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Last version
[jalview.git]
/
src
/
jalview
/
schemes
/
ClustalxColourScheme.java
diff --git
a/src/jalview/schemes/ClustalxColourScheme.java
b/src/jalview/schemes/ClustalxColourScheme.java
index
14f0ce6
..
d363764
100755
(executable)
--- a/
src/jalview/schemes/ClustalxColourScheme.java
+++ b/
src/jalview/schemes/ClustalxColourScheme.java
@@
-17,11
+17,15
@@
*/
package jalview.schemes;
*/
package jalview.schemes;
-import java.util.*;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
-import java.awt.*;
-
-import jalview.datamodel.*;
+import java.awt.Color;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.Vector;
public class ClustalxColourScheme extends ResidueColourScheme // implements
// IParameterizable
public class ClustalxColourScheme extends ResidueColourScheme // implements
// IParameterizable
@@
-55,13
+59,13
@@
public class ClustalxColourScheme extends ResidueColourScheme // implements
colhash.put("YELLOW", new Color((float) 0.8, (float) 0.8, (float) 0.0));
}
colhash.put("YELLOW", new Color((float) 0.8, (float) 0.8, (float) 0.0));
}
- public ClustalxColourScheme(Vector seqs, int maxWidth)
+ public ClustalxColourScheme(AnnotatedCollectionI alignment, Map<SequenceI, SequenceCollectionI> hiddenReps)
{
{
- resetClustalX(seqs, maxWidth);
+ alignmentChanged(alignment,hiddenReps);
}
}
-
- public void resetClustalX(Vector seqs, int maxWidth)
- {
+ public void alignmentChanged(AnnotatedCollectionI alignment, Map<SequenceI, SequenceCollectionI> hiddenReps) {
+ int maxWidth=alignment.getWidth();
+ List<SequenceI> seqs=alignment.getSequences(hiddenReps);
cons2 = new int[maxWidth][24];
includeGaps = isIncludeGaps(); // does nothing - TODO replace with call to
// get the current setting of the
cons2 = new int[maxWidth][24];
includeGaps = isIncludeGaps(); // does nothing - TODO replace with call to
// get the current setting of the
@@
-82,9
+86,9
@@
public class ClustalxColourScheme extends ResidueColourScheme // implements
int j = 0;
char[] seq;
int j = 0;
char[] seq;
- while (j < seqs.size())
+ for (SequenceI sq: seqs)
{
{
- seq = ((SequenceI) seqs.elementAt(j)).getSequence();
+ seq = sq.getSequence();
int end_j = seq.length - 1;
int end_j = seq.length - 1;
@@
-251,12
+255,14
@@
public class ClustalxColourScheme extends ResidueColourScheme // implements
ResidueColour[19] = colours[0]; // V
}
ResidueColour[19] = colours[0]; // V
}
+ @Override
public Color findColour(char c)
{
return Color.pink;
}
public Color findColour(char c)
{
return Color.pink;
}
- public Color findColour(char c, int j)
+ @Override
+ public Color findColour(char c, int j, SequenceI seq)
{
Color currentColour;
{
Color currentColour;