+ /* if (av.cursorMode && cursorY == i && cursorX >= startRes
+ && cursorX <= endRes)
+ {
+ seqRdr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * charWidth,
+ offset + ((i - startSeq) * charHeight));
+ }*/
+ }
+
+ if (av.getSelectionGroup() != null
+ || av.getAlignment().getGroups().size() > 0)
+ {
+ drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset);
+ }
+
+ }
+
+ void drawGroupsBoundaries(Graphics g1, int startRes, int endRes,
+ int startSeq, int endSeq, int offset)
+ {
+ Graphics2D g = (Graphics2D) g1;
+ //
+ // ///////////////////////////////////
+ // Now outline any areas if necessary
+ // ///////////////////////////////////
+
+ SequenceGroup group = null;
+ int groupIndex = -1;
+
+ if (av.getAlignment().getGroups().size() > 0)
+ {
+ group = av.getAlignment().getGroups().get(0);
+ groupIndex = 0;
+ }
+
+ if (group != null)
+ {
+ g.setStroke(new BasicStroke());
+ g.setColor(group.getOutlineColour());
+
+ do
+ {
+ drawPartialGroupOutline(g, group, startRes, endRes, startSeq,
+ endSeq, offset);
+
+ groupIndex++;
+
+ g.setStroke(new BasicStroke());
+
+ if (groupIndex >= av.getAlignment().getGroups().size())
+ {
+ break;
+ }
+
+ group = av.getAlignment().getGroups().get(groupIndex);
+
+ } while (groupIndex < av.getAlignment().getGroups().size());
+
+ }
+
+ }
+
+
+ /*
+ * Draw the selection group as a separate image and overlay
+ */
+ private BufferedImage drawSelectionGroup(int startRes, int endRes,
+ int startSeq, int endSeq)
+ {
+ // get a new image of the correct size
+ BufferedImage selectionImage = setupImage();
+
+ if (selectionImage == null)
+ {
+ return null;
+ }
+
+ SequenceGroup group = av.getSelectionGroup();
+ if (group == null)
+ {
+ // nothing to draw
+ return null;
+ }
+
+ // set up drawing colour
+ Graphics2D g = (Graphics2D) selectionImage.getGraphics();
+
+ setupSelectionGroup(g, selectionImage);
+
+ if (!av.getWrapAlignment())
+ {
+ drawUnwrappedSelection(g, group, startRes, endRes, startSeq, endSeq,
+ 0);
+ }
+ else
+ {
+ drawWrappedSelection(g, group, getWidth(), getHeight(),
+ av.getRanges().getStartRes());
+ }
+
+ g.dispose();
+ return selectionImage;
+ }
+
+ /**
+ * Draw the cursor as a separate image and overlay
+ *
+ * @param startRes
+ * start residue of area to draw cursor in
+ * @param endRes
+ * end residue of area to draw cursor in
+ * @param startSeq
+ * start sequence of area to draw cursor in
+ * @param endSeq
+ * end sequence of are to draw cursor in
+ * @return a transparent image of the same size as the sequence canvas, with
+ * the cursor drawn on it, if any
+ */
+ private BufferedImage drawCursor(int startRes, int endRes, int startSeq,
+ int endSeq)
+ {
+ // define our cursor image
+ BufferedImage cursorImage = null;
+
+ if (av.cursorMode && cursorY >= startSeq && cursorY <= endSeq
+ && cursorX >= startRes && cursorX <= endRes)
+ {
+ // get a new image of the correct size
+ cursorImage = setupImage();
+ Graphics2D g = (Graphics2D) cursorImage.getGraphics();
+
+ // get the character the cursor is drawn at
+ SequenceI seq = av.getAlignment().getSequenceAt(cursorY);
+ char s = seq.getCharAt(cursorX);
+
+ int offset = 0;
+ if (av.getWrapAlignment())