+
+ /**
+ * Redraws any positions in the search results in the visible region. Any
+ * highlights are drawn depending on the search results set on the Viewport,
+ * not the results parameter. This allows this method to be called to either
+ * clear highlighting (passing the previous search results), or set new
+ * highlighting.
+ *
+ * @param results
+ * @return
+ */
+ protected boolean drawWrappedMappedPositions(SearchResultsI results)
+ {
+ if (results == null)
+ {
+ return false;
+ }
+
+ boolean matchFound = false;
+
+ /*
+ * Viewport ranges are set for the 'row' of the wrapped alignment
+ * the cursor is in, not the whole visible region; really we want
+ * the latter; +-6 a temporary fudge for codons wrapping across lines
+ */
+ ViewportRanges ranges = av.getRanges();
+ int firstVisibleColumn = ranges.getStartRes() - 6;
+ int lastVisibleColumn = ranges.getEndRes() + 6;
+ AlignmentI alignment = av.getAlignment();
+ if (av.hasHiddenColumns())
+ {
+ firstVisibleColumn = alignment.getHiddenColumns()
+ .adjustForHiddenColumns(firstVisibleColumn);
+ lastVisibleColumn = alignment.getHiddenColumns()
+ .adjustForHiddenColumns(lastVisibleColumn);
+ }
+
+ /*
+ * find width of alignment in residues, and height of alignment,
+ * so we can calculate where to render each matched position
+ */
+ int wrappedWidth = av.getWrappedWidth();
+ int wrappedHeight = av.getAlignment().getHeight() * av.getCharHeight();
+ int gapHeight = av.getCharHeight()
+ * (av.getScaleAboveWrapped() ? 2 : 1);
+ wrappedHeight += gapHeight;
+ wrappedHeight += getAnnotationHeight();
+
+ for (int seqNo = ranges.getStartSeq(); seqNo <= ranges
+ .getEndSeq(); seqNo++)
+ {
+ SequenceI seq = alignment.getSequenceAt(seqNo);
+
+ int[] visibleResults = results.getResults(seq, firstVisibleColumn,
+ lastVisibleColumn);
+ if (visibleResults != null)
+ {
+ for (int i = 0; i < visibleResults.length - 1; i += 2)
+ {
+ int firstMatchedColumn = visibleResults[i];
+ int lastMatchedColumn = visibleResults[i + 1];
+ if (firstMatchedColumn <= lastVisibleColumn
+ && lastMatchedColumn >= firstVisibleColumn)
+ {
+ /*
+ * found a search results match in the visible region
+ */
+ firstMatchedColumn = Math.max(firstMatchedColumn,
+ firstVisibleColumn);
+ lastMatchedColumn = Math.min(lastMatchedColumn,
+ lastVisibleColumn);
+
+ /*
+ * draw each mapped position separately (as contiguous positions may
+ * wrap across lines)
+ */
+ for (int mappedPos = firstMatchedColumn; mappedPos <= lastMatchedColumn; mappedPos++)
+ {
+ int displayColumn = mappedPos;
+ if (av.hasHiddenColumns())
+ {
+ displayColumn = alignment.getHiddenColumns()
+ .findColumnPosition(displayColumn);
+ }
+
+ /*
+ * transX: offset from left edge of canvas to residue position
+ */
+ int transX = labelWidthWest
+ + ((displayColumn - ranges.getStartRes()) % wrappedWidth)
+ * av.getCharWidth();
+
+ /*
+ * transY: offset from top edge of canvas to residue position
+ */
+ int transY = gapHeight;
+ transY += (displayColumn / wrappedWidth) * wrappedHeight;
+ transY += (seqNo - ranges.getStartSeq()) * av.getCharHeight();
+
+ /*
+ * yOffset is from graphics origin to start of visible region
+ */
+ int yOffset = 0;// (displayColumn / wrappedWidth) * wrappedHeight;
+ if (transY < getHeight())
+ {
+ matchFound = true;
+ gg.translate(transX, transY);
+ drawPanel(gg, displayColumn, displayColumn, seqNo, seqNo,
+ yOffset);
+ gg.translate(-transX, -transY);
+ }
+ }
+ }
+ }
+ }
+ }
+
+ return matchFound;
+ }