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Merge branch 'bug/JAL-2791exportFilteredFeature' into merge/JAL-2791
[jalview.git]
/
src
/
jalview
/
gui
/
TreePanel.java
diff --git
a/src/jalview/gui/TreePanel.java
b/src/jalview/gui/TreePanel.java
index
2727db1
..
ca4f84e
100755
(executable)
--- a/
src/jalview/gui/TreePanel.java
+++ b/
src/jalview/gui/TreePanel.java
@@
-85,11
+85,11
@@
public class TreePanel extends GTreePanel
SimilarityParamsI similarityParams;
SimilarityParamsI similarityParams;
- TreeCanvas treeCanvas;
+ private TreeCanvas treeCanvas;
TreeModel tree;
TreeModel tree;
- AlignViewport av;
+ private AlignViewport av;
/**
* Creates a new TreePanel object.
/**
* Creates a new TreePanel object.
@@
-121,24
+121,24
@@
public class TreePanel extends GTreePanel
public AlignmentI getAlignment()
{
public AlignmentI getAlignment()
{
- return treeCanvas.av.getAlignment();
+ return getTreeCanvas().getViewport().getAlignment();
}
public AlignmentViewport getViewPort()
{
}
public AlignmentViewport getViewPort()
{
- return treeCanvas.av;
+ return getTreeCanvas().getViewport();
}
void initTreePanel(AlignmentPanel ap, String type, String modelName,
NewickFile newTree, AlignmentView inputData)
{
}
void initTreePanel(AlignmentPanel ap, String type, String modelName,
NewickFile newTree, AlignmentView inputData)
{
- av = ap.av;
+ setViewport(ap.av);
this.treeType = type;
this.scoreModelName = modelName;
treeCanvas = new TreeCanvas(this, ap, scrollPane);
this.treeType = type;
this.scoreModelName = modelName;
treeCanvas = new TreeCanvas(this, ap, scrollPane);
- scrollPane.setViewportView(treeCanvas);
+ scrollPane.setViewportView(getTreeCanvas());
PaintRefresher.Register(this, ap.av.getSequenceSetId());
PaintRefresher.Register(this, ap.av.getSequenceSetId());
@@
-155,9
+155,9
@@
public class TreePanel extends GTreePanel
@Override
public void internalFrameClosed(InternalFrameEvent evt)
{
@Override
public void internalFrameClosed(InternalFrameEvent evt)
{
- if (av != null)
+ if (getViewport() != null)
{
{
- av.removePropertyChangeListener(listener);
+ getViewport().removePropertyChangeListener(listener);
}
}
});
}
}
});
@@
-194,13
+194,13
@@
public class TreePanel extends GTreePanel
}
tree.updatePlaceHolders((List<SequenceI>) evt.getNewValue());
}
tree.updatePlaceHolders((List<SequenceI>) evt.getNewValue());
- treeCanvas.nameHash.clear(); // reset the mapping between canvas
+ getTreeCanvas().nameHash.clear(); // reset the mapping between canvas
// rectangles and leafnodes
repaint();
}
}
};
// rectangles and leafnodes
repaint();
}
}
};
- av.addPropertyChangeListener(listener);
+ getViewport().addPropertyChangeListener(listener);
return listener;
}
return listener;
}
@@
-213,8
+213,8
@@
public class TreePanel extends GTreePanel
void buildAssociatedViewMenu()
{
AlignmentPanel[] aps = PaintRefresher
void buildAssociatedViewMenu()
{
AlignmentPanel[] aps = PaintRefresher
- .getAssociatedPanels(av.getSequenceSetId());
- if (aps.length == 1 && treeCanvas.ap == aps[0])
+ .getAssociatedPanels(getViewport().getSequenceSetId());
+ if (aps.length == 1 && getTreeCanvas().getAssociatedPanel() == aps[0])
{
associateLeavesMenu.setVisible(false);
return;
{
associateLeavesMenu.setVisible(false);
return;
@@
-237,16
+237,16
@@
public class TreePanel extends GTreePanel
for (i = 0; i < iSize; i++)
{
final AlignmentPanel ap = aps[i];
for (i = 0; i < iSize; i++)
{
final AlignmentPanel ap = aps[i];
- item = new JRadioButtonMenuItem(ap.av.viewName, ap == treeCanvas.ap);
+ item = new JRadioButtonMenuItem(ap.av.getViewName(), ap == getTreeCanvas().getAssociatedPanel());
buttonGroup.add(item);
item.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent evt)
{
buttonGroup.add(item);
item.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent evt)
{
- treeCanvas.applyToAllViews = false;
- treeCanvas.ap = ap;
- treeCanvas.av = ap.av;
+ getTreeCanvas().applyToAllViews = false;
+ getTreeCanvas().setAssociatedPanel(ap);
+ getTreeCanvas().setViewport(ap.av);
PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId());
}
});
PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId());
}
});
@@
-257,13
+257,13
@@
public class TreePanel extends GTreePanel
final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
MessageManager.getString("label.all_views"));
buttonGroup.add(itemf);
final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
MessageManager.getString("label.all_views"));
buttonGroup.add(itemf);
- itemf.setSelected(treeCanvas.applyToAllViews);
+ itemf.setSelected(getTreeCanvas().applyToAllViews);
itemf.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent evt)
{
itemf.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent evt)
{
- treeCanvas.applyToAllViews = itemf.isSelected();
+ getTreeCanvas().applyToAllViews = itemf.isSelected();
}
});
associateLeavesMenu.add(itemf);
}
});
associateLeavesMenu.add(itemf);
@@
-296,7
+296,7
@@
public class TreePanel extends GTreePanel
if (newtree != null)
{
if (newtree != null)
{
- tree = new TreeModel(av.getAlignment().getSequencesArray(), odata,
+ tree = new TreeModel(getViewport().getAlignment().getSequencesArray(), odata,
newtree);
if (tree.getOriginalData() == null)
{
newtree);
if (tree.getOriginalData() == null)
{
@@
-306,20
+306,20
@@
public class TreePanel extends GTreePanel
else
{
ScoreModelI sm = ScoreModels.getInstance()
else
{
ScoreModelI sm = ScoreModels.getInstance()
- .getScoreModel(scoreModelName, treeCanvas.ap);
+ .getScoreModel(scoreModelName, getTreeCanvas().getAssociatedPanel());
TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING)
TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING)
- ? new NJTree(av, sm, similarityParams)
- : new AverageDistanceTree(av, sm, similarityParams);
+ ? new NJTree(getViewport(), sm, similarityParams)
+ : new AverageDistanceTree(getViewport(), sm, similarityParams);
tree = new TreeModel(njtree);
showDistances(true);
}
tree.reCount(tree.getTopNode());
tree.findHeight(tree.getTopNode());
tree = new TreeModel(njtree);
showDistances(true);
}
tree.reCount(tree.getTopNode());
tree.findHeight(tree.getTopNode());
- treeCanvas.setTree(tree);
- treeCanvas.repaint();
- av.setCurrentTree(tree);
- if (av.getSortByTree())
+ getTreeCanvas().setTree(tree);
+ getTreeCanvas().repaint();
+ getViewport().setCurrentTree(tree);
+ if (getViewport().getSortByTree())
{
sortByTree_actionPerformed();
}
{
sortByTree_actionPerformed();
}
@@
-328,20
+328,20
@@
public class TreePanel extends GTreePanel
public void showDistances(boolean b)
{
public void showDistances(boolean b)
{
- treeCanvas.setShowDistances(b);
+ getTreeCanvas().setShowDistances(b);
distanceMenu.setSelected(b);
}
public void showBootstrap(boolean b)
{
distanceMenu.setSelected(b);
}
public void showBootstrap(boolean b)
{
- treeCanvas.setShowBootstrap(b);
+ getTreeCanvas().setShowBootstrap(b);
bootstrapMenu.setSelected(b);
}
public void showPlaceholders(boolean b)
{
placeholdersMenu.setState(b);
bootstrapMenu.setSelected(b);
}
public void showPlaceholders(boolean b)
{
placeholdersMenu.setState(b);
- treeCanvas.setMarkPlaceholders(b);
+ getTreeCanvas().setMarkPlaceholders(b);
}
/**
}
/**
@@
-432,7
+432,7
@@
public class TreePanel extends GTreePanel
public void printMenu_actionPerformed(ActionEvent e)
{
// Putting in a thread avoids Swing painting problems
public void printMenu_actionPerformed(ActionEvent e)
{
// Putting in a thread avoids Swing painting problems
- treeCanvas.startPrinting();
+ getTreeCanvas().startPrinting();
}
@Override
}
@Override
@@
-456,7
+456,7
@@
public class TreePanel extends GTreePanel
{
// we try to get the associated view's gap character
// but this may fail if the view was closed...
{
// we try to get the associated view's gap character
// but this may fail if the view was closed...
- gc = av.getGapCharacter();
+ gc = getViewport().getGapCharacter();
} catch (Exception ex)
{
} catch (Exception ex)
{
@@
-469,8
+469,8
@@
public class TreePanel extends GTreePanel
// AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
// AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
- AlignmentI dataset = (av != null && av.getAlignment() != null)
- ? av.getAlignment().getDataset()
+ AlignmentI dataset = (getViewport() != null && getViewport().getAlignment() != null)
+ ? getViewport().getAlignment().getDataset()
: null;
if (dataset != null)
{
: null;
if (dataset != null)
{
@@
-507,7
+507,7
@@
public class TreePanel extends GTreePanel
@Override
public void fitToWindow_actionPerformed(ActionEvent e)
{
@Override
public void fitToWindow_actionPerformed(ActionEvent e)
{
- treeCanvas.fitToWindow = fitToWindow.isSelected();
+ getTreeCanvas().fitToWindow = fitToWindow.isSelected();
repaint();
}
repaint();
}
@@
-520,15
+520,15
@@
public class TreePanel extends GTreePanel
public void sortByTree_actionPerformed()
{
public void sortByTree_actionPerformed()
{
- if (treeCanvas.applyToAllViews)
+ if (getTreeCanvas().applyToAllViews)
{
final ArrayList<CommandI> commands = new ArrayList<>();
for (AlignmentPanel ap : PaintRefresher
{
final ArrayList<CommandI> commands = new ArrayList<>();
for (AlignmentPanel ap : PaintRefresher
- .getAssociatedPanels(av.getSequenceSetId()))
+ .getAssociatedPanels(getViewport().getSequenceSetId()))
{
commands.add(sortAlignmentIn(ap.av.getAlignPanel()));
}
{
commands.add(sortAlignmentIn(ap.av.getAlignPanel()));
}
- av.getAlignPanel().alignFrame.addHistoryItem(new CommandI()
+ getViewport().getAlignPanel().alignFrame.addHistoryItem(new CommandI()
{
@Override
{
@Override
@@
-563,7
+563,7
@@
public class TreePanel extends GTreePanel
}
});
for (AlignmentPanel ap : PaintRefresher
}
});
for (AlignmentPanel ap : PaintRefresher
- .getAssociatedPanels(av.getSequenceSetId()))
+ .getAssociatedPanels(getViewport().getSequenceSetId()))
{
// ensure all the alignFrames refresh their GI after adding an undo item
ap.alignFrame.updateEditMenuBar();
{
// ensure all the alignFrames refresh their GI after adding an undo item
ap.alignFrame.updateEditMenuBar();
@@
-571,8
+571,8
@@
public class TreePanel extends GTreePanel
}
else
{
}
else
{
- treeCanvas.ap.alignFrame
- .addHistoryItem(sortAlignmentIn(treeCanvas.ap));
+ getTreeCanvas().getAssociatedPanel().alignFrame
+ .addHistoryItem(sortAlignmentIn(getTreeCanvas().getAssociatedPanel()));
}
}
}
}
@@
-599,7
+599,7
@@
public class TreePanel extends GTreePanel
@Override
public void font_actionPerformed(ActionEvent e)
{
@Override
public void font_actionPerformed(ActionEvent e)
{
- if (treeCanvas == null)
+ if (getTreeCanvas() == null)
{
return;
}
{
return;
}
@@
-609,14
+609,14
@@
public class TreePanel extends GTreePanel
public Font getTreeFont()
{
public Font getTreeFont()
{
- return treeCanvas.font;
+ return getTreeCanvas().font;
}
public void setTreeFont(Font f)
{
}
public void setTreeFont(Font f)
{
- if (treeCanvas != null)
+ if (getTreeCanvas() != null)
{
{
- treeCanvas.setFont(f);
+ getTreeCanvas().setFont(f);
}
}
}
}
@@
-629,7
+629,7
@@
public class TreePanel extends GTreePanel
@Override
public void distanceMenu_actionPerformed(ActionEvent e)
{
@Override
public void distanceMenu_actionPerformed(ActionEvent e)
{
- treeCanvas.setShowDistances(distanceMenu.isSelected());
+ getTreeCanvas().setShowDistances(distanceMenu.isSelected());
}
/**
}
/**
@@
-641,7
+641,7
@@
public class TreePanel extends GTreePanel
@Override
public void bootstrapMenu_actionPerformed(ActionEvent e)
{
@Override
public void bootstrapMenu_actionPerformed(ActionEvent e)
{
- treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
+ getTreeCanvas().setShowBootstrap(bootstrapMenu.isSelected());
}
/**
}
/**
@@
-653,7
+653,7
@@
public class TreePanel extends GTreePanel
@Override
public void placeholdersMenu_actionPerformed(ActionEvent e)
{
@Override
public void placeholdersMenu_actionPerformed(ActionEvent e)
{
- treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
+ getTreeCanvas().setMarkPlaceholders(placeholdersMenu.isSelected());
}
/**
}
/**
@@
-691,8
+691,8
@@
public class TreePanel extends GTreePanel
accurateText = false;
}
accurateText = false;
}
- int width = treeCanvas.getWidth();
- int height = treeCanvas.getHeight();
+ int width = getTreeCanvas().getWidth();
+ int height = getTreeCanvas().getHeight();
try
{
try
{
@@
-720,7
+720,7
@@
public class TreePanel extends GTreePanel
pg.setAccurateTextMode(accurateText);
pg.setAccurateTextMode(accurateText);
- treeCanvas.draw(pg, width, height);
+ getTreeCanvas().draw(pg, width, height);
pg.flush();
pg.close();
pg.flush();
pg.close();
@@
-739,8
+739,8
@@
public class TreePanel extends GTreePanel
@Override
public void pngTree_actionPerformed(ActionEvent e)
{
@Override
public void pngTree_actionPerformed(ActionEvent e)
{
- int width = treeCanvas.getWidth();
- int height = treeCanvas.getHeight();
+ int width = getTreeCanvas().getWidth();
+ int height = getTreeCanvas().getHeight();
try
{
try
{
@@
-769,7
+769,7
@@
public class TreePanel extends GTreePanel
BufferedImage.TYPE_INT_RGB);
Graphics png = bi.getGraphics();
BufferedImage.TYPE_INT_RGB);
Graphics png = bi.getGraphics();
- treeCanvas.draw(png, width, height);
+ getTreeCanvas().draw(png, width, height);
ImageIO.write(bi, "png", out);
out.close();
ImageIO.write(bi, "png", out);
out.close();
@@
-879,8
+879,23
@@
public class TreePanel extends GTreePanel
/*
* put them together as <method> Using <model>
*/
/*
* put them together as <method> Using <model>
*/
- final String ttl = MessageManager.formatMessage("label.treecalc_title",
+ final String ttl = MessageManager.formatMessage("label.calc_title",
treecalcnm, smn);
return ttl;
}
treecalcnm, smn);
return ttl;
}
+
+ public AlignViewport getViewport()
+ {
+ return av;
+ }
+
+ public void setViewport(AlignViewport av)
+ {
+ this.av = av;
+ }
+
+ public TreeCanvas getTreeCanvas()
+ {
+ return treeCanvas;
+ }
}
}