mg.setColor(Color.orange);
mg.fillRect(0, 0, od.getWidth(), miniMe.getHeight());
- // calculate scale based on current alignment width and height
- od.updateScales();
-
// calculate sampleCol and sampleRow
// alignment width is max number of residues/bases
// alignment height is number of sequences
int alwidth = av.getAlignment().getWidth();
- int alheight = av.getAlignment().getHeight()
- + av.getAlignment().getHiddenSequences().getSize();
+ int alheight = av.getAlignment().getAbsoluteHeight();
// sampleCol or sampleRow is the width/height allocated to each residue
// in particular, sometimes we may need more than one row/col of the
int color = Color.white.getRGB();
jalview.datamodel.SequenceI seq = null;
- final boolean hasHiddenRows = av.hasHiddenRows();
+
final boolean hasHiddenCols = av.hasHiddenColumns();
boolean hiddenRow = false;
// get hidden row and hidden column map once at beginning.
lastrow = currentrow;
- hiddenRow = false;
- // should be method(s) in Alignment
- if (hasHiddenRows)
- {
- seq = av.getAlignment().getHiddenSequences()
- .getHiddenSequence(lastrow);
- if (seq == null)
- {
- int index = av.getAlignment().getHiddenSequences()
- .findIndexWithoutHiddenSeqs(lastrow);
-
- seq = av.getAlignment().getSequenceAt(index);
- }
- else
- {
- hiddenRow = true;
- }
- }
- else
- {
- seq = av.getAlignment().getSequenceAt(lastrow);
- }
- // end of Alignment method(s)
+ // get the sequence which would be at alignment index 'lastrow' if no
+ // columns were hidden, and determine whether it is hidden or not
+ hiddenRow = av.getAlignment().isHidden(lastrow);
+ seq = av.getAlignment().getSequenceAtAbsoluteIndex(lastrow);
}
if (seq == null)