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CurrentColour must not be accessed by multiple sequence renderers
author
amwaterhouse
<Andrew Waterhouse>
Tue, 28 Nov 2006 17:18:23 +0000
(17:18 +0000)
committer
amwaterhouse
<Andrew Waterhouse>
Tue, 28 Nov 2006 17:18:23 +0000
(17:18 +0000)
src/jalview/schemes/AnnotationColourGradient.java
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src/jalview/schemes/Blosum62ColourScheme.java
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src/jalview/schemes/ClustalxColourScheme.java
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src/jalview/schemes/NucleotideColourScheme.java
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src/jalview/schemes/PIDColourScheme.java
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src/jalview/schemes/ResidueColourScheme.java
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src/jalview/schemes/ScoreColourScheme.java
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src/jalview/schemes/UserColourScheme.java
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diff --git
a/src/jalview/schemes/AnnotationColourGradient.java
b/src/jalview/schemes/AnnotationColourGradient.java
index
8367cad
..
4a78aa1
100755
(executable)
--- a/
src/jalview/schemes/AnnotationColourGradient.java
+++ b/
src/jalview/schemes/AnnotationColourGradient.java
@@
-179,7
+179,7
@@
public class AnnotationColourGradient extends ResidueColourScheme
}
\r
\r
if(conservationColouring)
\r
}
\r
\r
if(conservationColouring)
\r
- applyConservation(currentColour, j);
\r
+ currentColour = applyConservation(currentColour, j);
\r
\r
return currentColour;
\r
}
\r
\r
return currentColour;
\r
}
\r
diff --git
a/src/jalview/schemes/Blosum62ColourScheme.java
b/src/jalview/schemes/Blosum62ColourScheme.java
index
d3b93bf
..
f2d2c98
100755
(executable)
--- a/
src/jalview/schemes/Blosum62ColourScheme.java
+++ b/
src/jalview/schemes/Blosum62ColourScheme.java
@@
-82,7
+82,7
@@
public class Blosum62ColourScheme
}
\r
\r
if(conservationColouring)
\r
}
\r
\r
if(conservationColouring)
\r
- applyConservation(currentColour, j);
\r
+ currentColour = applyConservation(currentColour, j);
\r
}
\r
else
\r
{
\r
}
\r
else
\r
{
\r
diff --git
a/src/jalview/schemes/ClustalxColourScheme.java
b/src/jalview/schemes/ClustalxColourScheme.java
index
ce30de8
..
4c20873
100755
(executable)
--- a/
src/jalview/schemes/ClustalxColourScheme.java
+++ b/
src/jalview/schemes/ClustalxColourScheme.java
@@
-281,7
+281,7
@@
public class ClustalxColourScheme
}
\r
\r
if(conservationColouring)
\r
}
\r
\r
if(conservationColouring)
\r
- applyConservation(currentColour, j);
\r
+ currentColour = applyConservation(currentColour, j);
\r
\r
return currentColour;
\r
}
\r
\r
return currentColour;
\r
}
\r
diff --git
a/src/jalview/schemes/NucleotideColourScheme.java
b/src/jalview/schemes/NucleotideColourScheme.java
index
f36bcad
..
4afb321
100755
(executable)
--- a/
src/jalview/schemes/NucleotideColourScheme.java
+++ b/
src/jalview/schemes/NucleotideColourScheme.java
@@
-78,7
+78,7
@@
public class NucleotideColourScheme extends ResidueColourScheme
}
\r
\r
if(conservationColouring)
\r
}
\r
\r
if(conservationColouring)
\r
- applyConservation(currentColour, j);
\r
+ currentColour = applyConservation(currentColour, j);
\r
\r
return currentColour;
\r
}
\r
\r
return currentColour;
\r
}
\r
diff --git
a/src/jalview/schemes/PIDColourScheme.java
b/src/jalview/schemes/PIDColourScheme.java
index
b287384
..
9bd092e
100755
(executable)
--- a/
src/jalview/schemes/PIDColourScheme.java
+++ b/
src/jalview/schemes/PIDColourScheme.java
@@
-83,7
+83,7
@@
public class PIDColourScheme
}
\r
\r
if(conservationColouring)
\r
}
\r
\r
if(conservationColouring)
\r
- applyConservation(currentColour, j);
\r
+ currentColour = applyConservation(currentColour, j);
\r
\r
return currentColour;
\r
}
\r
\r
return currentColour;
\r
}
\r
diff --git
a/src/jalview/schemes/ResidueColourScheme.java
b/src/jalview/schemes/ResidueColourScheme.java
index
bf83665
..
b905c45
100755
(executable)
--- a/
src/jalview/schemes/ResidueColourScheme.java
+++ b/
src/jalview/schemes/ResidueColourScheme.java
@@
-97,7
+97,7
@@
public class ResidueColourScheme implements ColourSchemeI
}
\r
\r
if(conservationColouring)
\r
}
\r
\r
if(conservationColouring)
\r
- applyConservation(currentColour, j);
\r
+ currentColour = applyConservation(currentColour, j);
\r
\r
\r
return currentColour;
\r
\r
\r
return currentColour;
\r
@@
-221,7
+221,7
@@
public class ResidueColourScheme implements ColourSchemeI
* @return DOCUMENT ME!
\r
*/
\r
\r
* @return DOCUMENT ME!
\r
*/
\r
\r
- void applyConservation(Color currentColour, int i)
\r
+ Color applyConservation(Color currentColour, int i)
\r
{
\r
\r
if ((conservation[i] != '*') && (conservation[i] != '+'))
\r
{
\r
\r
if ((conservation[i] != '*') && (conservation[i] != '+'))
\r
@@
-235,8
+235,7
@@
public class ResidueColourScheme implements ColourSchemeI
float t = 11 - (conservation[i] - '0');
\r
if(t==0)
\r
{
\r
float t = 11 - (conservation[i] - '0');
\r
if(t==0)
\r
{
\r
- currentColour = Color.white;
\r
- return;
\r
+ return Color.white;
\r
}
\r
\r
int red = currentColour.getRed();
\r
}
\r
\r
int red = currentColour.getRed();
\r
@@
-261,6
+260,7
@@
public class ResidueColourScheme implements ColourSchemeI
currentColour = new Color(red, green, blue);
\r
}
\r
}
\r
currentColour = new Color(red, green, blue);
\r
}
\r
}
\r
+ return currentColour;
\r
}
\r
\r
\r
}
\r
\r
\r
diff --git
a/src/jalview/schemes/ScoreColourScheme.java
b/src/jalview/schemes/ScoreColourScheme.java
index
c9f7fc8
..
4cd9fd3
100755
(executable)
--- a/
src/jalview/schemes/ScoreColourScheme.java
+++ b/
src/jalview/schemes/ScoreColourScheme.java
@@
-102,7
+102,7
@@
public class ScoreColourScheme extends ResidueColourScheme
Color currentColour = colors[ ResidueProperties.aaIndex[c] ];
\r
\r
if(conservationColouring)
\r
Color currentColour = colors[ ResidueProperties.aaIndex[c] ];
\r
\r
if(conservationColouring)
\r
- applyConservation(currentColour, j);
\r
+ currentColour = applyConservation(currentColour, j);
\r
\r
return currentColour;
\r
}
\r
\r
return currentColour;
\r
}
\r
diff --git
a/src/jalview/schemes/UserColourScheme.java
b/src/jalview/schemes/UserColourScheme.java
index
9d61279
..
c029b31
100755
(executable)
--- a/
src/jalview/schemes/UserColourScheme.java
+++ b/
src/jalview/schemes/UserColourScheme.java
@@
-204,7
+204,7
@@
public class UserColourScheme
}
\r
\r
if(conservationColouring)
\r
}
\r
\r
if(conservationColouring)
\r
- applyConservation(currentColour, j);
\r
+ currentColour = applyConservation(currentColour, j);
\r
\r
\r
return currentColour;
\r
\r
\r
return currentColour;
\r