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JAL-1065 JAL-1066 generic 'annotation collection updated' method called when alignmen...
author
jprocter
<jprocter@compbio.dundee.ac.uk>
Fri, 4 May 2012 15:46:07 +0000
(16:46 +0100)
committer
jprocter
<jprocter@compbio.dundee.ac.uk>
Fri, 4 May 2012 15:46:07 +0000
(16:46 +0100)
src/jalview/appletgui/AlignViewport.java
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src/jalview/datamodel/SequenceGroup.java
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src/jalview/gui/AlignViewport.java
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src/jalview/schemes/ColourSchemeI.java
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src/jalview/schemes/ResidueColourScheme.java
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diff --git
a/src/jalview/appletgui/AlignViewport.java
b/src/jalview/appletgui/AlignViewport.java
index
ff8f7df
..
46945b6
100644
(file)
--- a/
src/jalview/appletgui/AlignViewport.java
+++ b/
src/jalview/appletgui/AlignViewport.java
@@
-1478,6
+1478,7
@@
public class AlignViewport implements SelectionSource, VamsasSource
ColourSchemeI cs = globalColourScheme;
if (cs != null)
{
ColourSchemeI cs = globalColourScheme;
if (cs != null)
{
+ cs.alignmentChanged(alignment);
if (cs instanceof ClustalxColourScheme)
{
((ClustalxColourScheme) cs).resetClustalX(alignment.getSequences(),
if (cs instanceof ClustalxColourScheme)
{
((ClustalxColourScheme) cs).resetClustalX(alignment.getSequences(),
diff --git
a/src/jalview/datamodel/SequenceGroup.java
b/src/jalview/datamodel/SequenceGroup.java
index
94e359a
..
b0eabff
100755
(executable)
--- a/
src/jalview/datamodel/SequenceGroup.java
+++ b/
src/jalview/datamodel/SequenceGroup.java
@@
-477,7
+477,10
@@
public class SequenceGroup implements AnnotatedCollectionI
{
return;
}
{
return;
}
-
+ if (cs!=null)
+ {
+ cs.alignmentChanged(this);
+ }
try
{
Hashtable cnsns[] = AAFrequency.calculate(sequences, startRes,
try
{
Hashtable cnsns[] = AAFrequency.calculate(sequences, startRes,
diff --git
a/src/jalview/gui/AlignViewport.java
b/src/jalview/gui/AlignViewport.java
index
13f66d9
..
ac364b9
100644
(file)
--- a/
src/jalview/gui/AlignViewport.java
+++ b/
src/jalview/gui/AlignViewport.java
@@
-1763,6
+1763,7
@@
public class AlignViewport implements SelectionSource, VamsasSource
ColourSchemeI cs = globalColourScheme;
if (cs != null)
{
ColourSchemeI cs = globalColourScheme;
if (cs != null)
{
+ cs.alignmentChanged(alignment);
if (cs instanceof ClustalxColourScheme)
{
((ClustalxColourScheme) cs).resetClustalX(alignment.getSequences(),
if (cs instanceof ClustalxColourScheme)
{
((ClustalxColourScheme) cs).resetClustalX(alignment.getSequences(),
diff --git
a/src/jalview/schemes/ColourSchemeI.java
b/src/jalview/schemes/ColourSchemeI.java
index
b197906
..
273273f
100755
(executable)
--- a/
src/jalview/schemes/ColourSchemeI.java
+++ b/
src/jalview/schemes/ColourSchemeI.java
@@
-19,7
+19,9
@@
package jalview.schemes;
import java.awt.Color;
import java.awt.Color;
+import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceI;
import jalview.datamodel.SequenceI;
+
public interface ColourSchemeI
{
public Color findColour(char c);
public interface ColourSchemeI
{
public Color findColour(char c);
@@
-40,4
+42,6
@@
public interface ColourSchemeI
public void setThreshold(int ct, boolean ignoreGaps);
public void setThreshold(int ct, boolean ignoreGaps);
+ public void alignmentChanged(AnnotatedCollectionI alignment);
+
}
}
diff --git
a/src/jalview/schemes/ResidueColourScheme.java
b/src/jalview/schemes/ResidueColourScheme.java
index
5c0aa53
..
ea9e44b
100755
(executable)
--- a/
src/jalview/schemes/ResidueColourScheme.java
+++ b/
src/jalview/schemes/ResidueColourScheme.java
@@
-19,6
+19,7
@@
package jalview.schemes;
import jalview.analysis.AAFrequency;
import jalview.analysis.Conservation;
import jalview.analysis.AAFrequency;
import jalview.analysis.Conservation;
+import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceI;
import java.awt.Color;
import jalview.datamodel.SequenceI;
import java.awt.Color;
@@
-104,6
+105,7
@@
public class ResidueColourScheme implements ColourSchemeI
return currentColour;
}
return currentColour;
}
+ @Override public void alignmentChanged(AnnotatedCollectionI alignment) {};
/**
* Get the percentage threshold for this colour scheme
/**
* Get the percentage threshold for this colour scheme