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Check for null colour
author
amwaterhouse
<Andrew Waterhouse>
Mon, 22 Aug 2005 17:10:39 +0000
(17:10 +0000)
committer
amwaterhouse
<Andrew Waterhouse>
Mon, 22 Aug 2005 17:10:39 +0000
(17:10 +0000)
src/jalview/appletgui/APopupMenu.java
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src/jalview/appletgui/AlignFrame.java
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src/jalview/appletgui/TreeCanvas.java
patch
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src/jalview/gui/AlignFrame.java
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src/jalview/gui/PopupMenu.java
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src/jalview/gui/TreeCanvas.java
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diff --git
a/src/jalview/appletgui/APopupMenu.java
b/src/jalview/appletgui/APopupMenu.java
index
abd76d6
..
80006c2
100755
(executable)
--- a/
src/jalview/appletgui/APopupMenu.java
+++ b/
src/jalview/appletgui/APopupMenu.java
@@
-379,6
+379,9
@@
public class APopupMenu
protected void abovePIDColour_itemStateChanged(ItemEvent ie)
\r
{
\r
SequenceGroup sg = getGroup();
\r
protected void abovePIDColour_itemStateChanged(ItemEvent ie)
\r
{
\r
SequenceGroup sg = getGroup();
\r
+ if(sg.cs==null)
\r
+ return;
\r
+
\r
if (abovePIDColour.getState())
\r
{
\r
sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
\r
if (abovePIDColour.getState())
\r
{
\r
sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
\r
@@
-435,6
+438,8
@@
public class APopupMenu
protected void conservationMenuItem_itemStateChanged(ItemEvent ie)
\r
{
\r
SequenceGroup sg = getGroup();
\r
protected void conservationMenuItem_itemStateChanged(ItemEvent ie)
\r
{
\r
SequenceGroup sg = getGroup();
\r
+ if(sg.cs==null)
\r
+ return;
\r
\r
if (conservationMenuItem.getState())
\r
{
\r
\r
if (conservationMenuItem.getState())
\r
{
\r
diff --git
a/src/jalview/appletgui/AlignFrame.java
b/src/jalview/appletgui/AlignFrame.java
index
6138257
..
010c73d
100755
(executable)
--- a/
src/jalview/appletgui/AlignFrame.java
+++ b/
src/jalview/appletgui/AlignFrame.java
@@
-879,10
+879,11
@@
public class AlignFrame
}
\r
}
\r
\r
}
\r
}
\r
\r
- if (viewport.getAbovePIDThreshold())
\r
+ if (viewport.getAbovePIDThreshold()
\r
+ || cs instanceof PIDColourScheme
\r
+ || cs instanceof Blosum62ColourScheme)
\r
{
\r
sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
{
\r
sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
-
\r
sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
\r
}
\r
\r
sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
\r
}
\r
\r
diff --git
a/src/jalview/appletgui/TreeCanvas.java
b/src/jalview/appletgui/TreeCanvas.java
index
a6bc5df
..
451d663
100755
(executable)
--- a/
src/jalview/appletgui/TreeCanvas.java
+++ b/
src/jalview/appletgui/TreeCanvas.java
@@
-490,8
+490,9
@@
System.out.println("called here");
false, 0, av.alignment.getWidth());
\r
\r
\r
false, 0, av.alignment.getWidth());
\r
\r
\r
- if (av.getGlobalColourScheme().conservationApplied())
\r
- {
\r
+ if ( av.getGlobalColourScheme()!=null
\r
+ && av.getGlobalColourScheme().conservationApplied())
\r
+ {
\r
Conservation c = new Conservation("Group",
\r
ResidueProperties.propHash, 3,
\r
sg.sequences, sg.getStartRes(),
\r
Conservation c = new Conservation("Group",
\r
ResidueProperties.propHash, 3,
\r
sg.sequences, sg.getStartRes(),
\r
diff --git
a/src/jalview/gui/AlignFrame.java
b/src/jalview/gui/AlignFrame.java
index
fc59062
..
692f258
100755
(executable)
--- a/
src/jalview/gui/AlignFrame.java
+++ b/
src/jalview/gui/AlignFrame.java
@@
-1448,7
+1448,9
@@
public class AlignFrame
}
\r
}
\r
\r
}
\r
}
\r
\r
- if (viewport.getAbovePIDThreshold())
\r
+ if (viewport.getAbovePIDThreshold()
\r
+ || cs instanceof PIDColourScheme
\r
+ || cs instanceof Blosum62ColourScheme)
\r
{
\r
sg.cs.setThreshold(threshold,
\r
viewport.getIgnoreGapsConsensus());
\r
{
\r
sg.cs.setThreshold(threshold,
\r
viewport.getIgnoreGapsConsensus());
\r
diff --git
a/src/jalview/gui/PopupMenu.java
b/src/jalview/gui/PopupMenu.java
index
137ca14
..
153e9fb
100755
(executable)
--- a/
src/jalview/gui/PopupMenu.java
+++ b/
src/jalview/gui/PopupMenu.java
@@
-606,6
+606,8
@@
public class PopupMenu extends JPopupMenu
protected void abovePIDColour_actionPerformed(ActionEvent e)
\r
{
\r
SequenceGroup sg = getGroup();
\r
protected void abovePIDColour_actionPerformed(ActionEvent e)
\r
{
\r
SequenceGroup sg = getGroup();
\r
+ if(sg.cs==null)
\r
+ return;
\r
\r
if (abovePIDColour.isSelected())
\r
{
\r
\r
if (abovePIDColour.isSelected())
\r
{
\r
@@
-696,6
+698,8
@@
public class PopupMenu extends JPopupMenu
protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
{
\r
SequenceGroup sg = getGroup();
\r
protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
{
\r
SequenceGroup sg = getGroup();
\r
+ if(sg.cs==null)
\r
+ return;
\r
\r
if (conservationMenuItem.isSelected())
\r
{
\r
\r
if (conservationMenuItem.isSelected())
\r
{
\r
diff --git
a/src/jalview/gui/TreeCanvas.java
b/src/jalview/gui/TreeCanvas.java
index
e923792
..
f0d63c4
100755
(executable)
--- a/
src/jalview/gui/TreeCanvas.java
+++ b/
src/jalview/gui/TreeCanvas.java
@@
-718,7
+718,8
@@
public class TreeCanvas extends JPanel implements MouseListener, Runnable,
sg.cs.setThreshold(25, av.getIgnoreGapsConsensus());
\r
}
\r
\r
sg.cs.setThreshold(25, av.getIgnoreGapsConsensus());
\r
}
\r
\r
- if (av.getGlobalColourScheme().conservationApplied())
\r
+ if ( av.getGlobalColourScheme()!=null
\r
+ && av.getGlobalColourScheme().conservationApplied())
\r
{
\r
Conservation c = new Conservation("Group",
\r
ResidueProperties.propHash, 3, sg.sequences,
\r
{
\r
Conservation c = new Conservation("Group",
\r
ResidueProperties.propHash, 3, sg.sequences,
\r