- hiddenRow = false;
- if (av.hasHiddenRows)
- {
- seq = av.alignment.getHiddenSequences().getHiddenSequence(lastrow);
- if (seq == null)
- {
- int index = av.alignment.getHiddenSequences()
- .findIndexWithoutHiddenSeqs(lastrow);
-
- seq = av.alignment.getSequenceAt(index);
- }
- else
- {
- hiddenRow = true;
- }
- }
- else
- {
- seq = av.alignment.getSequenceAt(lastrow);
- }
-
- if (seq == null)
- {
- System.out.println(lastrow + " null");
- continue;
- }
-
- for (col = 0; col < width; col++)
- {
- if ((int) (col * sampleCol) == lastcol
- && (int) (row * sampleRow) == lastrow)
- {
- miniMe.setRGB(col, row, color);
- continue;
- }
-
- lastcol = (int) (col * sampleCol);
-
- if (seq.getLength() > lastcol)
- {
- color = sr.getResidueBoxColour(seq, lastcol).getRGB();
-
- if (av.showSequenceFeatures)
- {
- color = fr.findFeatureColour(color, seq, lastcol);
- }
- }
- else
- {
- color = -1; // White
- }
-
- if (hiddenRow
- || (av.hasHiddenColumns && !av.getColumnSelection()
- .isVisible(lastcol)))
- {
- color = new Color(color).darker().darker().getRGB();
- }
-
- miniMe.setRGB(col, row, color);
-
- }
- }
-
- if (av.conservation != null)