if (av.hasHiddenColumns())
{
HiddenColumns hiddenColumns = av.getAlignment().getHiddenColumns();
- startX = hiddenColumns.adjustForHiddenColumns(startx);
- endX = hiddenColumns.adjustForHiddenColumns(endx);
+ startX = hiddenColumns.visibleToAbsoluteColumn(startx);
+ endX = hiddenColumns.visibleToAbsoluteColumn(endx);
}
FontMetrics fm = getFontMetrics(av.getFont());
int endSeq = ranges.getEndSeq();
int transX = 0;
int transY = 0;
-
+
gg.copyArea(horizontal * charWidth, vertical * charHeight,
img.getWidth(), img.getHeight(), -horizontal * charWidth,
-vertical * charHeight);
drawPanel(gg, startRes, endRes, startSeq, endSeq, 0);
gg.translate(-transX, -transY);
- repaint();
+ // Call repaint on alignment panel so that repaints from other alignment
+ // panel components can be aggregated. Otherwise performance of the
+ // overview window and others may be adversely affected.
+ av.getAlignPanel().repaint();
} finally
{
fastpainting = false;
int charHeight = av.getCharHeight();
int charWidth = av.getCharWidth();
-
+
ViewportRanges ranges = av.getRanges();
-
+
int width = getWidth();
int height = getHeight();
-
+
width -= (width % charWidth);
height -= (height % charHeight);
-
+
// selectImage is the selection group outline image
BufferedImage selectImage = drawSelectionGroup(
ranges.getStartRes(), ranges.getEndRes(),
ranges.getStartSeq(), ranges.getEndSeq());
-
+
if ((img != null) && (fastPaint
|| (getVisibleRect().width != g.getClipBounds().width)
|| (getVisibleRect().height != g.getClipBounds().height)))
gg = (Graphics2D) img.getGraphics();
gg.setFont(av.getFont());
}
-
+
if (av.antiAlias)
{
gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
RenderingHints.VALUE_ANTIALIAS_ON);
}
-
+
gg.setColor(Color.white);
gg.fillRect(0, 0, img.getWidth(), img.getHeight());
-
+
if (av.getWrapAlignment())
{
drawWrappedPanel(gg, getWidth(), getHeight(), ranges.getStartRes());
drawPanel(gg, ranges.getStartRes(), ranges.getEndRes(),
ranges.getStartSeq(), ranges.getEndSeq(), 0);
}
-
+
// lcimg is a local *copy* of img which we'll draw selectImage on top of
BufferedImage lcimg = buildLocalImage(selectImage);
g.drawImage(lcimg, 0, 0, this);
private BufferedImage buildLocalImage(BufferedImage selectImage)
{
// clone the cached image
- BufferedImage lcimg = new BufferedImage(img.getWidth(), img.getHeight(),
- img.getType());
+ BufferedImage lcimg = new BufferedImage(img.getWidth(), img.getHeight(),
+ img.getType());
+
+ // BufferedImage lcimg = new BufferedImage(img.getWidth(), img.getHeight(),
+ // img.getType());
Graphics2D g2d = lcimg.createGraphics();
g2d.drawImage(img, 0, 0, null);
try
{
- lcimg = new BufferedImage(width, height,
- BufferedImage.TYPE_INT_ARGB); // ARGB so alpha compositing works
+ lcimg = new BufferedImage(width, height,
+ BufferedImage.TYPE_INT_ARGB); // ARGB so alpha compositing works
} catch (OutOfMemoryError er)
{
System.gc();
* white fill the region to be drawn (so incremental fast paint doesn't
* scribble over an existing image)
*/
- gg.setColor(Color.white);
- gg.fillRect(0, ypos, (endx - startColumn + 1) * charWidth,
+ g.setColor(Color.white);
+ g.fillRect(0, ypos, (endx - startColumn + 1) * charWidth,
wrappedRepeatHeightPx);
drawPanel(g, startColumn, endx, 0, av.getAlignment().getHeight() - 1,
int res;
HiddenColumns hidden = av.getAlignment().getHiddenColumns();
- Iterator<Integer> it = hidden.getBoundedStartIterator(startColumn,
+ Iterator<Integer> it = hidden.getStartRegionIterator(startColumn,
endColumn);
while (it.hasNext())
{
if (av.hasHiddenColumns())
{
maxwidth = av.getAlignment().getHiddenColumns()
- .findColumnPosition(maxwidth);
+ .absoluteToVisibleColumn(maxwidth);
}
// chop the wrapped alignment extent up into panel-sized blocks and treat
int blockEnd;
HiddenColumns hidden = av.getAlignment().getHiddenColumns();
- VisibleContigsIterator regions = (VisibleContigsIterator) hidden
+ VisibleContigsIterator regions = hidden
.getVisContigsIterator(startRes, endRes + 1, true);
while (regions.hasNext())
if (av.hasSearchResults())
{
SearchResultsI searchResults = av.getSearchResults();
- int[] visibleResults = searchResults.getResults(nextSeq,
- startRes, endRes);
+ int[] visibleResults = searchResults.getResults(nextSeq, startRes,
+ endRes);
if (visibleResults != null)
{
for (int r = 0; r < visibleResults.length; r += 2)
{
seqRdr.drawHighlightedText(nextSeq, visibleResults[r],
- visibleResults[r + 1], (visibleResults[r] - startRes)
- * charWidth, offset
- + ((i - startSeq) * charHeight));
+ visibleResults[r + 1],
+ (visibleResults[r] - startRes) * charWidth,
+ offset + ((i - startSeq) * charHeight));
}
}
}
// convert the cursorX into a position on the visible alignment
int cursor_xpos = av.getAlignment().getHiddenColumns()
- .findColumnPosition(cursorX);
+ .absoluteToVisibleColumn(cursorX);
if (av.getAlignment().getHiddenColumns().isVisible(cursorX))
{
int blockEnd;
HiddenColumns hidden = av.getAlignment().getHiddenColumns();
- VisibleContigsIterator regions = (VisibleContigsIterator) hidden
+ VisibleContigsIterator regions = hidden
.getVisContigsIterator(startRes, endRes + 1, true);
while (regions.hasNext())
{
int startRes, int endRes, int startSeq, int endSeq,
int verticalOffset)
{
- int charHeight = av.getCharHeight();
- int charWidth = av.getCharWidth();
-
+ int charHeight = av.getCharHeight();
+ int charWidth = av.getCharWidth();
int visWidth = (endRes - startRes + 1) * charWidth;
int oldY = -1;
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;
+ List<SequenceI> seqs = group.getSequences(null);
- sy = verticalOffset + (i - startSeq) * charHeight;
+ // position of start residue of group relative to startRes, in pixels
+ int sx = (group.getStartRes() - startRes) * charWidth;
- if (sx + xwidth < 0 || sx > visWidth)
- {
- continue;
- }
+ // width of group in pixels
+ int xwidth = (((group.getEndRes() + 1) - group.getStartRes())
+ * charWidth) - 1;
- if ((sx <= (endRes - startRes) * charWidth)
- && group.getSequences(null)
- .contains(av.getAlignment().getSequenceAt(i)))
+ if (!(sx + xwidth < 0 || sx > visWidth))
+ {
+ for (i = startSeq; i <= endSeq; i++)
{
- if ((bottom == -1) && !group.getSequences(null)
- .contains(av.getAlignment().getSequenceAt(i + 1)))
- {
- bottom = sy + charHeight;
- }
+ sy = verticalOffset + (i - startSeq) * charHeight;
- if (!inGroup)
+ if ((sx <= (endRes - startRes) * charWidth)
+ && seqs.contains(av.getAlignment().getSequenceAt(i)))
{
- if (((top == -1) && (i == 0)) || !group.getSequences(null)
- .contains(av.getAlignment().getSequenceAt(i - 1)))
+ if ((bottom == -1)
+ && !seqs.contains(av.getAlignment().getSequenceAt(i + 1)))
{
- top = sy;
+ bottom = sy + charHeight;
}
- oldY = sy;
- inGroup = true;
- }
- }
- else
- {
- if (inGroup)
- {
- // 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);
- }
-
- if (sx < 0)
- {
- xwidth += sx;
- sx = 0;
- }
-
- // don't let width extend beyond current block, or group extent
- // fixes JAL-2672
- if (sx + xwidth >= (endRes - startRes + 1) * charWidth)
- {
- xwidth = (endRes - startRes + 1) * charWidth - sx;
- }
-
- // draw horizontal line at top of group
- if (top != -1)
+ if (!inGroup)
{
- g.drawLine(sx, top, sx + xwidth, top);
- top = -1;
- }
+ if (((top == -1) && (i == 0)) || !seqs
+ .contains(av.getAlignment().getSequenceAt(i - 1)))
+ {
+ top = sy;
+ }
- // draw horizontal line at bottom of group
- if (bottom != -1)
- {
- g.drawLine(sx, bottom, sx + xwidth, bottom);
- bottom = -1;
+ oldY = sy;
+ inGroup = true;
}
+ }
+ else if (inGroup)
+ {
+ drawVerticals(g, sx, xwidth, visWidth, oldY, sy);
+ drawHorizontals(g, sx, xwidth, visWidth, top, bottom);
+ // reset top and bottom
+ top = -1;
+ bottom = -1;
inGroup = false;
}
}
- }
-
- if (inGroup)
- {
- sy = verticalOffset + ((i - startSeq) * charHeight);
- if (sx >= 0 && sx < visWidth)
+ if (inGroup)
{
- g.drawLine(sx, oldY, sx, sy);
+ sy = verticalOffset + ((i - startSeq) * charHeight);
+ drawVerticals(g, sx, xwidth, visWidth, oldY, sy);
+ drawHorizontals(g, sx, xwidth, visWidth, top, bottom);
}
+ }
+ }
- if (sx + xwidth < visWidth)
- {
- g.drawLine(sx + xwidth, oldY, sx + xwidth, sy);
- }
+ /**
+ * 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;
+ }
- if (sx < 0)
- {
- xwidth += sx;
- sx = 0;
- }
+ // don't let width extend beyond current block, or group extent
+ // fixes JAL-2672
+ if (startx + width >= visWidth)
+ {
+ width = visWidth - startx;
+ }
- if (sx + xwidth > visWidth)
- {
- xwidth = visWidth;
- }
- else if (sx + xwidth >= (endRes - startRes + 1) * charWidth)
- {
- xwidth = (endRes - startRes + 1) * charWidth;
- }
+ if (top != -1)
+ {
+ g.drawLine(startx, top, startx + width, top);
+ }
- if (top != -1)
- {
- g.drawLine(sx, top, sx + xwidth, top);
- top = -1;
- }
+ if (bottom != -1)
+ {
+ g.drawLine(startx, bottom - 1, startx + width, bottom - 1);
+ }
+ }
- if (bottom != -1)
- {
- g.drawLine(sx, bottom - 1, sx + xwidth, bottom - 1);
- 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);
+ }
- inGroup = false;
+ // if end position is visible, draw vertical line to right of
+ // group
+ if (sx + xwidth < visWidth)
+ {
+ g.drawLine(sx + xwidth, oldY, sx + xwidth, sy);
}
}
*/
protected boolean drawMappedPositions(SearchResultsI results)
{
- if (results == null)
+ if ((results == null) || (gg == null)) // JAL-2784 check gg is not null
{
return false;
}
if (av.hasHiddenColumns())
{
firstVisibleColumn = alignment.getHiddenColumns()
- .adjustForHiddenColumns(firstVisibleColumn);
+ .visibleToAbsoluteColumn(firstVisibleColumn);
lastVisibleColumn = alignment.getHiddenColumns()
- .adjustForHiddenColumns(lastVisibleColumn);
+ .visibleToAbsoluteColumn(lastVisibleColumn);
}
for (int seqNo = ranges.getStartSeq(); seqNo <= ranges
if (av.hasHiddenColumns())
{
firstCol = alignment.getHiddenColumns()
- .findColumnPosition(firstCol);
- lastCol = alignment.getHiddenColumns().findColumnPosition(lastCol);
+ .absoluteToVisibleColumn(firstCol);
+ lastCol = alignment.getHiddenColumns().absoluteToVisibleColumn(lastCol);
}
int transX = (firstCol - ranges.getStartRes()) * av.getCharWidth();
int transY = (firstSeq - ranges.getStartSeq()) * av.getCharHeight();
{
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
{
fastPaint(scrollX, 0);
}
- // bizarrely, we only need to scroll on the x value here as fastpaint
- // copies the full height of the image anyway. Passing in the y value
- // causes nasty repaint artefacts, which only disappear on a full
- // repaint.
+ }
+ else if (eventName.equals(ViewportRanges.STARTSEQ))
+ {
+ // scroll
+ fastPaint(0, (int) evt.getNewValue() - (int) evt.getOldValue());
+ }
+ else if (eventName.equals(ViewportRanges.STARTRESANDSEQ))
+ {
+ if (av.getWrapAlignment())
+ {
+ fastPaintWrapped(scrollX);
}
}
}
{
ViewportRanges ranges = av.getRanges();
- // if (Math.abs(scrollX) > ranges.getViewportWidth())
- // JAL-2836, 2836 temporarily removed wrapped fastpaint for release 2.10.3
- if (true)
+ if (Math.abs(scrollX) > ranges.getViewportWidth())
{
/*
* shift of more than one view width is
*/
protected boolean drawMappedPositionsWrapped(SearchResultsI results)
{
- if (results == null)
+ if ((results == null) || (gg == null)) // JAL-2784 check gg is not null
{
return false;
}
if (av.hasHiddenColumns())
{
firstVisibleColumn = alignment.getHiddenColumns()
- .adjustForHiddenColumns(firstVisibleColumn);
+ .visibleToAbsoluteColumn(firstVisibleColumn);
lastVisibleColumn = alignment.getHiddenColumns()
- .adjustForHiddenColumns(lastVisibleColumn);
+ .visibleToAbsoluteColumn(lastVisibleColumn);
}
int gapHeight = charHeight * (av.getScaleAboveWrapped() ? 2 : 1);
if (av.hasHiddenColumns())
{
displayColumn = alignment.getHiddenColumns()
- .findColumnPosition(displayColumn);
+ .absoluteToVisibleColumn(displayColumn);
}
/*
git://source.jalview.org / jalview.git / blobdiff