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package jalview.gui; |
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import java.awt.Color; |
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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.Point; |
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import java.awt.RenderingHints; |
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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.event.MouseEvent; |
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import java.awt.event.MouseListener; |
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import java.awt.event.MouseMotionListener; |
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import java.beans.PropertyChangeEvent; |
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import java.util.Iterator; |
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import java.util.List; |
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import javax.swing.JMenuItem; |
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import javax.swing.JPanel; |
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import javax.swing.JPopupMenu; |
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import javax.swing.ToolTipManager; |
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import jalview.api.AlignViewportI; |
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import jalview.datamodel.AlignedCodonFrame; |
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import jalview.datamodel.AlignmentI; |
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import jalview.datamodel.ColumnSelection; |
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import jalview.datamodel.HiddenColumns; |
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import jalview.datamodel.SearchResults; |
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import jalview.datamodel.SearchResultsI; |
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import jalview.datamodel.SequenceGroup; |
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import jalview.renderer.ScaleRenderer; |
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import jalview.renderer.ScaleRenderer.ScaleMark; |
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import jalview.structure.StructureSelectionManager; |
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import jalview.util.MappingUtils; |
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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 jalview.workers.AlignmentComparisonThread; |
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| 67% |
Uncovered Elements: 88 (267) |
Complexity: 59 |
Complexity Density: 0.33 |
|
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public class ScalePanel extends JPanel |
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implements MouseMotionListener, MouseListener, ViewportListenerI |
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{ |
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protected int offy = 4; |
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public int width; |
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protected AlignViewport av; |
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AlignmentPanel ap; |
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boolean stretchingGroup = false; |
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int min; |
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int max; |
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boolean mouseDragging = false; |
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int[] reveal; |
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@param |
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@param |
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| 100% |
Uncovered Elements: 0 (5) |
Complexity: 1 |
Complexity Density: 0.2 |
|
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public ScalePanel(AlignViewport av, AlignmentPanel ap)... |
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{ |
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this.av = av; |
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this.ap = ap; |
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addMouseListener(this); |
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addMouseMotionListener(this); |
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av.getRanges().addPropertyChangeListener(this); |
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} |
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@param |
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| 61.5% |
Uncovered Elements: 5 (13) |
Complexity: 3 |
Complexity Density: 0.33 |
|
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3 |
@Override... |
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public void mousePressed(MouseEvent evt) |
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{ |
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int res = ap.getSeqPanel().findAlignmentColumn(evt); |
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min = res; |
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max = res; |
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if (evt.isPopupTrigger()) |
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{ |
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rightMouseButtonPressed(evt, res); |
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return; |
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} |
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if (Platform.isWinRightButton(evt)) |
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{ |
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return; |
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} |
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leftMouseButtonPressed(evt, res); |
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} |
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@param |
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@param |
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| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
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protected void rightMouseButtonPressed(MouseEvent evt, final int res)... |
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{ |
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JPopupMenu pop = buildPopupMenu(res); |
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if (pop.getSubElements().length > 0) |
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{ |
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pop.show(this, evt.getX(), evt.getY()); |
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} |
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} |
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@param |
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@return |
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| 100% |
Uncovered Elements: 0 (21) |
Complexity: 4 |
Complexity Density: 0.27 |
|
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protected JPopupMenu buildPopupMenu(final int res)... |
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{ |
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JPopupMenu pop = new JPopupMenu(); |
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final int[] hiddenRange = reveal; |
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if (hiddenRange != null) |
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{ |
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JMenuItem item = new JMenuItem( |
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MessageManager.getString("label.reveal")); |
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item.addActionListener(new ActionListener() |
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{ |
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| 0% |
Uncovered Elements: 5 (5) |
Complexity: 1 |
Complexity Density: 0.2 |
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@Override... |
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public void actionPerformed(ActionEvent e) |
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{ |
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av.showColumn(hiddenRange[0]); |
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reveal = null; |
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ap.updateLayout(); |
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ap.paintAlignment(true, true); |
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av.sendSelection(); |
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} |
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}); |
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pop.add(item); |
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if (av.getAlignment().getHiddenColumns() |
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.hasMultiHiddenColumnRegions()) |
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{ |
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item = new JMenuItem(MessageManager.getString("action.reveal_all")); |
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item.addActionListener(new ActionListener() |
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{ |
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| 0% |
Uncovered Elements: 5 (5) |
Complexity: 1 |
Complexity Density: 0.2 |
|
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0 |
@Override... |
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public void actionPerformed(ActionEvent e) |
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{ |
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av.showAllHiddenColumns(); |
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reveal = null; |
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ap.updateLayout(); |
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ap.paintAlignment(true, true); |
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av.sendSelection(); |
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} |
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}); |
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pop.add(item); |
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} |
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} |
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if (av.getColumnSelection().contains(res)) |
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{ |
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JMenuItem item = new JMenuItem( |
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MessageManager.getString("label.hide_columns")); |
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item.addActionListener(new ActionListener() |
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{ |
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| 0% |
Uncovered Elements: 8 (8) |
Complexity: 3 |
Complexity Density: 0.5 |
|
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0 |
@Override... |
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public void actionPerformed(ActionEvent e) |
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{ |
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av.hideColumns(res, res); |
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if (av.getSelectionGroup() != null && av.getSelectionGroup() |
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.getSize() == av.getAlignment().getHeight()) |
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{ |
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av.setSelectionGroup(null); |
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} |
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ap.updateLayout(); |
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ap.paintAlignment(true, true); |
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av.sendSelection(); |
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} |
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}); |
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pop.add(item); |
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} |
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return pop; |
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} |
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@param |
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@param |
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| 56.5% |
Uncovered Elements: 10 (23) |
Complexity: 5 |
Complexity Density: 0.29 |
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protected void leftMouseButtonPressed(MouseEvent evt, final int res)... |
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{ |
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if (!Platform.isControlDown(evt) && !evt.isShiftDown()) |
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{ |
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av.getColumnSelection().clear(); |
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} |
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3 |
av.getColumnSelection().addElement(res); |
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3 |
SequenceGroup sg = new SequenceGroup(av.getAlignment().getSequences()); |
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sg.setStartRes(res); |
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sg.setEndRes(res); |
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3 |
if (evt.isShiftDown()) |
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{ |
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int min = Math.min(av.getColumnSelection().getMin(), res); |
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0 |
int max = Math.max(av.getColumnSelection().getMax(), res); |
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for (int i = min; i < max; i++) |
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{ |
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0 |
av.getColumnSelection().addElement(i); |
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} |
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sg.setStartRes(min); |
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sg.setEndRes(max); |
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} |
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3 |
av.setSelectionGroup(sg); |
272 |
3 |
ap.paintAlignment(false, false); |
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3 |
PaintRefresher.Refresh(this, av.getSequenceSetId()); |
274 |
3 |
av.sendSelection(); |
275 |
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} |
276 |
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277 |
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278 |
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279 |
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280 |
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281 |
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@param |
282 |
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| 70.3% |
Uncovered Elements: 11 (37) |
Complexity: 7 |
Complexity Density: 0.28 |
|
283 |
3 |
@Override... |
284 |
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public void mouseReleased(MouseEvent evt) |
285 |
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{ |
286 |
3 |
boolean wasDragging = mouseDragging; |
287 |
3 |
mouseDragging = false; |
288 |
3 |
ap.getSeqPanel().stopScrolling(); |
289 |
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|
290 |
3 |
int res = ap.getSeqPanel().findAlignmentColumn(evt); |
291 |
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|
292 |
3 |
if (!stretchingGroup) |
293 |
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{ |
294 |
0 |
if (evt.isPopupTrigger()) |
295 |
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{ |
296 |
0 |
rightMouseButtonPressed(evt, res); |
297 |
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} |
298 |
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else |
299 |
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{ |
300 |
0 |
ap.paintAlignment(false, false); |
301 |
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} |
302 |
0 |
return; |
303 |
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} |
304 |
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|
305 |
3 |
SequenceGroup sg = av.getSelectionGroup(); |
306 |
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|
307 |
3 |
if (sg != null) |
308 |
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{ |
309 |
3 |
if (res > sg.getStartRes()) |
310 |
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{ |
311 |
2 |
sg.setEndRes(res); |
312 |
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} |
313 |
1 |
else if (res < sg.getStartRes()) |
314 |
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{ |
315 |
0 |
sg.setStartRes(res); |
316 |
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} |
317 |
3 |
if (wasDragging) |
318 |
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{ |
319 |
3 |
min = Math.min(res, min); |
320 |
3 |
max = Math.max(res, max); |
321 |
3 |
av.getColumnSelection().stretchGroup(res, sg, min, max); |
322 |
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} |
323 |
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} |
324 |
3 |
stretchingGroup = false; |
325 |
3 |
ap.paintAlignment(false, false); |
326 |
3 |
av.isSelectionGroupChanged(true); |
327 |
3 |
av.isColSelChanged(true); |
328 |
3 |
PaintRefresher.Refresh(ap, av.getSequenceSetId()); |
329 |
3 |
av.sendSelection(); |
330 |
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} |
331 |
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334 |
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336 |
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337 |
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338 |
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339 |
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@param |
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| 92.3% |
Uncovered Elements: 1 (13) |
Complexity: 2 |
Complexity Density: 0.18 |
|
341 |
3 |
@Override... |
342 |
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public void mouseDragged(MouseEvent evt) |
343 |
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{ |
344 |
3 |
mouseDragging = true; |
345 |
3 |
int res = ap.getSeqPanel().findAlignmentColumn(evt); |
346 |
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|
347 |
3 |
ColumnSelection cs = av.getColumnSelection(); |
348 |
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|
349 |
3 |
min = Math.min(res, min); |
350 |
3 |
max = Math.max(res, max); |
351 |
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|
352 |
3 |
SequenceGroup sg = av.getSelectionGroup(); |
353 |
3 |
if (sg != null) |
354 |
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{ |
355 |
3 |
stretchingGroup = true; |
356 |
3 |
cs.stretchGroup(res, sg, min, max); |
357 |
3 |
ap.paintAlignment(false, false); |
358 |
3 |
PaintRefresher.Refresh(ap, av.getSequenceSetId()); |
359 |
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} |
360 |
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} |
361 |
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|
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|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
362 |
0 |
@Override... |
363 |
|
public void mouseEntered(MouseEvent evt) |
364 |
|
{ |
365 |
0 |
if (mouseDragging) |
366 |
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{ |
367 |
0 |
mouseDragging = false; |
368 |
0 |
ap.getSeqPanel().stopScrolling(); |
369 |
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} |
370 |
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} |
371 |
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372 |
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373 |
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374 |
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375 |
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|
376 |
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|
377 |
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| 0% |
Uncovered Elements: 4 (4) |
Complexity: 2 |
Complexity Density: 1 |
|
378 |
0 |
@Override... |
379 |
|
public void mouseExited(MouseEvent evt) |
380 |
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{ |
381 |
0 |
if (mouseDragging) |
382 |
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{ |
383 |
0 |
ap.getSeqPanel().startScrolling(new Point(evt.getX(), 0)); |
384 |
|
} |
385 |
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} |
386 |
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| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
387 |
0 |
@Override... |
388 |
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public void mouseClicked(MouseEvent evt) |
389 |
|
{ |
390 |
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} |
391 |
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|
392 |
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|
393 |
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|
394 |
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|
|
| 59.3% |
Uncovered Elements: 11 (27) |
Complexity: 5 |
Complexity Density: 0.26 |
|
395 |
8 |
@Override... |
396 |
|
public void mouseMoved(MouseEvent evt) |
397 |
|
{ |
398 |
8 |
this.setToolTipText(null); |
399 |
8 |
reveal = null; |
400 |
8 |
final int res = ap.getSeqPanel().findAlignmentColumn(evt); |
401 |
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|
402 |
8 |
highlightAllStructPos(res); |
403 |
8 |
if (av.getCalcManager().getRegisteredWorkersOfClass(AlignmentComparisonThread.class)!=null) |
404 |
|
{ |
405 |
0 |
AlignmentI alignment = av.getAlignment(); |
406 |
0 |
AlignViewportI codingComplement = av.getCodingComplement(); |
407 |
0 |
List<AlignedCodonFrame> ourMappings = alignment |
408 |
|
.getCodonFrames(); |
409 |
0 |
SearchResultsI mappedPos = MappingUtils.allMappedRegionsForColumn(res, |
410 |
|
ourMappings, alignment.getSequences(),codingComplement.getAlignment().getSequences(), |
411 |
|
alignment.getGapCharacter()); |
412 |
0 |
if (mappedPos.getCount()>0) |
413 |
|
{ |
414 |
0 |
Desktop.getAlignFrameFor(codingComplement).alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(mappedPos,true); |
415 |
|
} |
416 |
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|
417 |
|
} |
418 |
8 |
if (!av.hasHiddenColumns()) |
419 |
|
{ |
420 |
0 |
return; |
421 |
|
} |
422 |
8 |
reveal = av.getAlignment().getHiddenColumns() |
423 |
|
.getRegionWithEdgeAtRes(av.getAlignment().getHiddenColumns() |
424 |
|
.absoluteToVisibleColumn(res)); |
425 |
8 |
if (reveal == null) |
426 |
|
{ |
427 |
3 |
return; |
428 |
|
} |
429 |
5 |
ToolTipManager.sharedInstance().registerComponent(this); |
430 |
5 |
this.setToolTipText( |
431 |
|
MessageManager.getString("label.reveal_hidden_columns")); |
432 |
5 |
repaint(); |
433 |
|
} |
434 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
435 |
8 |
public void highlightAllStructPos(int col)... |
436 |
|
{ |
437 |
8 |
ap.getStructureSelectionManager().highlightPositionsOnMany( |
438 |
|
ap.av.getAlignment().getSequencesArray(), new int[] |
439 |
|
{ col, col }, ap); |
440 |
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|
441 |
|
} |
442 |
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|
443 |
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|
444 |
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|
445 |
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|
446 |
|
@param |
447 |
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|
448 |
|
|
|
|
| 75% |
Uncovered Elements: 1 (4) |
Complexity: 2 |
Complexity Density: 1 |
|
449 |
707 |
@Override... |
450 |
|
public void paintComponent(Graphics g) |
451 |
|
{ |
452 |
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|
453 |
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|
454 |
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|
455 |
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|
456 |
|
|
457 |
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|
458 |
707 |
if (!av.getWrapAlignment()) |
459 |
|
{ |
460 |
707 |
drawScale(g, av.getRanges().getStartRes(), av.getRanges().getEndRes(), |
461 |
|
getWidth(), getHeight()); |
462 |
|
} |
463 |
|
} |
464 |
|
|
465 |
|
|
|
|
| 85.5% |
Uncovered Elements: 10 (69) |
Complexity: 13 |
Complexity Density: 0.28 |
|
466 |
719 |
public void drawScale(Graphics g, int startx, int endx, int width,... |
467 |
|
int height) |
468 |
|
{ |
469 |
719 |
Graphics2D gg = (Graphics2D) g; |
470 |
719 |
gg.setFont(av.getFont()); |
471 |
|
|
472 |
719 |
if (av.antiAlias) |
473 |
|
{ |
474 |
510 |
gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING, |
475 |
|
RenderingHints.VALUE_ANTIALIAS_ON); |
476 |
|
} |
477 |
|
|
478 |
|
|
479 |
719 |
gg.setColor(Color.white); |
480 |
719 |
gg.fillRect(0, 0, width, height); |
481 |
719 |
gg.setColor(Color.black); |
482 |
|
|
483 |
|
|
484 |
719 |
ColumnSelection cs = av.getColumnSelection(); |
485 |
719 |
HiddenColumns hidden = av.getAlignment().getHiddenColumns(); |
486 |
719 |
int avCharWidth = av.getCharWidth(); |
487 |
719 |
int avCharHeight = av.getCharHeight(); |
488 |
|
|
489 |
719 |
if (cs != null) |
490 |
|
{ |
491 |
719 |
gg.setColor(new Color(220, 0, 0)); |
492 |
|
|
493 |
719 |
for (int sel : cs.getSelected()) |
494 |
|
{ |
495 |
|
|
496 |
|
|
497 |
|
|
498 |
42 |
if (av.hasHiddenColumns()) |
499 |
|
{ |
500 |
0 |
if (hidden.isVisible(sel)) |
501 |
|
{ |
502 |
0 |
sel = hidden.absoluteToVisibleColumn(sel); |
503 |
|
} |
504 |
|
else |
505 |
|
{ |
506 |
0 |
continue; |
507 |
|
} |
508 |
|
} |
509 |
|
|
510 |
42 |
if ((sel >= startx) && (sel <= endx)) |
511 |
|
{ |
512 |
42 |
gg.fillRect((sel - startx) * avCharWidth, 0, avCharWidth, |
513 |
|
getHeight()); |
514 |
|
} |
515 |
|
} |
516 |
|
} |
517 |
|
|
518 |
719 |
int widthx = 1 + endx - startx; |
519 |
|
|
520 |
719 |
FontMetrics fm = gg.getFontMetrics(av.getFont()); |
521 |
719 |
int y = avCharHeight; |
522 |
719 |
int yOf = fm.getDescent(); |
523 |
719 |
y -= yOf; |
524 |
719 |
if (av.hasHiddenColumns()) |
525 |
|
{ |
526 |
|
|
527 |
9 |
gg.setColor(Color.blue); |
528 |
9 |
int res; |
529 |
|
|
530 |
9 |
if (av.getShowHiddenMarkers()) |
531 |
|
{ |
532 |
9 |
Iterator<Integer> it = hidden.getStartRegionIterator(startx, |
533 |
|
startx + widthx + 1); |
534 |
20 |
while (it.hasNext()) |
535 |
|
{ |
536 |
11 |
res = it.next() - startx; |
537 |
|
|
538 |
11 |
gg.fillPolygon( |
539 |
|
new int[] |
540 |
|
{ -1 + res * avCharWidth - avCharHeight / 4, |
541 |
|
-1 + res * avCharWidth + avCharHeight / 4, |
542 |
|
-1 + res * avCharWidth }, |
543 |
|
new int[] |
544 |
|
{ y, y, y + 2 * yOf }, 3); |
545 |
|
} |
546 |
|
} |
547 |
|
} |
548 |
|
|
549 |
719 |
gg.setColor(Color.black); |
550 |
|
|
551 |
719 |
int maxX = 0; |
552 |
719 |
List<ScaleMark> marks = new ScaleRenderer().calculateMarks(av, startx, |
553 |
|
endx); |
554 |
|
|
555 |
719 |
for (ScaleMark mark : marks) |
556 |
|
{ |
557 |
1374 |
boolean major = mark.major; |
558 |
1374 |
int mpos = mark.column; |
559 |
1374 |
String mstring = mark.text; |
560 |
1374 |
if (mstring != null) |
561 |
|
{ |
562 |
649 |
if (mpos * avCharWidth > maxX) |
563 |
|
{ |
564 |
649 |
gg.drawString(mstring, mpos * avCharWidth, y); |
565 |
649 |
maxX = (mpos + 2) * avCharWidth + fm.stringWidth(mstring); |
566 |
|
} |
567 |
|
} |
568 |
1374 |
if (major) |
569 |
|
{ |
570 |
649 |
gg.drawLine((mpos * avCharWidth) + (avCharWidth / 2), y + 2, |
571 |
|
(mpos * avCharWidth) + (avCharWidth / 2), y + (yOf * 2)); |
572 |
|
} |
573 |
|
else |
574 |
|
{ |
575 |
725 |
gg.drawLine((mpos * avCharWidth) + (avCharWidth / 2), y + yOf, |
576 |
|
(mpos * avCharWidth) + (avCharWidth / 2), y + (yOf * 2)); |
577 |
|
} |
578 |
|
} |
579 |
|
} |
580 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (4) |
Complexity: 4 |
Complexity Density: 2 |
|
581 |
167 |
@Override... |
582 |
|
public void propertyChange(PropertyChangeEvent evt) |
583 |
|
{ |
584 |
|
|
585 |
|
|
586 |
|
|
587 |
|
|
588 |
|
|
589 |
|
|
590 |
167 |
if (evt.getPropertyName().equals(ViewportRanges.STARTRES) |
591 |
|
|| evt.getPropertyName().equals(ViewportRanges.STARTRESANDSEQ) |
592 |
|
|| evt.getPropertyName().equals(ViewportRanges.MOVE_VIEWPORT)) |
593 |
|
{ |
594 |
|
|
595 |
|
|
596 |
|
|
597 |
|
|
598 |
|
|
599 |
|
|
600 |
8 |
av.getAlignPanel().repaint(); |
601 |
|
} |
602 |
|
} |
603 |
|
|
604 |
|
} |