*/
package jalview.schemes;
-import jalview.datamodel.AlignmentI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import java.awt.Color;
/**
* Find a colour without an index in a sequence
*/
- @Override
public Color findColour(char c)
{
- return colors == null ? Color.white : colors[symbolIndex[c]];
+ Color colour = Color.white;
+
+ if (colors != null && symbolIndex != null
+ && c < symbolIndex.length
+ && symbolIndex[c] < colors.length)
+ {
+ colour = colors[symbolIndex[c]];
+ }
+
+ return colour;
}
/**
return findColour(c, j, seq);
}
+ /**
+ * Default implementation looks up the residue colour in a fixed scheme, or
+ * returns White if not found. Override this method for a colour scheme that
+ * depends on the column position or sequence.
+ *
+ * @param c
+ * @param j
+ * @param seq
+ * @return
+ */
protected Color findColour(char c, int j, SequenceI seq)
{
- Color colour = Color.white;
-
- if (colors != null && symbolIndex != null && c < symbolIndex.length
- && symbolIndex[c] < colors.length)
- {
- colour = colors[symbolIndex[c]];
- }
- // colour = adjustColour(c, j, colour);
-
- return colour;
+ return findColour(c);
}
@Override
{
return true;
}
-
- /*
- * inspect the data context (alignment) for residue type
- */
- boolean nucleotide = false;
- if (ac instanceof AlignmentI)
+ if (ac == null)
{
- nucleotide = ((AlignmentI) ac).isNucleotide();
+ return true;
}
- else
+ /*
+ * pop-up menu on selection group before group created
+ * (no alignment context)
+ */
+ // TODO: add nucleotide flag to SequenceGroup?
+ if (ac instanceof SequenceGroup && ac.getContext() == null)
{
- AnnotatedCollectionI context = ac.getContext();
- if (context instanceof AlignmentI)
- {
- nucleotide = ((AlignmentI) context).isNucleotide();
- }
- else
- {
- // not sure what's going on, play safe
- return true;
- }
+ return true;
}
/*
+ * inspect the data context (alignment) for residue type
+ */
+ boolean nucleotide = ac.isNucleotide();
+
+ /*
* does data type match colour scheme type?
*/
return (nucleotide && isNucleotideSpecific())