colhash.put("YELLOW", new Color((float) 0.8, (float) 0.8, (float) 0.0));
}
- public ClustalxColourScheme(AnnotatedCollectionI alignment, Map<SequenceI, SequenceCollectionI> hiddenReps)
+ public ClustalxColourScheme(AnnotatedCollectionI alignment,
+ Map<SequenceI, SequenceCollectionI> hiddenReps)
{
- alignmentChanged(alignment,hiddenReps);
+ alignmentChanged(alignment, hiddenReps);
}
- public void alignmentChanged(AnnotatedCollectionI alignment, Map<SequenceI, SequenceCollectionI> hiddenReps) {
- int maxWidth=alignment.getWidth();
- List<SequenceI> seqs=alignment.getSequences(hiddenReps);
+
+ 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;
- for (SequenceI sq: seqs)
+ for (SequenceI sq : seqs)
{
seq = sq.getSequence();