Stack historyList = new Stack();
Stack redoList = new Stack();
+ Hashtable sequenceColours;
+
+ int thresholdTextColour = 0;
+ Color textColour = Color.black;
+ Color textColour2 = Color.white;
+
+ boolean rightAlignIds = false;
+
+
/**
* Creates a new AlignViewport object.
*
showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true);
showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);
+ rightAlignIds = Cache.getDefault("RIGHT_ALIGN_IDS", false);
+
autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
padGaps = Cache.getDefault("PAD_GAPS", true);
public void invertColumnSelection()
{
- int column;
for(int i=0; i<alignment.getWidth(); i++)
{
- column = i;
-
- if(colSel.contains(column))
- colSel.removeElement(column);
+ if(colSel.contains(i))
+ colSel.removeElement(i);
else
- colSel.addElement(column);
+ {
+ if (!hasHiddenColumns || colSel.isVisible(i))
+ {
+ colSel.addElement(i);
+ }
+ }
}
}
+ public Color getSequenceColour(SequenceI seq)
+ {
+ if(sequenceColours==null || !sequenceColours.containsKey(seq))
+ return Color.white;
+ else
+ return (Color)sequenceColours.get(seq);
+ }
+
+ public void setSequenceColour(SequenceI seq, Color col)
+ {
+ if(sequenceColours==null)
+ sequenceColours = new Hashtable();
+
+ if(col == null)
+ sequenceColours.remove(seq);
+ else
+ sequenceColours.put(seq, col);
+ }
+
}