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JAL-4235 JAL-3599 Try and report Eclipse Product Version for jalviewjsTranspile....
[jalview.git]
/
src
/
jalview
/
schemes
/
ClustalxColourScheme.java
diff --git
a/src/jalview/schemes/ClustalxColourScheme.java
b/src/jalview/schemes/ClustalxColourScheme.java
index
f13a90c
..
5a2d5dc
100755
(executable)
--- a/
src/jalview/schemes/ClustalxColourScheme.java
+++ b/
src/jalview/schemes/ClustalxColourScheme.java
@@
-20,15
+20,16
@@
*/
package jalview.schemes;
*/
package jalview.schemes;
+import java.awt.Color;
+import java.util.List;
+import java.util.Map;
+
+import jalview.api.AlignViewportI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
import jalview.util.Comparison;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
import jalview.util.Comparison;
-import java.awt.Color;
-import java.util.List;
-import java.util.Map;
-
public class ClustalxColourScheme extends ResidueColourScheme
{
private static final int EIGHTY_FIVE = 85;
public class ClustalxColourScheme extends ResidueColourScheme
{
private static final int EIGHTY_FIVE = 85;
@@
-43,8
+44,8
@@
public class ClustalxColourScheme extends ResidueColourScheme
{
RED(0.9f, 0.2f, 0.1f), BLUE(0.5f, 0.7f, 0.9f), GREEN(0.1f, 0.8f, 0.1f),
ORANGE(0.9f, 0.6f, 0.3f), CYAN(0.1f, 0.7f, 0.7f),
{
RED(0.9f, 0.2f, 0.1f), BLUE(0.5f, 0.7f, 0.9f), GREEN(0.1f, 0.8f, 0.1f),
ORANGE(0.9f, 0.6f, 0.3f), CYAN(0.1f, 0.7f, 0.7f),
- PINK(0.9f, 0.5f, 0.5f), MAGENTA(0.8f, 0.3f, 0.8f), YELLOW(0.8f, 0.8f,
- 0.0f);
+ PINK(0.9f, 0.5f, 0.5f), MAGENTA(0.8f, 0.3f, 0.8f),
+ YELLOW(0.8f, 0.8f, 0.0f);
final Color colour;
final Color colour;
@@
-53,6
+54,7
@@
public class ClustalxColourScheme extends ResidueColourScheme
colour = new Color(r, g, b);
}
}
colour = new Color(r, g, b);
}
}
+
private class ConsensusColour
{
Consensus[] cons;
private class ConsensusColour
{
Consensus[] cons;
@@
-93,7
+95,7
@@
public class ClustalxColourScheme extends ResidueColourScheme
}
@Override
}
@Override
- public void alignmentChanged(AnnotatedCollectionI alignment,
+ public synchronized void alignmentChanged(AnnotatedCollectionI alignment,
Map<SequenceI, SequenceCollectionI> hiddenReps)
{
int maxWidth = alignment.getWidth();
Map<SequenceI, SequenceCollectionI> hiddenReps)
{
int maxWidth = alignment.getWidth();
@@
-106,19
+108,18
@@
public class ClustalxColourScheme extends ResidueColourScheme
for (SequenceI sq : seqs)
{
for (SequenceI sq : seqs)
{
- char[] seq = sq.getSequence();
-
- int end_j = seq.length - 1;
+ int end_j = sq.getLength() - 1;
+ int length = sq.getLength();
for (int i = 0; i <= end_j; i++)
{
for (int i = 0; i <= end_j; i++)
{
- if ((seq.length - 1) < i)
+ if (length - 1 < i)
{
res = 23;
}
else
{
{
res = 23;
}
else
{
- res = ResidueProperties.aaIndex[seq[i]];
+ res = ResidueProperties.aaIndex[sq.getCharAt(i)];
}
cons2[i][res]++;
}
}
cons2[i][res]++;
}
@@
-277,7
+278,7
@@
public class ClustalxColourScheme extends ResidueColourScheme
}
@Override
}
@Override
- protected Color findColour(char c, int j, SequenceI seq)
+ protected synchronized Color findColour(char c, int j, SequenceI seq)
{
// TODO why the test for includeGaps here?
if (cons2.length <= j || Comparison.isGap(c)
{
// TODO why the test for includeGaps here?
if (cons2.length <= j || Comparison.isGap(c)
@@
-297,8
+298,7
@@
public class ClustalxColourScheme extends ResidueColourScheme
for (int k = 0; k < residueColour[i].cons.length; k++)
{
for (int k = 0; k < residueColour[i].cons.length; k++)
{
- if (residueColour[i].cons[k].isConserved(cons2, j, size,
- includeGaps))
+ if (residueColour[i].cons[k].isConserved(cons2, j, size, includeGaps))
{
colour = residueColour[i].c;
}
{
colour = residueColour[i].c;
}
@@
-336,11
+336,11
@@
public class ClustalxColourScheme extends ResidueColourScheme
}
@Override
}
@Override
- public ColourSchemeI getInstance(AnnotatedCollectionI sg,
- Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+ public ColourSchemeI getInstance(AlignViewportI view,
+ AnnotatedCollectionI sg)
{
ClustalxColourScheme css = new ClustalxColourScheme(sg,
{
ClustalxColourScheme css = new ClustalxColourScheme(sg,
- hiddenRepSequences);
+ view == null ? null : view.getHiddenRepSequences());
css.includeGaps = includeGaps;
return css;
}
css.includeGaps = includeGaps;
return css;
}