* 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 boolean highlightSearchResults(SearchResultsI results,
boolean noFastPaint)
{
if (fastpainting)
{
return false;
}
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
* 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;
}
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;
}
}
/**
* Redraws the minimal rectangle in the visible region (if any) that includes
* mapped positions of the given search results. Whether or not positions are
* highlighted depends on the SearchResults set on the Viewport. This allows
* this method to be called to either clear or set highlighting. Answers true
* if any positions were drawn (in which case a repaint is still required),
* else false.
*
* @param results
* @return
*/
protected boolean drawMappedPositions(SearchResultsI results)
{
if (results == null)
{
return false;
}
/*
* calculate the minimal rectangle to redraw that
* includes both new and existing search results
*/
int firstSeq = Integer.MAX_VALUE;
int lastSeq = -1;
int firstCol = Integer.MAX_VALUE;
int lastCol = -1;
boolean matchFound = false;
ViewportRanges ranges = av.getRanges();
int firstVisibleColumn = ranges.getStartRes();
int lastVisibleColumn = ranges.getEndRes();
AlignmentI alignment = av.getAlignment();
if (av.hasHiddenColumns())
{
firstVisibleColumn = alignment.getHiddenColumns()
.adjustForHiddenColumns(firstVisibleColumn);
lastVisibleColumn = alignment.getHiddenColumns()
.adjustForHiddenColumns(lastVisibleColumn);
}
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 -
* remember the first and last sequence matched, and the first
* and last visible columns in the matched positions
*/
matchFound = true;
firstSeq = Math.min(firstSeq, seqNo);
lastSeq = Math.max(lastSeq, seqNo);
firstMatchedColumn = Math.max(firstMatchedColumn,
firstVisibleColumn);
lastMatchedColumn = Math.min(lastMatchedColumn,
lastVisibleColumn);
firstCol = Math.min(firstCol, firstMatchedColumn);
lastCol = Math.max(lastCol, lastMatchedColumn);
}
}
}
}
if (matchFound)
{
if (av.hasHiddenColumns())
{
firstCol = alignment.getHiddenColumns()
.findColumnPosition(firstCol);
lastCol = alignment.getHiddenColumns().findColumnPosition(lastCol);
}
int transX = (firstCol - ranges.getStartRes()) * av.getCharWidth();
int transY = (firstSeq - ranges.getStartSeq()) * av.getCharHeight();
gg.translate(transX, transY);
drawPanel(gg, firstCol, lastCol, firstSeq, lastSeq, 0);
gg.translate(-transX, -transY);
}
return matchFound;
}
@Override
public void propertyChange(PropertyChangeEvent evt)
{
String eventName = evt.getPropertyName();
// if (av.getWrapAlignment())
// {
// 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();
scrollX = (int) evt.getNewValue() - (int) evt.getOldValue();
int range = vpRanges.getEndRes() - vpRanges.getStartRes();
if (scrollX > range)
{
scrollX = range;
}
else if (scrollX < -range)
{
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
if (av.getWrapAlignment())
{
fastPaintWrapped(scrollX);
// fastPaintWrapped(scrollX > 0 ? 1 : -1); // to debug: 1 at a time
}
else
{
fastPaint(scrollX, 0);
}
}
else if (eventName.equals(ViewportRanges.STARTSEQ))
{
fastPaint(0, (int) evt.getNewValue() - (int) evt.getOldValue());
}
}
}
/**
* Does a minimal update of the image for a scroll movement. This method
* handles scroll movements of up to one width of the wrapped alignment (one
* click in the vertical scrollbar). Larger movements (for example after a
* scroll to highlight a mapped position) trigger a full redraw instead.
*
* @param scrollX
* number of positions scrolled (right if positive, left if negative)
*/
protected void fastPaintWrapped(int scrollX)
{
if (Math.abs(scrollX) > av.getRanges().getViewportWidth())
{
/*
* shift of more than one view width is
* too complicated to handle in this method
*/
fastPaint = false;
repaint();
return;
}
fastPaint = true;
/*
* relocate the regions of the alignment that are still visible
*/
shiftWrappedAlignment(-scrollX);
/*
* add new columns (scale above, sequence, annotation)
* - at top left if scrollX < 0
* - at right of last two widths if scrollX > 0
* also West scale top left or East scale bottom right if shown
*/
if (scrollX < 0)
{
fastPaintWrappedAddLeft(-scrollX);
}
else
{
fastPaintWrappedAddRight(scrollX);
}
repaint();
}
/**
* Draws the specified number of columns at the 'end' (bottom right) of a
* wrapped alignment view, including scale above and right and annotations if
* shown. Also draws the same number of columns at the right hand end of the
* second last width shown, if the last width is not full height (so cannot
* simply be copied from the graphics image).
*
* @param columns
*/
protected void fastPaintWrappedAddRight(int columns)
{
if (columns == 0)
{
return;
}
/*
* how many widths are visible? we will be adding
* columns to the last visible width, right hand end
*/
int repeatHeight = getRepeatHeightWrapped();
int canvasHeight = getHeight();
int visibleWidths = canvasHeight / repeatHeight;
int remainder = canvasHeight % repeatHeight;
int hgap = charHeight * (av.getScaleAboveWrapped() ? 2 : 1);
boolean lastWidthPartHeight = false;
if (remainder >= (hgap + charHeight))
{
visibleWidths++;
lastWidthPartHeight = true;
}
/*
* limit visible widths to max widths of alignment
*/
ViewportRanges ranges = av.getRanges();
int visibleAlignmentWidth = ranges.getVisibleAlignmentWidth();
int viewportWidth = ranges.getViewportWidth();
int maxWidths = visibleAlignmentWidth / viewportWidth;
if (visibleAlignmentWidth % viewportWidth > 0)
{
maxWidths++;
}
visibleWidths = Math.min(visibleWidths, maxWidths);
int widthInColumns = (getWidth() - labelWidthEast - labelWidthWest)
/ charWidth;
/**
* draw full height alignment in the second last row, last columns, if the
* last row was not full height
*/
if (lastWidthPartHeight)
{
int widthsAbove = visibleWidths - 2;
int ypos = repeatHeight * widthsAbove + hgap;
int endRes = ranges.getEndRes();
endRes += widthsAbove * viewportWidth;
int startRes = endRes - columns;
int xOffset = ((startRes - ranges.getStartRes()) % viewportWidth)
* charWidth;
gg.translate(xOffset, 0);
/*
* white fill first to erase annotations
*/
gg.setColor(Color.white);
gg.fillRect(labelWidthWest, ypos,
(endRes - startRes + 1) * charWidth, repeatHeight);
drawWrappedRegion(gg, startRes, endRes, canvasHeight, widthInColumns,
ypos);
gg.translate(-xOffset, 0);
}
/*
* y-offset for drawing is height of widths above,
* plus one gap row
*/
int widthsAbove = visibleWidths - 1;
int ypos = repeatHeight * widthsAbove + hgap;
int endRes = ranges.getEndRes();
endRes += widthsAbove * viewportWidth;
endRes = Math.min(endRes, ranges.getVisibleAlignmentWidth());
/*
* draw one extra column than strictly needed - this is a (harmless)
* fudge to ensure scale marks get drawn (JAL-2636)
*/
int startRes = endRes - columns;
/*
* x-offset is x-start modulo viewport start residue;
* doesn't include label West (offset is applied in drawWrappedRegion)
*/
int leftEndColumn = ranges.getStartRes() + widthsAbove
* ranges.getViewportWidth();
// startRes = Math.max(startRes - 0, leftEndColumn);
int xOffset = ((startRes - ranges.getStartRes()) % viewportWidth)
* charWidth;
gg.translate(xOffset, 0);
/*
* white fill the region to be drawn including scale left or above;
* extend to right hand margin so as to erase scale above when
* scrolling right beyond end of alignment
*/
gg.setColor(Color.white);
int width = getWidth() - labelWidthWest - xOffset;
gg.fillRect(labelWidthWest, ypos - hgap, width, repeatHeight);
gg.setFont(av.getFont());
gg.setColor(Color.black);
drawWrappedRegion(gg, startRes, endRes, canvasHeight, widthInColumns,
ypos);
gg.translate(-xOffset, 0);
/*
* draw scale right if shown, passing in the start/end columns
* for the whole line, not just the last few columns
*/
if (av.getScaleRightWrapped())
{
drawVerticalScale(gg, leftEndColumn, endRes, ypos, false);
}
}
/**
* Draws the specified number of columns at the 'start' (top left) of a
* wrapped alignment view, including scale above and left and annotations if
* shown
*
* @param columns
*/
protected void fastPaintWrappedAddLeft(int columns)
{
int startRes = av.getRanges().getStartRes();
/*
* draw one extra column than strictly needed - this is a (harmless)
* fudge to ensure scale marks get drawn (JAL-2636)
*/
int endx = startRes + columns;
int ypos = 0;
/*
* white fill the region to be drawn including scale left or above
*/
gg.setColor(Color.white);
int height = getRepeatHeightWrapped();
gg.fillRect(0, ypos, labelWidthWest + columns * charWidth, height);
ypos += charHeight * (av.getScaleAboveWrapped() ? 2 : 1);
gg.setFont(av.getFont());
gg.setColor(Color.black);
if (av.getScaleLeftWrapped())
{
drawVerticalScale(gg, startRes, endx, ypos, true);
}
int cWidth = (getWidth() - labelWidthEast - labelWidthWest) / charWidth;
drawWrappedRegion(gg, startRes, endx, getHeight(), cWidth, ypos);
}
/**
* Shifts the visible alignment by the specified number of columns - left if
* negative, right if positive. Includes scale above, left or right and
* annotations (if shown). Does not draw newly visible columns.
*
* @param positions
*/
protected void shiftWrappedAlignment(int positions)
{
if (positions == 0)
{
return;
}
int repeatHeight = getRepeatHeightWrapped();
ViewportRanges ranges = av.getRanges();
int xMax = ranges.getVisibleAlignmentWidth();
int widthToCopy = (ranges.getViewportWidth() - Math.abs(positions))
* charWidth;
int canvasHeight = getHeight();
int visibleWidths = canvasHeight / repeatHeight;
if (canvasHeight % repeatHeight > 0)
{
visibleWidths++;
}
int viewportWidth = ranges.getViewportWidth();
int hgap = charHeight * (av.getScaleAboveWrapped() ? 2 : 1);
int remainder = canvasHeight % repeatHeight;
if (remainder >= (hgap + charHeight))
{
visibleWidths++;
}
if (positions > 0)
{
/*
* shift right (after scroll left)
* for each wrapped width (starting with the last), copy (width-positions)
* columns from the left margin to the right margin, and copy positions
* columns from the right margin of the row above (if any) to the
* left margin of the current row
*/
int xpos = ranges.getStartRes() + (visibleWidths - 1) * viewportWidth;
/*
* get y-offset of last wrapped width
*/
int y = canvasHeight / repeatHeight * repeatHeight;
int copyFromLeftStart = labelWidthWest;
int copyFromRightStart = copyFromLeftStart + widthToCopy;
while (y >= 0)
{
gg.copyArea(copyFromLeftStart, y, widthToCopy, repeatHeight,
positions * charWidth, 0);
if (y > 0)
{
gg.copyArea(copyFromRightStart, y - repeatHeight, positions
* charWidth, repeatHeight, -widthToCopy, repeatHeight);
}
if (av.getScaleLeftWrapped())
{
drawVerticalScale(gg, xpos, xpos + viewportWidth - 1, y + hgap,
true);
}
if (av.getScaleRightWrapped())
{
drawVerticalScale(gg, xpos, xpos + viewportWidth - 1, y + hgap,
false);
}
y -= repeatHeight;
xpos -= viewportWidth;
}
}
else
{
/*
* shift left (after scroll right)
* for each wrapped width (starting with the first), copy (width-positions)
* columns from the right margin to the left margin, and copy positions
* columns from the left margin of the row below (if any) to the
* right margin of the current row
*/
int xpos = ranges.getStartRes();
int y = 0;
int copyFromRightStart = labelWidthWest - positions * charWidth;
while (y < canvasHeight)
{
gg.copyArea(copyFromRightStart, y, widthToCopy, repeatHeight,
positions * charWidth, 0);
if (y + repeatHeight < canvasHeight - repeatHeight
&& (xpos + viewportWidth <= xMax))
{
gg.copyArea(labelWidthWest, y + repeatHeight, -positions
* charWidth, repeatHeight, widthToCopy, -repeatHeight);
}
if (av.getScaleLeftWrapped())
{
drawVerticalScale(gg, xpos, xpos + viewportWidth, y + hgap, true);
}
if (av.getScaleRightWrapped())
{
drawVerticalScale(gg, xpos, xpos + viewportWidth, y + hgap, false);
}
y += repeatHeight;
xpos += viewportWidth;
}
}
}
/**
* 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 results
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;
}
}