+ 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;
+
+ int yoffset = 0;
+ int xoffset = 0;
+ int startx = startRes;
+ int endx = endRes;
+ if (av.getWrapAlignment())
+ {
+ // work out the correct offsets for the cursor
+ int charHeight = av.getCharHeight();
+ int charWidth = av.getCharWidth();
+ int canvasWidth = getWidth();
+ int canvasHeight = getHeight();
+
+ // height gap above each panel
+ int hgap = charHeight;
+ if (av.getScaleAboveWrapped())
+ {
+ hgap += charHeight;
+ }
+
+ int cWidth = (canvasWidth - labelWidthEast - labelWidthWest)
+ / charWidth;
+ int cHeight = av.getAlignment().getHeight() * charHeight;
+
+ endx = startx + cWidth - 1;
+ int ypos = hgap; // vertical offset
+
+ // iterate down the wrapped panels
+ while ((ypos <= canvasHeight) && (endx < cursorX))
+ {
+ // update vertical offset
+ ypos += cHeight + getAnnotationHeight() + hgap;
+
+ // update horizontal offset
+ startx += cWidth;
+ endx = startx + cWidth - 1;
+ }
+ yoffset = ypos;
+ xoffset = labelWidthWest;
+ }
+
+ if (av.cursorMode && cursorY >= startSeq && cursorY <= endSeq
+ && cursorX >= startx && cursorX <= endx)
+ {
+ // 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);
+
+ seqRdr.drawCursor(g, s,
+ xoffset + (cursorX - startx) * av.getCharWidth(),
+ yoffset + (cursorY - startSeq) * av.getCharHeight());
+ g.dispose();
+ }
+
+ return cursorImage;
+ }
+
+
+ /*
+ * Set up graphics for selection group
+ */
+ private void setupSelectionGroup(Graphics2D g,
+ BufferedImage selectionImage)
+ {
+ // set background to transparent
+ g.setComposite(AlphaComposite.getInstance(AlphaComposite.CLEAR, 0.0f));
+ g.fillRect(0, 0, selectionImage.getWidth(), selectionImage.getHeight());
+
+ // set up foreground to draw red dashed line
+ g.setComposite(AlphaComposite.Src);
+ g.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT,
+ BasicStroke.JOIN_ROUND, 3f, new float[]
+ { 5f, 3f }, 0f));
+ g.setColor(Color.RED);
+ }
+
+ /*
+ * Draw a selection group over an unwrapped alignment
+ * @param g graphics object to draw with
+ * @param group selection group
+ * @param startRes start residue of area to draw
+ * @param endRes end residue of area to draw
+ * @param startSeq start sequence of area to draw
+ * @param endSeq end sequence of area to draw
+ * @param offset vertical offset (used when called from wrapped alignment code)
+ */
+ private void drawUnwrappedSelection(Graphics2D g, SequenceGroup group,
+ int startRes, int endRes, int startSeq, int endSeq, int offset)
+ {
+ int charWidth = av.getCharWidth();
+
+ if (!av.hasHiddenColumns())
+ {
+ drawPartialGroupOutline(g, group, startRes, endRes, startSeq, endSeq,
+ offset);
+ }
+ else
+ {
+ // package into blocks of visible columns
+ int screenY = 0;
+ int blockStart = startRes;
+ int blockEnd = endRes;
+
+ for (int[] region : av.getAlignment().getHiddenColumns()
+ .getHiddenColumnsCopy())
+ {
+ int hideStart = region[0];
+ int hideEnd = region[1];
+
+ if (hideStart <= blockStart)
+ {
+ blockStart += (hideEnd - hideStart) + 1;
+ continue;
+ }
+
+ blockEnd = hideStart - 1;
+
+ g.translate(screenY * charWidth, 0);
+ drawPartialGroupOutline(g, group,
+ blockStart, blockEnd, startSeq, endSeq, offset);
+
+ g.translate(-screenY * charWidth, 0);
+ screenY += blockEnd - blockStart + 1;
+ blockStart = hideEnd + 1;
+
+ if (screenY > (endRes - startRes))
+ {
+ // already rendered last block
+ break;
+ }
+ }
+
+ if (screenY <= (endRes - startRes))
+ {
+ // remaining visible region to render
+ blockEnd = blockStart + (endRes - startRes) - screenY;
+ g.translate(screenY * charWidth, 0);
+ drawPartialGroupOutline(g, group,
+ blockStart, blockEnd, startSeq, endSeq, offset);
+
+ g.translate(-screenY * charWidth, 0);
+ }
+ }
+ }
+
+ /*
+ * Draw the selection group as a separate image and overlay
+ */
+ private void drawPartialGroupOutline(Graphics2D g, SequenceGroup group,
+ int startRes, int endRes, int startSeq, int endSeq,
+ int verticalOffset)
+ {
+ int charHeight = av.getCharHeight();
+ int charWidth = av.getCharWidth();
+
+ int visWidth = (endRes - startRes + 1) * charWidth;
+
+ int oldY = -1;
+ int i = 0;
+ boolean inGroup = false;
+ int top = -1;
+ int bottom = -1;
+
+ int sx = -1;
+ int sy = -1;
+ int xwidth = -1;
+
+ for (i = startSeq; i <= endSeq; i++)
+ {
+ // position of start residue of group relative to startRes, in pixels
+ sx = (group.getStartRes() - startRes) * charWidth;
+
+ // width of group in pixels
+ xwidth = (((group.getEndRes() + 1) - group.getStartRes()) * charWidth)
+ - 1;
+
+ sy = verticalOffset + (i - startSeq) * charHeight;
+
+ if (sx + xwidth < 0 || sx > visWidth)
+ {
+ continue;
+ }
+
+ if ((sx <= (endRes - startRes) * charWidth)
+ && group.getSequences(null)
+ .contains(av.getAlignment().getSequenceAt(i)))
+ {
+ if ((bottom == -1) && !group.getSequences(null)
+ .contains(av.getAlignment().getSequenceAt(i + 1)))
+ {
+ bottom = sy + charHeight;