*/
package jalview.schemes;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
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
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
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;