+ // now selection groups
+ if (av.getSelectionGroup() != null
+ || av.getAlignment().getGroups().size() > 0)
+ {
+ drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset);
+ }
+
+ }
+
+ /**
+ * Draw a single sequence
+ *
+ * @param nextSeq
+ * the next sequence to draw
+ * @param g
+ * graphics context
+ * @param startRes
+ * offset of the first column in the visible region (0..)
+ * @param endRes
+ * offset of the last column in the visible region (0..)
+ * @param heightPosition
+ * vertical location of the sequence in the alignment
+ * @param i
+ * index of sequence
+ */
+ private void drawSequence(SequenceI nextSeq, Graphics g, int startRes,
+ int endRes, int heightPosition, int i)
+ {
+ int charWidth = av.getCharWidth();
+
+ if (nextSeq == null)
+ {
+ // occasionally, a race condition occurs such that the alignment row is
+ // empty
+ // TODO Don't think this will happen any more?
+ return;
+ }
+ seqRdr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq),
+ startRes, endRes, heightPosition);
+
+ if (av.isShowSequenceFeatures())
+ {
+ fr.drawSequence(g, nextSeq, startRes, endRes, heightPosition, false);
+ }
+
+ /*
+ * highlight search Results once sequence has been drawn
+ */
+ if (av.hasSearchResults())
+ {
+ SearchResultsI searchResults = av.getSearchResults();
+ int[] visibleResults = searchResults.getResults(nextSeq, startRes,
+ endRes);
+ if (visibleResults != null)