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trap NPE possiblity for trees that have no associated alignment panels (usually becau...
author
jprocter
<Jim Procter>
Wed, 8 Sep 2010 14:10:29 +0000
(14:10 +0000)
committer
jprocter
<Jim Procter>
Wed, 8 Sep 2010 14:10:29 +0000
(14:10 +0000)
src/jalview/gui/TreeCanvas.java
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diff --git
a/src/jalview/gui/TreeCanvas.java
b/src/jalview/gui/TreeCanvas.java
index
c2b9b7f
..
a66f251
100755
(executable)
--- a/
src/jalview/gui/TreeCanvas.java
+++ b/
src/jalview/gui/TreeCanvas.java
@@
-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());
}
@@
-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();
@@
-893,8
+894,9
@@
public class TreeCanvas extends JPanel implements MouseListener, Runnable,
{
if (av.getGlobalColourScheme() instanceof UserColourScheme)
{
{
if (av.getGlobalColourScheme() instanceof UserColourScheme)
{
- cs = new UserColourScheme(((UserColourScheme) av
- .getGlobalColourScheme()).getColours());
+ cs = new UserColourScheme(
+ ((UserColourScheme) av.getGlobalColourScheme())
+ .getColours());
}
else
}
else
@@
-904,8
+906,8
@@
public class TreeCanvas extends JPanel implements MouseListener, Runnable,
.getGlobalColourScheme()));
}
.getGlobalColourScheme()));
}
- cs.setThreshold(av.getGlobalColourScheme().getThreshold(), av
- .getIgnoreGapsConsensus());
+ cs.setThreshold(av.getGlobalColourScheme().getThreshold(),
+ av.getIgnoreGapsConsensus());
}
SequenceGroup sg = new SequenceGroup(sequences, null, cs, true, true,
}
SequenceGroup sg = new SequenceGroup(sequences, null, cs, true, true,
@@
-919,8
+921,8
@@
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.verdict(false, aps[a].av.ConsPercGaps);
c.calculate();
c.verdict(false, aps[a].av.ConsPercGaps);
@@
-931,7
+933,7
@@
public class TreeCanvas extends JPanel implements MouseListener, Runnable,
}
}
// 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();
}