+ if (inGroup)
+ {
+ sy = verticalOffset + ((i - startSeq) * charHeight);
+ drawVerticals(g, sx, xwidth, visWidth, oldY, sy);
+ drawHorizontals(g, sx, xwidth, visWidth, top, bottom);
+ }
+ }
+ }
+
+ /**
+ * Draw horizontal selection group boundaries at top and bottom positions
+ *
+ * @param g
+ * graphics object to draw on
+ * @param sx
+ * start x position
+ * @param xwidth
+ * width of gap
+ * @param visWidth
+ * visWidth maximum available width
+ * @param top
+ * position to draw top of group at
+ * @param bottom
+ * position to draw bottom of group at
+ */
+ private void drawHorizontals(Graphics2D g, int sx, int xwidth,
+ int visWidth, int top, int bottom)
+ {
+ int width = xwidth;
+ int startx = sx;
+ if (startx < 0)
+ {
+ width += startx;
+ startx = 0;
+ }
+
+ // don't let width extend beyond current block, or group extent
+ // fixes JAL-2672
+ if (startx + width >= visWidth)
+ {
+ width = visWidth - startx;
+ }
+
+ if (top != -1)
+ {
+ g.drawLine(startx, top, startx + width, top);
+ }
+
+ if (bottom != -1)
+ {
+ g.drawLine(startx, bottom - 1, startx + width, bottom - 1);
+ }
+ }
+
+ /**
+ * Draw vertical lines at sx and sx+xwidth providing they lie within
+ * [0,visWidth)
+ *
+ * @param g
+ * graphics object to draw on
+ * @param sx
+ * start x position
+ * @param xwidth
+ * width of gap
+ * @param visWidth
+ * visWidth maximum available width
+ * @param oldY
+ * top y value
+ * @param sy
+ * bottom y value
+ */
+ private void drawVerticals(Graphics2D g, int sx, int xwidth, int visWidth,
+ int oldY, int sy)
+ {
+ // if start position is visible, draw vertical line to left of
+ // group
+ if (sx >= 0 && sx < visWidth)
+ {
+ g.drawLine(sx, oldY, sx, sy);
+ }
+
+ // if end position is visible, draw vertical line to right of
+ // group
+ if (sx + xwidth < visWidth)
+ {
+ g.drawLine(sx + xwidth, oldY, sx + xwidth, sy);
+ }
+ }
+
+ /**
+ * Highlights search results in the visible region by rendering as white text
+ * on a black background. Any previous highlighting is removed. Answers true
+ * if any highlight was left on the visible alignment (so status bar should be
+ * set to match), else false. This method does _not_ set the 'fastPaint' flag,
+ * so allows the next repaint to update the whole display.
+ *
+ * @param results
+ * @return
+ */
+ public boolean highlightSearchResults(SearchResultsI results)
+ {
+ return highlightSearchResults(results, false);
+
+ }
+
+ /**
+ * Highlights search results in the visible region by rendering as white text
+ * on a black background. Any previous highlighting is removed. Answers true
+ * if any highlight was left on the visible alignment (so status bar should be
+ * set to match), else false.
+ * <p>
+ * Optionally, set the 'fastPaint' flag for a faster redraw if only the
+ * highlighted regions are modified. This speeds up highlighting across linked
+ * alignments.
+ * <p>
+ * Currently fastPaint is not implemented for scrolled wrapped alignments. If
+ * a wrapped alignment had to be scrolled to show the highlighted region, then
+ * it should be fully redrawn, otherwise a fast paint can be performed. This
+ * argument could be removed if fast paint of scrolled wrapped alignment is
+ * coded in future (JAL-2609).
+ *
+ * @param results
+ * @param doFastPaint
+ * if true, sets a flag so the next repaint only redraws the modified
+ * image
+ * @return
+ */
+ public boolean highlightSearchResults(SearchResultsI results,
+ boolean doFastPaint)
+ {
+ if (fastpainting)
+ {
+ return false;
+ }
+ boolean wrapped = av.getWrapAlignment();
+ try
+ {
+ fastPaint = doFastPaint;
+ fastpainting = fastPaint;
+
+ /*
+ * to avoid redrawing the whole visible region, we instead
+ * redraw just the minimal regions to remove previous highlights
+ * and add new ones
+ */
+ SearchResultsI previous = av.getSearchResults();
+ av.setSearchResults(results);
+ boolean redrawn = false;
+ boolean drawn = false;
+ if (wrapped)
+ {
+ redrawn = drawMappedPositionsWrapped(previous);
+ drawn = drawMappedPositionsWrapped(results);
+ redrawn |= drawn;
+ }