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JAL-1118 - hack to try and get rid of flicker. consider moving greyed out image rende...
[jalview.git]
/
src
/
jalview
/
gui
/
TreeCanvas.java
diff --git
a/src/jalview/gui/TreeCanvas.java
b/src/jalview/gui/TreeCanvas.java
index
c2b9b7f
..
9f65511
100755
(executable)
--- a/
src/jalview/gui/TreeCanvas.java
+++ b/
src/jalview/gui/TreeCanvas.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-125,7
+125,7
@@
public class TreeCanvas extends JPanel implements MouseListener, Runnable,
aps[a].av.setSelectionGroup(selected);
}
aps[a].av.setSelectionGroup(selected);
}
- selected.setEndRes(aps[a].av.alignment.getWidth() - 1);
+ selected.setEndRes(aps[a].av.getAlignment().getWidth() - 1);
selected.addOrRemove(sequence, true);
}
}
selected.addOrRemove(sequence, true);
}
}
@@
-247,8
+247,7
@@
public class TreeCanvas extends JPanel implements MouseListener, Runnable,
}
String name = (markPlaceholders && node.isPlaceholder()) ? (PLACEHOLDER + node
}
String name = (markPlaceholders && node.isPlaceholder()) ? (PLACEHOLDER + node
- .getName())
- : node.getName();
+ .getName()) : node.getName();
int charWidth = fm.stringWidth(name) + 3;
int charHeight = font.getSize();
int charWidth = fm.stringWidth(name) + 3;
int charHeight = font.getSize();
@@
-487,9
+486,12
@@
public class TreeCanvas extends JPanel implements MouseListener, Runnable,
if (node.element() instanceof SequenceI)
{
AlignmentPanel[] aps = getAssociatedPanels();
if (node.element() instanceof SequenceI)
{
AlignmentPanel[] aps = getAssociatedPanels();
- for (int a = 0; a < aps.length; a++)
+ if (aps != null)
{
{
- aps[a].av.setSequenceColour((SequenceI) node.element(), c);
+ for (int a = 0; a < aps.length; a++)
+ {
+ aps[a].av.setSequenceColour((SequenceI) node.element(), c);
+ }
}
}
}
}
}
}
@@
-626,9
+628,8
@@
public class TreeCanvas extends JPanel implements MouseListener, Runnable,
}
else
{
}
else
{
- setPreferredSize(new Dimension(scrollPane.getWidth(), fm
- .getHeight()
- * nameHash.size()));
+ setPreferredSize(new Dimension(scrollPane.getWidth(),
+ fm.getHeight() * nameHash.size()));
draw(g, scrollPane.getWidth(), fm.getHeight() * nameHash.size());
}
draw(g, scrollPane.getWidth(), fm.getHeight() * nameHash.size());
}
@@
-850,7
+851,7
@@
public class TreeCanvas extends JPanel implements MouseListener, Runnable,
for (int a = 0; a < aps.length; a++)
{
aps[a].av.setSelectionGroup(null);
for (int a = 0; a < aps.length; a++)
{
aps[a].av.setSelectionGroup(null);
- aps[a].av.alignment.deleteAllGroups();
+ aps[a].av.getAlignment().deleteAllGroups();
aps[a].av.sequenceColours = null;
}
colourGroups();
aps[a].av.sequenceColours = null;
}
colourGroups();
@@
-867,12
+868,12
@@
public class TreeCanvas extends JPanel implements MouseListener, Runnable,
AlignmentPanel[] aps = getAssociatedPanels();
for (int i = 0; i < tree.getGroups().size(); i++)
{
AlignmentPanel[] aps = getAssociatedPanels();
for (int i = 0; i < tree.getGroups().size(); i++)
{
- Color col = new Color((int) (Math.random() * 255), (int) (Math
- .random() * 255), (int) (Math.random() * 255));
+ Color col = new Color((int) (Math.random() * 255),
+ (int) (Math.random() * 255), (int) (Math.random() * 255));
setColor((SequenceNode) tree.getGroups().elementAt(i), col.brighter());
setColor((SequenceNode) tree.getGroups().elementAt(i), col.brighter());
- Vector l = tree.findLeaves((SequenceNode) tree.getGroups().elementAt(
- i), new Vector());
+ Vector l = tree.findLeaves(
+ (SequenceNode) tree.getGroups().elementAt(i), new Vector());
Vector sequences = new Vector();
Vector sequences = new Vector();
@@
-888,29
+889,32
@@
public class TreeCanvas extends JPanel implements MouseListener, Runnable,
}
ColourSchemeI cs = null;
}
ColourSchemeI cs = null;
+ SequenceGroup sg = new SequenceGroup(sequences, null, cs, true, true,
+ false, 0, av.getAlignment().getWidth() - 1);
if (av.getGlobalColourScheme() != null)
{
if (av.getGlobalColourScheme() instanceof UserColourScheme)
{
if (av.getGlobalColourScheme() != null)
{
if (av.getGlobalColourScheme() instanceof UserColourScheme)
{
- cs = new UserColourScheme(((UserColourScheme) av
- .getGlobalColourScheme()).getColours());
+ cs = new UserColourScheme(
+ ((UserColourScheme) av.getGlobalColourScheme())
+ .getColours());
}
else
{
}
else
{
- cs = ColourSchemeProperty.getColour(sequences, av.alignment
- .getWidth(), ColourSchemeProperty.getColourName(av
+ cs = ColourSchemeProperty.getColour(sg, ColourSchemeProperty.getColourName(av
.getGlobalColourScheme()));
}
.getGlobalColourScheme()));
}
-
- cs.setThreshold(av.getGlobalColourScheme().getThreshold(), av
- .getIgnoreGapsConsensus());
+ // cs is null if shading is an annotationColourGradient
+ if (cs!=null)
+ {
+ cs.setThreshold(av.getGlobalColourScheme().getThreshold(),
+ av.getIgnoreGapsConsensus());
+ }
}
}
-
- SequenceGroup sg = new SequenceGroup(sequences, null, cs, true, true,
- false, 0, av.alignment.getWidth() - 1);
-
+ sg.cs=cs;
+// sg.recalcConservation();
sg.setName("JTreeGroup:" + sg.hashCode());
sg.setIdColour(col);
for (int a = 0; a < aps.length; a++)
sg.setName("JTreeGroup:" + sg.hashCode());
sg.setIdColour(col);
for (int a = 0; a < aps.length; a++)
@@
-919,21
+923,22
@@
public class TreeCanvas extends JPanel implements MouseListener, Runnable,
&& aps[a].av.getGlobalColourScheme().conservationApplied())
{
Conservation c = new Conservation("Group",
&& aps[a].av.getGlobalColourScheme().conservationApplied())
{
Conservation c = new Conservation("Group",
- ResidueProperties.propHash, 3, sg.getSequences(null), sg
- .getStartRes(), sg.getEndRes());
+ ResidueProperties.propHash, 3, sg.getSequences(null),
+ sg.getStartRes(), sg.getEndRes());
c.calculate();
c.calculate();
- c.verdict(false, aps[a].av.ConsPercGaps);
+ c.verdict(false, aps[a].av.getConsPercGaps());
sg.cs.setConservation(c);
}
sg.cs.setConservation(c);
}
- aps[a].av.alignment.addGroup(sg);
+ aps[a].av.getAlignment().addGroup(sg);
}
}
// notify the panel to redo any group specific stuff.
}
}
// notify the panel to redo any group specific stuff.
- for (int a=0;a<aps.length;a++)
+ for (int a = 0; a < aps.length; a++)
{
aps[a].updateAnnotation();
{
aps[a].updateAnnotation();
+ // TODO: JAL-868 - need to ensure view colour change message is broadcast to any Jmols listening in
}
}
}
}