*/
public class SeqCanvas extends JComponent implements ViewportListenerI
{
+ private static String ZEROS = "0000000000";
+
final FeatureRenderer fr;
final SequenceRenderer sr;
boolean fastPaint = false;
- int LABEL_WEST;
+ int labelWidthWest;
- int LABEL_EAST;
+ int labelWidthEast;
int cursorX = 0;
if (value != -1)
{
- int x = LABEL_WEST - fm.stringWidth(String.valueOf(value))
+ int x = labelWidthWest - fm.stringWidth(String.valueOf(value))
- charWidth / 2;
g.drawString(value + "", x, (ypos + (i * charHeight))
- (charHeight / 5));
fastpainting = true;
fastPaint = true;
updateViewport();
- gg.copyArea(horizontal * charWidth, vertical * charHeight, imgWidth,
- imgHeight, -horizontal * charWidth, -vertical * charHeight);
ViewportRanges ranges = av.getRanges();
int startRes = ranges.getStartRes();
int transX = 0;
int transY = 0;
+ gg.copyArea(horizontal * charWidth, vertical * charHeight, imgWidth,
+ imgHeight, -horizontal * charWidth, -vertical * charHeight);
+
if (horizontal > 0) // scrollbar pulled right, image to the left
{
transX = (endRes - startRes - horizontal) * charWidth;
}
/**
- * DOCUMENT ME!
+ * Returns the visible width of the canvas in residues, after allowing for
+ * East or West scales (if shown)
*
- * @param cwidth
- * DOCUMENT ME!
+ * @param canvasWidth
+ * the width in pixels (possibly including scales)
*
- * @return DOCUMENT ME!
+ * @return
*/
- public int getWrappedCanvasWidth(int cwidth)
+ public int getWrappedCanvasWidth(int canvasWidth)
{
FontMetrics fm = getFontMetrics(av.getFont());
- LABEL_EAST = 0;
- LABEL_WEST = 0;
+ labelWidthEast = 0;
+ labelWidthWest = 0;
if (av.getScaleRightWrapped())
{
- LABEL_EAST = fm.stringWidth(getMask());
+ labelWidthEast = getLabelWidth(fm);
}
if (av.getScaleLeftWrapped())
{
- LABEL_WEST = fm.stringWidth(getMask());
+ labelWidthWest = labelWidthEast > 0 ? labelWidthEast
+ : getLabelWidth(fm);
}
- return (cwidth - LABEL_EAST - LABEL_WEST) / charWidth;
+ return (canvasWidth - labelWidthEast - labelWidthWest) / charWidth;
}
/**
- * Generates a string of zeroes.
+ * Returns a pixel width suitable for showing the largest sequence coordinate
+ * (end position) in the alignment. Returns 2 plus the number of decimal
+ * digits to be shown (3 for 1-10, 4 for 11-99 etc).
*
- * @return String
+ * @param fm
+ * @return
*/
- String getMask()
+ protected int getLabelWidth(FontMetrics fm)
{
- String mask = "00";
+ /*
+ * find the biggest sequence end position we need to show
+ * (note this is not necessarily the sequence length)
+ */
int maxWidth = 0;
- int tmp;
- for (int i = 0; i < av.getAlignment().getHeight(); i++)
+ AlignmentI alignment = av.getAlignment();
+ for (int i = 0; i < alignment.getHeight(); i++)
{
- tmp = av.getAlignment().getSequenceAt(i).getEnd();
- if (tmp > maxWidth)
- {
- maxWidth = tmp;
- }
+ maxWidth = Math.max(maxWidth, alignment.getSequenceAt(i).getEnd());
}
+ int length = 2;
for (int i = maxWidth; i > 0; i /= 10)
{
- mask += "0";
+ length++;
}
- return mask;
+
+ return fm.stringWidth(ZEROS.substring(0, length));
}
/**
updateViewport();
AlignmentI al = av.getAlignment();
- FontMetrics fm = getFontMetrics(av.getFont());
-
- if (av.getScaleRightWrapped())
+ int labelWidth = 0;
+ if (av.getScaleRightWrapped() || av.getScaleLeftWrapped())
{
- LABEL_EAST = fm.stringWidth(getMask());
+ FontMetrics fm = getFontMetrics(av.getFont());
+ labelWidth = getLabelWidth(fm);
}
- if (av.getScaleLeftWrapped())
- {
- LABEL_WEST = fm.stringWidth(getMask());
- }
+ labelWidthEast = av.getScaleRightWrapped() ? labelWidth : 0;
+ labelWidthWest = av.getScaleLeftWrapped() ? labelWidth : 0;
int hgap = charHeight;
if (av.getScaleAboveWrapped())
hgap += charHeight;
}
- int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / charWidth;
+ int cWidth = (canvasWidth - labelWidthEast - labelWidthWest) / charWidth;
int cHeight = av.getAlignment().getHeight() * charHeight;
av.setWrappedWidth(cWidth);
- av.getRanges().setEndRes(av.getRanges().getStartRes() + cWidth - 1);
+ av.getRanges().setViewportStartAndWidth(startRes, cWidth);
int endx;
int ypos = hgap;
- int maxwidth = av.getAlignment().getWidth() - 1;
+ int maxwidth = av.getAlignment().getWidth();
if (av.hasHiddenColumns())
{
maxwidth = av.getAlignment().getHiddenColumns()
- .findColumnPosition(maxwidth) - 1;
+ .findColumnPosition(maxwidth);
}
+ int annotationHeight = getAnnotationHeight();
+
while ((ypos <= canvasHeight) && (startRes < maxwidth))
{
endx = startRes + cWidth - 1;
if (av.getScaleRightWrapped())
{
- g.translate(canvasWidth - LABEL_EAST, 0);
+ g.translate(canvasWidth - labelWidthEast, 0);
drawEastScale(g, startRes, endx, ypos);
- g.translate(-(canvasWidth - LABEL_EAST), 0);
+ g.translate(-(canvasWidth - labelWidthEast), 0);
}
- g.translate(LABEL_WEST, 0);
+ g.translate(labelWidthWest, 0);
if (av.getScaleAboveWrapped())
{
g.setColor(Color.blue);
int res;
HiddenColumns hidden = av.getAlignment().getHiddenColumns();
- for (int i = 0; i < hidden.getHiddenRegions().size(); i++)
+ List<Integer> positions = hidden.findHiddenRegionPositions();
+ for (int pos : positions)
{
- res = hidden.findHiddenRegionPosition(i) - startRes;
+ res = pos - startRes;
if (res < 0 || res > endx - startRes)
{
g.translate(0, -cHeight - ypos - 3);
}
g.setClip(clip);
- g.translate(-LABEL_WEST, 0);
+ g.translate(-labelWidthWest, 0);
- ypos += cHeight + getAnnotationHeight() + hgap;
+ ypos += cHeight + annotationHeight + hgap;
startRes += cWidth;
}
}
else
{
- List<int[]> regions = av.getAlignment().getHiddenColumns()
- .getHiddenRegions();
-
int screenY = 0;
final int screenYMax = endRes - startRes;
int blockStart = startRes;
int blockEnd = endRes;
- for (int[] region : regions)
+ for (int[] region : av.getAlignment().getHiddenColumns()
+ .getHiddenColumnsCopy())
{
int hideStart = region[0];
int hideEnd = region[1];
/**
* Highlights search results in the visible region by rendering as white text
- * on a black background. Any previous highlighting is removed.
+ * 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>
+ * Currently fastPaint is not implemented for 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 noFastPaint
+ * @return
*/
- public void highlightSearchResults(SearchResultsI results)
+ public boolean highlightSearchResults(SearchResultsI results,
+ boolean noFastPaint)
{
- updateViewport();
-
- /*
- * for now, don't attempt fastpaint if wrapped format
- */
- if (av.getWrapAlignment())
+ if (fastpainting)
{
- img = null;
- av.setSearchResults(results);
- repaint();
- return;
+ return false;
}
-
- fastpainting = true;
- fastPaint = true;
+ boolean wrapped = av.getWrapAlignment();
try
{
+ fastPaint = !noFastPaint;
+ fastpainting = fastPaint;
+
+ updateViewport();
+
/*
* to avoid redrawing the whole visible region, we instead
* redraw just the minimal regions to remove previous highlights
*/
SearchResultsI previous = av.getSearchResults();
av.setSearchResults(results);
- boolean redrawn = drawMappedPositions(previous);
- redrawn |= drawMappedPositions(results);
+ boolean redrawn = false;
+ boolean drawn = false;
+ if (wrapped)
+ {
+ redrawn = drawMappedPositionsWrapped(previous);
+ drawn = drawMappedPositionsWrapped(results);
+ redrawn |= drawn;
+ }
+ else
+ {
+ redrawn = drawMappedPositions(previous);
+ drawn = drawMappedPositions(results);
+ redrawn |= drawn;
+ }
+
+ /*
+ * if highlights were either removed or added, repaint
+ */
if (redrawn)
{
repaint();
}
+
+ /*
+ * return true only if highlights were added
+ */
+ return drawn;
+
} finally
{
fastpainting = false;
@Override
public void propertyChange(PropertyChangeEvent evt)
{
- if (!av.getWrapAlignment())
+ String eventName = evt.getPropertyName();
+
+ if (av.getWrapAlignment())
{
- if (evt.getPropertyName().equals("startres")
- || evt.getPropertyName().equals("endres"))
+ if (eventName.equals(ViewportRanges.STARTRES))
+ {
+ repaint();
+ }
+ }
+ else
+ {
+ int scrollX = 0;
+ if (eventName.equals(ViewportRanges.STARTRES))
{
// Make sure we're not trying to draw a panel
// larger than the visible window
ViewportRanges vpRanges = av.getRanges();
- int scrollX = (int) evt.getNewValue() - (int) evt.getOldValue();
- if (scrollX > vpRanges.getEndRes() - vpRanges.getStartRes())
+ scrollX = (int) evt.getNewValue() - (int) evt.getOldValue();
+ int range = vpRanges.getEndRes() - vpRanges.getStartRes();
+ if (scrollX > range)
{
- scrollX = vpRanges.getEndRes() - vpRanges.getStartRes();
+ scrollX = range;
}
- else if (scrollX < vpRanges.getStartRes() - vpRanges.getEndRes())
+ else if (scrollX < -range)
{
- scrollX = vpRanges.getStartRes() - vpRanges.getEndRes();
+ scrollX = -range;
}
+ }
+
+ // Both scrolling and resizing change viewport ranges: scrolling changes
+ // both start and end points, but resize only changes end values.
+ // Here we only want to fastpaint on a scroll, with resize using a normal
+ // paint, so scroll events are identified as changes to the horizontal or
+ // vertical start value.
+ if (eventName.equals(ViewportRanges.STARTRES))
+ {
+ // scroll - startres and endres both change
fastPaint(scrollX, 0);
}
- else if (evt.getPropertyName().equals("startseq")
- || evt.getPropertyName().equals("endseq"))
+ else if (eventName.equals(ViewportRanges.STARTSEQ))
{
+ // scroll
fastPaint(0, (int) evt.getNewValue() - (int) evt.getOldValue());
}
}
}
+
+ /**
+ * Redraws any positions in the search results in the visible region of a
+ * wrapped alignment. Any highlights are drawn depending on the search results
+ * set on the Viewport, not the <code>results</code> argument. This allows
+ * this method to be called either to clear highlights (passing the previous
+ * search results), or to draw new highlights.
+ *
+ * @param results
+ * @return
+ */
+ protected boolean drawMappedPositionsWrapped(SearchResultsI results)
+ {
+ if (results == null)
+ {
+ return false;
+ }
+
+ boolean matchFound = false;
+
+ int wrappedWidth = av.getWrappedWidth();
+ int wrappedHeight = getRepeatHeightWrapped();
+
+ ViewportRanges ranges = av.getRanges();
+ int canvasHeight = getHeight();
+ int repeats = canvasHeight / wrappedHeight;
+ if (canvasHeight / wrappedHeight > 0)
+ {
+ repeats++;
+ }
+
+ int firstVisibleColumn = ranges.getStartRes();
+ int lastVisibleColumn = ranges.getStartRes() + repeats
+ * ranges.getViewportWidth() - 1;
+
+ AlignmentI alignment = av.getAlignment();
+ if (av.hasHiddenColumns())
+ {
+ firstVisibleColumn = alignment.getHiddenColumns()
+ .adjustForHiddenColumns(firstVisibleColumn);
+ lastVisibleColumn = alignment.getHiddenColumns()
+ .adjustForHiddenColumns(lastVisibleColumn);
+ }
+
+ int gapHeight = charHeight * (av.getScaleAboveWrapped() ? 2 : 1);
+
+ 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 - ranges.getStartRes())
+ / 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;
+ }
+
+ /**
+ * Answers the height in pixels of a repeating section of the wrapped
+ * alignment, including space above, scale above if shown, sequences, and
+ * annotation panel if shown
+ *
+ * @return
+ */
+ protected int getRepeatHeightWrapped()
+ {
+ // gap (and maybe scale) above
+ int repeatHeight = charHeight * (av.getScaleAboveWrapped() ? 2 : 1);
+
+ // add sequences
+ repeatHeight += av.getRanges().getViewportHeight() * charHeight;
+
+ // add annotations panel height if shown
+ repeatHeight += getAnnotationHeight();
+
+ return repeatHeight;
+ }
}
git://source.jalview.org / jalview.git / blobdiff