedPanel(int topLeftColumn)... |
898 |
|
{ |
899 |
178 |
ViewportRanges ranges = av.getRanges(); |
900 |
178 |
int scrollPosition = ranges.getWrappedScrollPosition(topLeftColumn); |
901 |
178 |
int maxScroll = ranges.getWrappedMaxScroll(topLeftColumn); |
902 |
|
|
903 |
|
|
904 |
|
|
905 |
|
|
906 |
|
|
907 |
178 |
vscroll.setUnitIncrement(1); |
908 |
178 |
vscroll.setValues(scrollPosition, 1, 0, maxScroll + 1); |
909 |
|
} |
910 |
|
|
911 |
|
|
912 |
|
|
913 |
|
|
914 |
|
@param |
915 |
|
|
916 |
|
@param |
917 |
|
|
918 |
|
@param |
919 |
|
|
920 |
|
|
921 |
|
@return |
922 |
|
|
923 |
|
@throws |
924 |
|
|
925 |
|
|
|
|
| 0% |
Uncovered Elements: 8 (8) |
Complexity: 2 |
Complexity Density: 0.33 |
|
926 |
0 |
@Override... |
927 |
|
public int print(Graphics pg, PageFormat pf, int pi) |
928 |
|
throws PrinterException |
929 |
|
{ |
930 |
0 |
pg.translate((int) pf.getImageableX(), (int) pf.getImageableY()); |
931 |
|
|
932 |
0 |
int pwidth = (int) pf.getImageableWidth(); |
933 |
0 |
int pheight = (int) pf.getImageableHeight(); |
934 |
|
|
935 |
0 |
if (av.getWrapAlignment()) |
936 |
|
{ |
937 |
0 |
return printWrappedAlignment(pwidth, pheight, pi, pg); |
938 |
|
} |
939 |
|
else |
940 |
|
{ |
941 |
0 |
return printUnwrapped(pwidth, pheight, pi, pg, pg); |
942 |
|
} |
943 |
|
} |
944 |
|
|
945 |
|
|
946 |
|
|
947 |
|
|
948 |
|
|
949 |
|
|
950 |
|
@param |
951 |
|
|
952 |
|
@param |
953 |
|
|
954 |
|
@param |
955 |
|
|
956 |
|
@param |
957 |
|
|
958 |
|
@param |
959 |
|
|
960 |
|
|
961 |
|
@return |
962 |
|
@throws |
963 |
|
|
|
|
| 0% |
Uncovered Elements: 55 (55) |
Complexity: 7 |
Complexity Density: 0.16 |
|
964 |
0 |
public int printUnwrapped(int pageWidth, int pageHeight, int pageIndex,... |
965 |
|
Graphics idGraphics, Graphics alignmentGraphics) |
966 |
|
throws PrinterException |
967 |
|
{ |
968 |
0 |
final int idWidth = getVisibleIdWidth(false); |
969 |
|
|
970 |
|
|
971 |
|
|
972 |
|
|
973 |
|
|
974 |
0 |
final int alignmentGraphicsOffset = idGraphics != alignmentGraphics ? 0 |
975 |
|
: idWidth; |
976 |
|
|
977 |
0 |
FontMetrics fm = getFontMetrics(av.getFont()); |
978 |
0 |
final int charHeight = av.getCharHeight(); |
979 |
0 |
final int scaleHeight = charHeight + fm.getDescent(); |
980 |
|
|
981 |
0 |
idGraphics.setColor(Color.white); |
982 |
0 |
idGraphics.fillRect(0, 0, pageWidth, pageHeight); |
983 |
0 |
idGraphics.setFont(av.getFont()); |
984 |
|
|
985 |
|
|
986 |
|
|
987 |
|
|
988 |
0 |
final int totalRes = (pageWidth - idWidth) / av.getCharWidth(); |
989 |
|
|
990 |
0 |
final int totalSeq = (pageHeight - scaleHeight) / charHeight - 1; |
991 |
|
|
992 |
0 |
final int alignmentWidth = av.getAlignment().getWidth(); |
993 |
0 |
final int pagesWide = (alignmentWidth / totalRes) + 1; |
994 |
|
|
995 |
0 |
final int startRes = (pageIndex % pagesWide) * totalRes; |
996 |
0 |
final int endRes = Math.min(startRes + totalRes - 1, |
997 |
|
alignmentWidth - 1); |
998 |
|
|
999 |
0 |
final int startSeq = (pageIndex / pagesWide) * totalSeq; |
1000 |
0 |
final int alignmentHeight = av.getAlignment().getHeight(); |
1001 |
0 |
final int endSeq = Math.min(startSeq + totalSeq, alignmentHeight); |
1002 |
|
|
1003 |
0 |
int pagesHigh = ((alignmentHeight / totalSeq) + 1) * pageHeight; |
1004 |
|
|
1005 |
0 |
if (av.isShowAnnotation()) |
1006 |
|
{ |
1007 |
0 |
pagesHigh += getAnnotationPanel().adjustPanelHeight() + 3; |
1008 |
|
} |
1009 |
|
|
1010 |
0 |
pagesHigh /= pageHeight; |
1011 |
|
|
1012 |
0 |
if (pageIndex >= (pagesWide * pagesHigh)) |
1013 |
|
{ |
1014 |
0 |
return Printable.NO_SUCH_PAGE; |
1015 |
|
} |
1016 |
0 |
final int alignmentDrawnHeight = (endSeq - startSeq) * charHeight + 3; |
1017 |
|
|
1018 |
|
|
1019 |
|
|
1020 |
|
|
1021 |
0 |
alignmentGraphics.translate(alignmentGraphicsOffset, 0); |
1022 |
0 |
getScalePanel().drawScale(alignmentGraphics, startRes, endRes, |
1023 |
|
pageWidth - idWidth, scaleHeight); |
1024 |
0 |
alignmentGraphics.translate(-alignmentGraphicsOffset, 0); |
1025 |
|
|
1026 |
|
|
1027 |
|
|
1028 |
|
|
1029 |
|
|
1030 |
0 |
idGraphics.translate(0, scaleHeight); |
1031 |
0 |
IdCanvas idCanvas = getIdPanel().getIdCanvas(); |
1032 |
0 |
List<SequenceI> selection = av.getSelectionGroup() == null ? null |
1033 |
|
: av.getSelectionGroup().getSequences(null); |
1034 |
0 |
idCanvas.drawIds((Graphics2D) idGraphics, av, startSeq, endSeq - 1, |
1035 |
|
selection); |
1036 |
|
|
1037 |
0 |
idGraphics.setFont(av.getFont()); |
1038 |
0 |
idGraphics.translate(0, -scaleHeight); |
1039 |
|
|
1040 |
|
|
1041 |
|
|
1042 |
|
|
1043 |
|
|
1044 |
0 |
alignmentGraphics.translate(alignmentGraphicsOffset, scaleHeight); |
1045 |
0 |
getSeqPanel().seqCanvas.drawPanelForPrinting(alignmentGraphics, startRes, |
1046 |
|
endRes, startSeq, endSeq - 1); |
1047 |
0 |
alignmentGraphics.translate(-alignmentGraphicsOffset, 0); |
1048 |
|
|
1049 |
0 |
if (av.isShowAnnotation() && (endSeq == alignmentHeight)) |
1050 |
|
{ |
1051 |
|
|
1052 |
|
|
1053 |
|
|
1054 |
|
|
1055 |
|
|
1056 |
0 |
int offset = getAlabels().getScrollOffset(); |
1057 |
0 |
idGraphics.translate(0, -offset); |
1058 |
0 |
idGraphics.translate(0, alignmentDrawnHeight); |
1059 |
0 |
getAlabels().drawComponent(idGraphics, idWidth); |
1060 |
0 |
idGraphics.translate(0, -alignmentDrawnHeight); |
1061 |
|
|
1062 |
|
|
1063 |
|
|
1064 |
|
|
1065 |
|
|
1066 |
0 |
alignmentGraphics.translate(alignmentGraphicsOffset, |
1067 |
|
alignmentDrawnHeight); |
1068 |
0 |
getAnnotationPanel().renderer.drawComponent(getAnnotationPanel(), av, |
1069 |
|
alignmentGraphics, -1, startRes, endRes + 1); |
1070 |
|
} |
1071 |
|
|
1072 |
0 |
return Printable.PAGE_EXISTS; |
1073 |
|
} |
1074 |
|
|
1075 |
|
|
1076 |
|
|
1077 |
|
|
1078 |
|
|
1079 |
|
|
1080 |
|
@param |
1081 |
|
@param |
1082 |
|
@param |
1083 |
|
|
1084 |
|
@param |
1085 |
|
|
1086 |
|
@return |
1087 |
|
|
1088 |
|
@throws |
1089 |
|
|
|
|
| 0% |
Uncovered Elements: 34 (34) |
Complexity: 5 |
Complexity Density: 0.19 |
|
1090 |
0 |
public int printWrappedAlignment(int pageWidth, int pageHeight, int pageNumber,... |
1091 |
|
Graphics g) throws PrinterException |
1092 |
|
{ |
1093 |
0 |
int annotationHeight = 0; |
1094 |
0 |
if (av.isShowAnnotation()) |
1095 |
|
{ |
1096 |
0 |
annotationHeight = getAnnotationPanel().adjustPanelHeight(); |
1097 |
|
} |
1098 |
|
|
1099 |
0 |
int hgap = av.getCharHeight(); |
1100 |
0 |
if (av.getScaleAboveWrapped()) |
1101 |
|
{ |
1102 |
0 |
hgap += av.getCharHeight(); |
1103 |
|
} |
1104 |
|
|
1105 |
0 |
int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap |
1106 |
|
+ annotationHeight; |
1107 |
|
|
1108 |
0 |
int idWidth = getVisibleIdWidth(false); |
1109 |
|
|
1110 |
0 |
int maxwidth = av.getAlignment().getWidth(); |
1111 |
0 |
if (av.hasHiddenColumns()) |
1112 |
|
{ |
1113 |
0 |
maxwidth = av.getAlignment().getHiddenColumns() |
1114 |
|
.absoluteToVisibleColumn(maxwidth) - 1; |
1115 |
|
} |
1116 |
|
|
1117 |
0 |
int resWidth = getSeqPanel().seqCanvas |
1118 |
|
.getWrappedCanvasWidth(pageWidth - idWidth); |
1119 |
|
|
1120 |
0 |
int totalHeight = cHeight * (maxwidth / resWidth + 1); |
1121 |
|
|
1122 |
0 |
g.setColor(Color.white); |
1123 |
0 |
g.fillRect(0, 0, pageWidth, pageHeight); |
1124 |
0 |
g.setFont(av.getFont()); |
1125 |
0 |
g.setColor(Color.black); |
1126 |
|
|
1127 |
|
|
1128 |
|
|
1129 |
|
|
1130 |
|
|
1131 |
|
|
1132 |
|
|
1133 |
0 |
g.translate(0, -pageNumber * pageHeight); |
1134 |
|
|
1135 |
0 |
g.setClip(0, pageNumber * pageHeight, pageWidth, pageHeight); |
1136 |
|
|
1137 |
|
|
1138 |
|
|
1139 |
|
|
1140 |
0 |
IdCanvas idCanvas = getIdPanel().getIdCanvas(); |
1141 |
0 |
idCanvas.drawIdsWrapped((Graphics2D) g, av, 0, totalHeight); |
1142 |
|
|
1143 |
0 |
g.translate(idWidth, 0); |
1144 |
|
|
1145 |
0 |
getSeqPanel().seqCanvas.drawWrappedPanelForPrinting(g, pageWidth - idWidth, |
1146 |
|
totalHeight, 0); |
1147 |
|
|
1148 |
0 |
if ((pageNumber * pageHeight) < totalHeight) |
1149 |
|
{ |
1150 |
0 |
return Printable.PAGE_EXISTS; |
1151 |
|
} |
1152 |
|
else |
1153 |
|
{ |
1154 |
0 |
return Printable.NO_SUCH_PAGE; |
1155 |
|
} |
1156 |
|
} |
1157 |
|
|
1158 |
|
|
1159 |
|
|
1160 |
|
|
1161 |
|
|
1162 |
|
@return |
1163 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1164 |
0 |
public int getVisibleIdWidth()... |
1165 |
|
{ |
1166 |
0 |
return getVisibleIdWidth(true); |
1167 |
|
} |
1168 |
|
|
1169 |
|
|
1170 |
|
|
1171 |
|
|
1172 |
|
|
1173 |
|
@param |
1174 |
|
|
1175 |
|
|
1176 |
|
@return |
1177 |
|
|
|
|
| 0% |
Uncovered Elements: 13 (13) |
Complexity: 6 |
Complexity Density: 0.86 |
|
1178 |
0 |
public int getVisibleIdWidth(boolean onscreen)... |
1179 |
|
{ |
1180 |
|
|
1181 |
0 |
if (!onscreen && Cache.getDefault("FIGURE_AUTOIDWIDTH", false)) |
1182 |
|
{ |
1183 |
0 |
return calculateIdWidth(-1).width + 4; |
1184 |
|
} |
1185 |
0 |
Integer idwidth = null; |
1186 |
0 |
if (onscreen || (idwidth = Cache |
1187 |
|
.getIntegerProperty("FIGURE_FIXEDIDWIDTH")) == null) |
1188 |
|
{ |
1189 |
0 |
int w = getIdPanel().getWidth(); |
1190 |
0 |
return (w > 0 ? w : calculateIdWidth().width + 4); |
1191 |
|
} |
1192 |
0 |
return idwidth.intValue() + 4; |
1193 |
|
} |
1194 |
|
|
1195 |
|
|
1196 |
|
|
1197 |
|
|
1198 |
|
|
1199 |
|
@param |
1200 |
|
@param |
1201 |
|
|
|
|
| 0% |
Uncovered Elements: 9 (9) |
Complexity: 1 |
Complexity Density: 0.11 |
|
1202 |
0 |
void makeAlignmentImage(ImageMaker.TYPE type, File file)... |
1203 |
|
{ |
1204 |
0 |
final int borderBottomOffset = 5; |
1205 |
|
|
1206 |
0 |
AlignmentDimension aDimension = getAlignmentDimension(); |
1207 |
|
|
1208 |
0 |
ImageWriterI writer = new ImageWriterI() |
1209 |
|
{ |
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
1210 |
0 |
@Override... |
1211 |
|
public void exportImage(Graphics graphics) throws Exception |
1212 |
|
{ |
1213 |
0 |
if (av.getWrapAlignment()) |
1214 |
|
{ |
1215 |
0 |
printWrappedAlignment(aDimension.getWidth(), |
1216 |
|
aDimension.getHeight() + borderBottomOffset, 0, graphics); |
1217 |
|
} |
1218 |
|
else |
1219 |
|
{ |
1220 |
0 |
printUnwrapped(aDimension.getWidth(), aDimension.getHeight(), 0, |
1221 |
|
graphics, graphics); |
1222 |
|
} |
1223 |
|
} |
1224 |
|
}; |
1225 |
|
|
1226 |
0 |
String fileTitle = alignFrame.getTitle(); |
1227 |
0 |
ImageExporter exporter = new ImageExporter(writer, alignFrame, type, |
1228 |
|
fileTitle); |
1229 |
0 |
int imageWidth = aDimension.getWidth(); |
1230 |
0 |
int imageHeight = aDimension.getHeight() + borderBottomOffset; |
1231 |
0 |
String of = MessageManager.getString("label.alignment"); |
1232 |
0 |
exporter.doExport(file, this, imageWidth, imageHeight, of); |
1233 |
|
} |
1234 |
|
|
1235 |
|
|
1236 |
|
|
1237 |
|
|
1238 |
|
|
1239 |
|
@return |
1240 |
|
|
|
|
| 0% |
Uncovered Elements: 21 (21) |
Complexity: 5 |
Complexity Density: 0.38 |
|
1241 |
0 |
public AlignmentDimension getAlignmentDimension()... |
1242 |
|
{ |
1243 |
0 |
int maxwidth = av.getAlignment().getWidth(); |
1244 |
0 |
if (av.hasHiddenColumns()) |
1245 |
|
{ |
1246 |
0 |
maxwidth = av.getAlignment().getHiddenColumns() |
1247 |
|
.absoluteToVisibleColumn(maxwidth); |
1248 |
|
} |
1249 |
|
|
1250 |
0 |
int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight()) |
1251 |
|
+ getScalePanel().getHeight(); |
1252 |
0 |
int width = getVisibleIdWidth(false) + (maxwidth * av.getCharWidth()); |
1253 |
|
|
1254 |
0 |
if (av.getWrapAlignment()) |
1255 |
|
{ |
1256 |
0 |
height = getWrappedHeight(); |
1257 |
0 |
if (Jalview.isHeadlessMode()) |
1258 |
|
{ |
1259 |
|
|
1260 |
|
|
1261 |
|
|
1262 |
|
|
1263 |
0 |
width = alignFrame.getWidth() - vscroll.getPreferredSize().width |
1264 |
|
- alignFrame.getInsets().left - alignFrame.getInsets().right |
1265 |
|
- getVisibleIdWidth() + getVisibleIdWidth(false); |
1266 |
|
} |
1267 |
|
else |
1268 |
|
{ |
1269 |
0 |
width = getSeqPanel().getWidth() + getVisibleIdWidth(false); |
1270 |
|
} |
1271 |
|
|
1272 |
|
} |
1273 |
0 |
else if (av.isShowAnnotation()) |
1274 |
|
{ |
1275 |
0 |
height += getAnnotationPanel().adjustPanelHeight() + 3; |
1276 |
|
} |
1277 |
0 |
return new AlignmentDimension(width, height); |
1278 |
|
|
1279 |
|
} |
1280 |
|
|
|
|
| 0% |
Uncovered Elements: 79 (79) |
Complexity: 19 |
Complexity Density: 0.37 |
|
1281 |
0 |
public void makePNGImageMap(File imgMapFile, String imageName)... |
1282 |
|
{ |
1283 |
|
|
1284 |
|
|
1285 |
0 |
int idWidth = getVisibleIdWidth(false); |
1286 |
0 |
FontMetrics fm = getFontMetrics(av.getFont()); |
1287 |
0 |
int scaleHeight = av.getCharHeight() + fm.getDescent(); |
1288 |
|
|
1289 |
|
|
1290 |
|
|
1291 |
0 |
if (imgMapFile != null) |
1292 |
|
{ |
1293 |
0 |
try |
1294 |
|
{ |
1295 |
0 |
int sSize = av.getAlignment().getHeight(); |
1296 |
0 |
int alwidth = av.getAlignment().getWidth(); |
1297 |
0 |
PrintWriter out = new PrintWriter(new FileWriter(imgMapFile)); |
1298 |
0 |
out.println(HTMLOutput.getImageMapHTML()); |
1299 |
0 |
out.println("<img src=\"" + imageName |
1300 |
|
+ "\" border=\"0\" usemap=\"#Map\" >" |
1301 |
|
+ "<map name=\"Map\">"); |
1302 |
|
|
1303 |
0 |
for (int s = 0; s < sSize; s++) |
1304 |
|
{ |
1305 |
0 |
int sy = s * av.getCharHeight() + scaleHeight; |
1306 |
|
|
1307 |
0 |
SequenceI seq = av.getAlignment().getSequenceAt(s); |
1308 |
0 |
SequenceGroup[] groups = av.getAlignment().findAllGroups(seq); |
1309 |
0 |
for (int column = 0; column < alwidth; column++) |
1310 |
|
{ |
1311 |
0 |
StringBuilder text = new StringBuilder(512); |
1312 |
0 |
String triplet = null; |
1313 |
0 |
if (av.getAlignment().isNucleotide()) |
1314 |
|
{ |
1315 |
0 |
triplet = ResidueProperties.nucleotideName.get(seq |
1316 |
|
.getCharAt(column) + ""); |
1317 |
|
} |
1318 |
|
else |
1319 |
|
{ |
1320 |
0 |
triplet = ResidueProperties.aa2Triplet.get(seq.getCharAt(column) |
1321 |
|
+ ""); |
1322 |
|
} |
1323 |
|
|
1324 |
0 |
if (triplet == null) |
1325 |
|
{ |
1326 |
0 |
continue; |
1327 |
|
} |
1328 |
|
|
1329 |
0 |
int seqPos = seq.findPosition(column); |
1330 |
0 |
int gSize = groups.length; |
1331 |
0 |
for (int g = 0; g < gSize; g++) |
1332 |
|
{ |
1333 |
0 |
if (text.length() < 1) |
1334 |
|
{ |
1335 |
0 |
text.append("<area shape=\"rect\" coords=\"") |
1336 |
|
.append((idWidth + column * av.getCharWidth())) |
1337 |
|
.append(",").append(sy).append(",") |
1338 |
|
.append((idWidth + (column + 1) * av.getCharWidth())) |
1339 |
|
.append(",").append((av.getCharHeight() + sy)) |
1340 |
|
.append("\"").append(" onMouseOver=\"toolTip('") |
1341 |
|
.append(seqPos).append(" ").append(triplet); |
1342 |
|
} |
1343 |
|
|
1344 |
0 |
if (groups[g].getStartRes() < column |
1345 |
|
&& groups[g].getEndRes() > column) |
1346 |
|
{ |
1347 |
0 |
text.append("<br><em>").append(groups[g].getName()) |
1348 |
|
.append("</em>"); |
1349 |
|
} |
1350 |
|
} |
1351 |
|
|
1352 |
0 |
if (text.length() < 1) |
1353 |
|
{ |
1354 |
0 |
text.append("<area shape=\"rect\" coords=\"") |
1355 |
|
.append((idWidth + column * av.getCharWidth())) |
1356 |
|
.append(",").append(sy).append(",") |
1357 |
|
.append((idWidth + (column + 1) * av.getCharWidth())) |
1358 |
|
.append(",").append((av.getCharHeight() + sy)) |
1359 |
|
.append("\"").append(" onMouseOver=\"toolTip('") |
1360 |
|
.append(seqPos).append(" ").append(triplet); |
1361 |
|
} |
1362 |
0 |
if (!Comparison.isGap(seq.getCharAt(column))) |
1363 |
|
{ |
1364 |
0 |
List<SequenceFeature> features = seq.findFeatures(column, column); |
1365 |
0 |
for (SequenceFeature sf : features) |
1366 |
|
{ |
1367 |
0 |
if (sf.isContactFeature()) |
1368 |
|
{ |
1369 |
0 |
text.append("<br>").append(sf.getType()).append(" ") |
1370 |
|
.append(sf.getBegin()).append(":") |
1371 |
|
.append(sf.getEnd()); |
1372 |
|
} |
1373 |
|
else |
1374 |
|
{ |
1375 |
0 |
text.append("<br>"); |
1376 |
0 |
text.append(sf.getType()); |
1377 |
0 |
String description = sf.getDescription(); |
1378 |
0 |
if (description != null |
1379 |
|
&& !sf.getType().equals(description)) |
1380 |
|
{ |
1381 |
0 |
description = description.replace("\"", """); |
1382 |
0 |
text.append(" ").append(description); |
1383 |
|
} |
1384 |
|
} |
1385 |
0 |
String status = sf.getStatus(); |
1386 |
0 |
if (status != null && !"".equals(status)) |
1387 |
|
{ |
1388 |
0 |
text.append(" (").append(status).append(")"); |
1389 |
|
} |
1390 |
|
} |
1391 |
0 |
if (text.length() > 1) |
1392 |
|
{ |
1393 |
0 |
text.append("')\"; onMouseOut=\"toolTip()\"; href=\"#\">"); |
1394 |
0 |
out.println(text.toString()); |
1395 |
|
} |
1396 |
|
} |
1397 |
|
} |
1398 |
|
} |
1399 |
0 |
out.println("</map></body></html>"); |
1400 |
0 |
out.close(); |
1401 |
|
|
1402 |
|
} catch (Exception ex) |
1403 |
|
{ |
1404 |
0 |
ex.printStackTrace(); |
1405 |
|
} |
1406 |
|
} |
1407 |
|
|
1408 |
|
} |
1409 |
|
|
|
|
| 0% |
Uncovered Elements: 24 (24) |
Complexity: 6 |
Complexity Density: 0.38 |
|
1410 |
0 |
int getWrappedHeight()... |
1411 |
|
{ |
1412 |
0 |
int seqPanelWidth = getSeqPanel().seqCanvas.getWidth(); |
1413 |
|
|
1414 |
0 |
if (System.getProperty("java.awt.headless") != null |
1415 |
|
&& System.getProperty("java.awt.headless").equals("true")) |
1416 |
|
{ |
1417 |
0 |
seqPanelWidth = alignFrame.getWidth() - getVisibleIdWidth() |
1418 |
|
- vscroll.getPreferredSize().width |
1419 |
|
- alignFrame.getInsets().left - alignFrame.getInsets().right; |
1420 |
|
} |
1421 |
|
|
1422 |
0 |
int chunkWidth = getSeqPanel().seqCanvas |
1423 |
|
.getWrappedCanvasWidth(seqPanelWidth); |
1424 |
|
|
1425 |
0 |
int hgap = av.getCharHeight(); |
1426 |
0 |
if (av.getScaleAboveWrapped()) |
1427 |
|
{ |
1428 |
0 |
hgap += av.getCharHeight(); |
1429 |
|
} |
1430 |
|
|
1431 |
0 |
int annotationHeight = 0; |
1432 |
0 |
if (av.isShowAnnotation()) |
1433 |
|
{ |
1434 |
0 |
annotationHeight = getAnnotationPanel().adjustPanelHeight(); |
1435 |
|
} |
1436 |
|
|
1437 |
0 |
int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap |
1438 |
|
+ annotationHeight; |
1439 |
|
|
1440 |
0 |
int maxwidth = av.getAlignment().getWidth(); |
1441 |
0 |
if (av.hasHiddenColumns()) |
1442 |
|
{ |
1443 |
0 |
maxwidth = av.getAlignment().getHiddenColumns() |
1444 |
|
.absoluteToVisibleColumn(maxwidth) - 1; |
1445 |
|
} |
1446 |
|
|
1447 |
0 |
int height = ((maxwidth / chunkWidth) + 1) * cHeight; |
1448 |
|
|
1449 |
0 |
return height; |
1450 |
|
} |
1451 |
|
|
1452 |
|
|
1453 |
|
|
1454 |
|
|
1455 |
|
|
|
|
| 76.9% |
Uncovered Elements: 6 (26) |
Complexity: 4 |
Complexity Density: 0.2 |
|
1456 |
91 |
public void closePanel()... |
1457 |
|
{ |
1458 |
91 |
PaintRefresher.RemoveComponent(getSeqPanel().seqCanvas); |
1459 |
91 |
PaintRefresher.RemoveComponent(getIdPanel().getIdCanvas()); |
1460 |
91 |
PaintRefresher.RemoveComponent(this); |
1461 |
|
|
1462 |
91 |
closeChildFrames(); |
1463 |
|
|
1464 |
|
|
1465 |
|
|
1466 |
|
|
1467 |
91 |
if (annotationPanel != null) |
1468 |
|
{ |
1469 |
91 |
annotationPanel.dispose(); |
1470 |
91 |
annotationPanel = null; |
1471 |
|
} |
1472 |
|
|
1473 |
91 |
if (av != null) |
1474 |
|
{ |
1475 |
91 |
av.removePropertyChangeListener(propertyChangeListener); |
1476 |
91 |
propertyChangeListener = null; |
1477 |
91 |
StructureSelectionManager ssm = av.getStructureSelectionManager(); |
1478 |
91 |
ssm.removeStructureViewerListener(getSeqPanel(), null); |
1479 |
91 |
ssm.removeSelectionListener(getSeqPanel()); |
1480 |
91 |
ssm.removeCommandListener(av); |
1481 |
91 |
ssm.removeStructureViewerListener(getSeqPanel(), null); |
1482 |
91 |
ssm.removeSelectionListener(getSeqPanel()); |
1483 |
91 |
av.dispose(); |
1484 |
91 |
av = null; |
1485 |
|
} |
1486 |
|
else |
1487 |
|
{ |
1488 |
0 |
if (Cache.log.isDebugEnabled()) |
1489 |
|
{ |
1490 |
0 |
Cache.log.warn("Closing alignment panel which is already closed."); |
1491 |
|
} |
1492 |
|
} |
1493 |
|
} |
1494 |
|
|
1495 |
|
|
1496 |
|
|
1497 |
|
|
|
|
| 40% |
Uncovered Elements: 6 (10) |
Complexity: 3 |
Complexity Density: 0.5 |
|
1498 |
91 |
protected void closeChildFrames()... |
1499 |
|
{ |
1500 |
91 |
if (overviewPanel != null) |
1501 |
|
{ |
1502 |
0 |
overviewPanel.dispose(); |
1503 |
0 |
overviewPanel = null; |
1504 |
|
} |
1505 |
91 |
if (calculationDialog != null) |
1506 |
|
{ |
1507 |
0 |
calculationDialog.closeFrame(); |
1508 |
0 |
calculationDialog = null; |
1509 |
|
} |
1510 |
|
} |
1511 |
|
|
1512 |
|
|
1513 |
|
|
1514 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1515 |
45 |
public void updateAnnotation()... |
1516 |
|
{ |
1517 |
45 |
updateAnnotation(false, false); |
1518 |
|
} |
1519 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1520 |
0 |
public void updateAnnotation(boolean applyGlobalSettings)... |
1521 |
|
{ |
1522 |
0 |
updateAnnotation(applyGlobalSettings, false); |
1523 |
|
} |
1524 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
1525 |
117 |
public void updateAnnotation(boolean applyGlobalSettings,... |
1526 |
|
boolean preserveNewGroupSettings) |
1527 |
|
{ |
1528 |
117 |
av.updateGroupAnnotationSettings(applyGlobalSettings, |
1529 |
|
preserveNewGroupSettings); |
1530 |
117 |
adjustAnnotationHeight(); |
1531 |
|
} |
1532 |
|
|
|
|
| 66.7% |
Uncovered Elements: 1 (3) |
Complexity: 2 |
Complexity Density: 2 |
|
1533 |
3872 |
@Override... |
1534 |
|
public AlignmentI getAlignment() |
1535 |
|
{ |
1536 |
3872 |
return av == null ? null : av.getAlignment(); |
1537 |
|
} |
1538 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1539 |
52 |
@Override... |
1540 |
|
public String getViewName() |
1541 |
|
{ |
1542 |
52 |
return av.viewName; |
1543 |
|
} |
1544 |
|
|
1545 |
|
|
1546 |
|
|
1547 |
|
|
1548 |
|
@param |
1549 |
|
|
|
|
| 0% |
Uncovered Elements: 10 (10) |
Complexity: 4 |
Complexity Density: 0.67 |
|
1550 |
0 |
public void setSelected(boolean b)... |
1551 |
|
{ |
1552 |
0 |
try |
1553 |
|
{ |
1554 |
0 |
if (alignFrame.getSplitViewContainer() != null) |
1555 |
|
{ |
1556 |
|
|
1557 |
|
|
1558 |
|
|
1559 |
0 |
((SplitFrame) alignFrame.getSplitViewContainer()).setSelected(b); |
1560 |
|
} |
1561 |
0 |
alignFrame.setSelected(b); |
1562 |
|
} catch (Exception ex) |
1563 |
|
{ |
1564 |
|
} |
1565 |
|
|
1566 |
0 |
if (b) |
1567 |
|
{ |
1568 |
0 |
alignFrame.setDisplayedView(this); |
1569 |
|
} |
1570 |
|
} |
1571 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1572 |
19 |
@Override... |
1573 |
|
public StructureSelectionManager getStructureSelectionManager() |
1574 |
|
{ |
1575 |
19 |
return av.getStructureSelectionManager(); |
1576 |
|
} |
1577 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1578 |
0 |
@Override... |
1579 |
|
public void raiseOOMWarning(String string, OutOfMemoryError error) |
1580 |
|
{ |
1581 |
0 |
new OOMWarning(string, error, this); |
1582 |
|
} |
1583 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1584 |
8 |
@Override... |
1585 |
|
public jalview.api.FeatureRenderer cloneFeatureRenderer() |
1586 |
|
{ |
1587 |
|
|
1588 |
8 |
return new FeatureRenderer(this); |
1589 |
|
} |
1590 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1591 |
32 |
@Override... |
1592 |
|
public jalview.api.FeatureRenderer getFeatureRenderer() |
1593 |
|
{ |
1594 |
32 |
return seqPanel.seqCanvas.getFeatureRenderer(); |
1595 |
|
} |
1596 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1597 |
0 |
public void updateFeatureRenderer(... |
1598 |
|
jalview.renderer.seqfeatures.FeatureRenderer fr) |
1599 |
|
{ |
1600 |
0 |
fr.transferSettings(getSeqPanel().seqCanvas.getFeatureRenderer()); |
1601 |
|
} |
1602 |
|
|
|
|
| 0% |
Uncovered Elements: 4 (4) |
Complexity: 2 |
Complexity Density: 1 |
|
1603 |
0 |
public void updateFeatureRendererFrom(jalview.api.FeatureRenderer fr)... |
1604 |
|
{ |
1605 |
0 |
if (getSeqPanel().seqCanvas.getFeatureRenderer() != null) |
1606 |
|
{ |
1607 |
0 |
getSeqPanel().seqCanvas.getFeatureRenderer().transferSettings(fr); |
1608 |
|
} |
1609 |
|
} |
1610 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1611 |
217 |
public ScalePanel getScalePanel()... |
1612 |
|
{ |
1613 |
217 |
return scalePanel; |
1614 |
|
} |
1615 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1616 |
217 |
public void setScalePanel(ScalePanel scalePanel)... |
1617 |
|
{ |
1618 |
217 |
this.scalePanel = scalePanel; |
1619 |
|
} |
1620 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1621 |
5418 |
public SeqPanel getSeqPanel()... |
1622 |
|
{ |
1623 |
5418 |
return seqPanel; |
1624 |
|
} |
1625 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1626 |
217 |
public void setSeqPanel(SeqPanel seqPanel)... |
1627 |
|
{ |
1628 |
217 |
this.seqPanel = seqPanel; |
1629 |
|
} |
1630 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1631 |
2773 |
public AnnotationPanel getAnnotationPanel()... |
1632 |
|
{ |
1633 |
2773 |
return annotationPanel; |
1634 |
|
} |
1635 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1636 |
217 |
public void setAnnotationPanel(AnnotationPanel annotationPanel)... |
1637 |
|
{ |
1638 |
217 |
this.annotationPanel = annotationPanel; |
1639 |
|
} |
1640 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1641 |
3285 |
public AnnotationLabels getAlabels()... |
1642 |
|
{ |
1643 |
3285 |
return alabels; |
1644 |
|
} |
1645 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1646 |
217 |
public void setAlabels(AnnotationLabels alabels)... |
1647 |
|
{ |
1648 |
217 |
this.alabels = alabels; |
1649 |
|
} |
1650 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1651 |
2234 |
public IdPanel getIdPanel()... |
1652 |
|
{ |
1653 |
2234 |
return idPanel; |
1654 |
|
} |
1655 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1656 |
217 |
public void setIdPanel(IdPanel idPanel)... |
1657 |
|
{ |
1658 |
217 |
this.idPanel = idPanel; |
1659 |
|
} |
1660 |
|
|
1661 |
|
|
1662 |
|
|
1663 |
|
|
1664 |
|
|
1665 |
|
@param |
1666 |
|
|
1667 |
|
|
1668 |
|
@param |
1669 |
|
|
1670 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1671 |
0 |
protected void scrollToCentre(SearchResultsI sr, int verticalOffset)... |
1672 |
|
{ |
1673 |
0 |
scrollToPosition(sr, verticalOffset, true, true); |
1674 |
|
} |
1675 |
|
|
1676 |
|
|
1677 |
|
|
1678 |
|
|
1679 |
|
@param |
1680 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1681 |
908 |
protected void setToScrollComplementPanel(boolean b)... |
1682 |
|
{ |
1683 |
908 |
this.scrollComplementaryPanel = b; |
1684 |
|
} |
1685 |
|
|
1686 |
|
|
1687 |
|
|
1688 |
|
|
1689 |
|
@return |
1690 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1691 |
452 |
protected boolean isSetToScrollComplementPanel()... |
1692 |
|
{ |
1693 |
452 |
return this.scrollComplementaryPanel; |
1694 |
|
} |
1695 |
|
|
1696 |
|
|
1697 |
|
|
1698 |
|
|
1699 |
|
|
1700 |
|
|
1701 |
|
|
|
|
| 0% |
Uncovered Elements: 7 (7) |
Complexity: 2 |
Complexity Density: 0.4 |
|
1702 |
0 |
protected void refresh(boolean adjustHeight)... |
1703 |
|
{ |
1704 |
0 |
validateAnnotationDimensions(adjustHeight); |
1705 |
0 |
addNotify(); |
1706 |
0 |
if (adjustHeight) |
1707 |
|
{ |
1708 |
|
|
1709 |
0 |
paintAlignment(true, false); |
1710 |
|
} |
1711 |
|
else |
1712 |
|
{ |
1713 |
|
|
1714 |
0 |
repaint(); |
1715 |
|
} |
1716 |
|
} |
1717 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (10) |
Complexity: 2 |
Complexity Density: 0.25 |
|
1718 |
452 |
@Override... |
1719 |
|
|
1720 |
|
|
1721 |
|
|
1722 |
|
|
1723 |
|
public void propertyChange(PropertyChangeEvent evt) |
1724 |
|
{ |
1725 |
|
|
1726 |
452 |
ViewportRanges ranges = av.getRanges(); |
1727 |
452 |
int x = ranges.getStartRes(); |
1728 |
452 |
int y = ranges.getStartSeq(); |
1729 |
452 |
setScrollValues(x, y); |
1730 |
|
|
1731 |
|
|
1732 |
|
|
1733 |
452 |
if (isSetToScrollComplementPanel()) |
1734 |
|
{ |
1735 |
451 |
setToScrollComplementPanel(false); |
1736 |
451 |
av.scrollComplementaryAlignment(); |
1737 |
451 |
setToScrollComplementPanel(true); |
1738 |
|
} |
1739 |
|
} |
1740 |
|
|
1741 |
|
|
1742 |
|
|
1743 |
|
|
1744 |
|
|
1745 |
|
@param |
1746 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1747 |
0 |
public void setCalculationDialog(CalculationChooser calculationChooser)... |
1748 |
|
{ |
1749 |
0 |
calculationDialog = calculationChooser; |
1750 |
|
} |
1751 |
|
|
1752 |
|
|
1753 |
|
|
1754 |
|
|
1755 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1756 |
345 |
public CalculationChooser getCalculationDialog()... |
1757 |
|
{ |
1758 |
345 |
return calculationDialog; |
1759 |
|
} |
1760 |
|
} |