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JAL-1065 JAL-1066 - use direct object reference rather then index into alignment
author
jprocter
<jprocter@compbio.dundee.ac.uk>
Fri, 4 May 2012 15:43:09 +0000
(16:43 +0100)
committer
jprocter
<jprocter@compbio.dundee.ac.uk>
Fri, 4 May 2012 15:43:09 +0000
(16:43 +0100)
13 files changed:
src/jalview/appletgui/SequenceRenderer.java
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src/jalview/appletgui/UserDefinedColours.java
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src/jalview/gui/SequenceRenderer.java
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src/jalview/gui/UserDefinedColours.java
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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/ColourSchemeI.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/appletgui/SequenceRenderer.java
b/src/jalview/appletgui/SequenceRenderer.java
index
32ff59a
..
2bd3a9e
100755
(executable)
--- a/
src/jalview/appletgui/SequenceRenderer.java
+++ b/
src/jalview/appletgui/SequenceRenderer.java
@@
-87,7
+87,7
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
{
if (cs != null)
{
{
if (cs != null)
{
- resBoxColour = cs.findColour(seq.getCharAt(i), i, seq.getIndex());
+ resBoxColour = cs.findColour(seq.getCharAt(i), i, seq);
}
else if (forOverview
&& !jalview.util.Comparison.isGap(seq.getCharAt(i)))
}
else if (forOverview
&& !jalview.util.Comparison.isGap(seq.getCharAt(i)))
diff --git
a/src/jalview/appletgui/UserDefinedColours.java
b/src/jalview/appletgui/UserDefinedColours.java
index
4ebe3b7
..
19ca45d
100755
(executable)
--- a/
src/jalview/appletgui/UserDefinedColours.java
+++ b/
src/jalview/appletgui/UserDefinedColours.java
@@
-397,7
+397,7
@@
public class UserDefinedColours extends Panel implements ActionListener,
{
try
{
{
try
{
- col = oldColourScheme.findColour(aa.charAt(0), -1, -1);
+ col = oldColourScheme.findColour(aa.charAt(0), -1, null);
} catch (Exception ex)
{
}
} catch (Exception ex)
{
}
diff --git
a/src/jalview/gui/SequenceRenderer.java
b/src/jalview/gui/SequenceRenderer.java
index
15f1928
..
9c25e0d
100755
(executable)
--- a/
src/jalview/gui/SequenceRenderer.java
+++ b/
src/jalview/gui/SequenceRenderer.java
@@
-115,7
+115,7
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
{
if (cs != null)
{
{
if (cs != null)
{
- resBoxColour = cs.findColour(seq.getCharAt(i), i, seq.getIndex());
+ resBoxColour = cs.findColour(seq.getCharAt(i), i, seq);
}
else if (forOverview
&& !jalview.util.Comparison.isGap(seq.getCharAt(i)))
}
else if (forOverview
&& !jalview.util.Comparison.isGap(seq.getCharAt(i)))
diff --git
a/src/jalview/gui/UserDefinedColours.java
b/src/jalview/gui/UserDefinedColours.java
index
8566e82
..
ca60354
100755
(executable)
--- a/
src/jalview/gui/UserDefinedColours.java
+++ b/
src/jalview/gui/UserDefinedColours.java
@@
-386,7
+386,7
@@
public class UserDefinedColours extends GUserDefinedColours implements
{
try
{
{
try
{
- col = oldColourScheme.findColour(aa.charAt(0), -1, -1);
+ col = oldColourScheme.findColour(aa.charAt(0), -1, null);
} catch (Exception ex)
{
}
} catch (Exception ex)
{
}
diff --git
a/src/jalview/schemes/AnnotationColourGradient.java
b/src/jalview/schemes/AnnotationColourGradient.java
index
5d12cce
..
b0365ce
100755
(executable)
--- a/
src/jalview/schemes/AnnotationColourGradient.java
+++ b/
src/jalview/schemes/AnnotationColourGradient.java
@@
-19,6
+19,7
@@
package jalview.schemes;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.GraphLine;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.GraphLine;
+import jalview.datamodel.SequenceI;
import java.awt.Color;
import java.awt.Color;
@@
-154,7
+155,7
@@
public class AnnotationColourGradient extends ResidueColourScheme
* @return DOCUMENT ME!
*/
@Override
* @return DOCUMENT ME!
*/
@Override
- public Color findColour(char c, int j, int sequenceIndex)
+ public Color findColour(char c, int j, SequenceI seq)
{
Color currentColour = Color.white;
{
Color currentColour = Color.white;
@@
-204,7
+205,7
@@
public class AnnotationColourGradient extends ResidueColourScheme
if (colourScheme != null)
{
if (colourScheme != null)
{
- currentColour = colourScheme.findColour(c, j, sequenceIndex);
+ currentColour = colourScheme.findColour(c, j, seq);
}
else if (range != 0)
{
}
else if (range != 0)
{
diff --git
a/src/jalview/schemes/Blosum62ColourScheme.java
b/src/jalview/schemes/Blosum62ColourScheme.java
index
c511ded
..
27b8996
100755
(executable)
--- a/
src/jalview/schemes/Blosum62ColourScheme.java
+++ b/
src/jalview/schemes/Blosum62ColourScheme.java
@@
-20,7
+20,7
@@
package jalview.schemes;
import jalview.analysis.AAFrequency;
import java.awt.Color;
import jalview.analysis.AAFrequency;
import java.awt.Color;
-
+import jalview.datamodel.SequenceI;
public class Blosum62ColourScheme extends ResidueColourScheme
{
public Blosum62ColourScheme()
public class Blosum62ColourScheme extends ResidueColourScheme
{
public Blosum62ColourScheme()
@@
-29,7
+29,7
@@
public class Blosum62ColourScheme extends ResidueColourScheme
}
@Override
}
@Override
- public Color findColour(char res, int j, int sequenceIndex)
+ public Color findColour(char res, int j, SequenceI seq)
{
if ('a' <= res && res <= 'z')
{
{
if ('a' <= res && res <= 'z')
{
diff --git
a/src/jalview/schemes/ClustalxColourScheme.java
b/src/jalview/schemes/ClustalxColourScheme.java
index
ad6d37f
..
7258605
100755
(executable)
--- a/
src/jalview/schemes/ClustalxColourScheme.java
+++ b/
src/jalview/schemes/ClustalxColourScheme.java
@@
-258,7
+258,7
@@
public class ClustalxColourScheme extends ResidueColourScheme // implements
}
@Override
}
@Override
- public Color findColour(char c, int j, int sequenceIndex)
+ public Color findColour(char c, int j, SequenceI seq)
{
Color currentColour;
{
Color currentColour;
diff --git
a/src/jalview/schemes/ColourSchemeI.java
b/src/jalview/schemes/ColourSchemeI.java
index
e8e5828
..
b197906
100755
(executable)
--- a/
src/jalview/schemes/ColourSchemeI.java
+++ b/
src/jalview/schemes/ColourSchemeI.java
@@
-19,11
+19,12
@@
package jalview.schemes;
import java.awt.Color;
import java.awt.Color;
+import jalview.datamodel.SequenceI;
public interface ColourSchemeI
{
public Color findColour(char c);
public interface ColourSchemeI
{
public Color findColour(char c);
- public Color findColour(char c, int j, int sequenceIndex);
+ public Color findColour(char c, int j, SequenceI seq);
public void setConsensus(java.util.Hashtable[] h);
public void setConsensus(java.util.Hashtable[] h);
diff --git
a/src/jalview/schemes/NucleotideColourScheme.java
b/src/jalview/schemes/NucleotideColourScheme.java
index
df4d9a9
..
1de5764
100755
(executable)
--- a/
src/jalview/schemes/NucleotideColourScheme.java
+++ b/
src/jalview/schemes/NucleotideColourScheme.java
@@
-17,6
+17,8
@@
*/
package jalview.schemes;
*/
package jalview.schemes;
+import jalview.datamodel.SequenceI;
+
import java.awt.Color;
/**
import java.awt.Color;
/**
@@
-61,7
+63,7
@@
public class NucleotideColourScheme extends ResidueColourScheme
* @return DOCUMENT ME!
*/
@Override
* @return DOCUMENT ME!
*/
@Override
- public Color findColour(char c, int j, int sequenceIndex)
+ public Color findColour(char c, int j, SequenceI seq)
{
Color currentColour;
if ((threshold == 0) || aboveThreshold(c, j))
{
Color currentColour;
if ((threshold == 0) || aboveThreshold(c, j))
diff --git
a/src/jalview/schemes/PIDColourScheme.java
b/src/jalview/schemes/PIDColourScheme.java
index
c4f7eb5
..
a64bf20
100755
(executable)
--- a/
src/jalview/schemes/PIDColourScheme.java
+++ b/
src/jalview/schemes/PIDColourScheme.java
@@
-19,6
+19,7
@@
package jalview.schemes;
import jalview.analysis.AAFrequency;
import jalview.datamodel.SequenceGroup;
import jalview.analysis.AAFrequency;
import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
import java.awt.Color;
import java.awt.Color;
@@
-38,7
+39,7
@@
public class PIDColourScheme extends ResidueColourScheme
@Override
@Override
- public Color findColour(char c, int j, int sequenceIndex)
+ public Color findColour(char c, int j, SequenceI seq)
{
if ('a' <= c && c <= 'z')
{
{
if ('a' <= c && c <= 'z')
{
diff --git
a/src/jalview/schemes/ResidueColourScheme.java
b/src/jalview/schemes/ResidueColourScheme.java
index
cc7f0d8
..
5c0aa53
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.SequenceI;
import java.awt.Color;
import java.util.Hashtable;
import java.awt.Color;
import java.util.Hashtable;
@@
-83,7
+84,7
@@
public class ResidueColourScheme implements ColourSchemeI
}
@Override
}
@Override
- public Color findColour(char c, int j, int sequenceIndex)
+ public Color findColour(char c, int j, SequenceI seq)
{
Color currentColour;
{
Color currentColour;
diff --git
a/src/jalview/schemes/ScoreColourScheme.java
b/src/jalview/schemes/ScoreColourScheme.java
index
49aeeeb
..
7cd5cb6
100755
(executable)
--- a/
src/jalview/schemes/ScoreColourScheme.java
+++ b/
src/jalview/schemes/ScoreColourScheme.java
@@
-17,6
+17,8
@@
*/
package jalview.schemes;
*/
package jalview.schemes;
+import jalview.datamodel.SequenceI;
+
import java.awt.Color;
/**
import java.awt.Color;
/**
@@
-86,7
+88,7
@@
public class ScoreColourScheme extends ResidueColourScheme
* @return DOCUMENT ME!
*/
@Override
* @return DOCUMENT ME!
*/
@Override
- public Color findColour(char c, int j, int sequenceIndex)
+ public Color findColour(char c, int j, SequenceI seq)
{
if (threshold > 0)
{
{
if (threshold > 0)
{
diff --git
a/src/jalview/schemes/UserColourScheme.java
b/src/jalview/schemes/UserColourScheme.java
index
0c1e688
..
62dfec5
100755
(executable)
--- a/
src/jalview/schemes/UserColourScheme.java
+++ b/
src/jalview/schemes/UserColourScheme.java
@@
-19,6
+19,7
@@
package jalview.schemes;
import java.awt.Color;
import java.util.StringTokenizer;
import java.awt.Color;
import java.util.StringTokenizer;
+import jalview.datamodel.SequenceI;
public class UserColourScheme extends ResidueColourScheme
{
public class UserColourScheme extends ResidueColourScheme
{
@@
-201,7
+202,7
@@
public class UserColourScheme extends ResidueColourScheme
}
@Override
}
@Override
- public Color findColour(char c, int j, int sequenceIndex)
+ public Color findColour(char c, int j, SequenceI seq)
{
Color currentColour;
int index = ResidueProperties.aaIndex[c];
{
Color currentColour;
int index = ResidueProperties.aaIndex[c];