import jalview.datamodel.SequenceI;
import jalview.renderer.ScaleRenderer;
import jalview.renderer.ScaleRenderer.ScaleMark;
+import jalview.util.Comparison;
import jalview.viewmodel.ViewportListenerI;
import jalview.viewmodel.ViewportRanges;
boolean fastPaint = false;
+ boolean fastpainting = false;
+
int labelWidthWest;
int labelWidthEast;
}
/**
- * DOCUMENT ME!
+ * Draw the scale to the left or right of a wrapped alignment
*
* @param g
- * DOCUMENT ME!
* @param startx
- * DOCUMENT ME!
+ * first column of wrapped width (0.. excluding any hidden columns)
* @param endx
- * DOCUMENT ME!
+ * last column of wrapped width (0.. excluding any hidden columns)
* @param ypos
- * DOCUMENT ME!
+ * vertical offset at which to begin the scale
+ * @param left
+ * if true, scale is left of residues, if false, scale is right
*/
- void drawWestScale(Graphics g, int startx, int endx, int ypos)
+ void drawVerticalScale(Graphics g, int startx, int endx, int ypos,
+ boolean left)
{
- FontMetrics fm = getFontMetrics(av.getFont());
ypos += charHeight;
if (av.hasHiddenColumns())
{
- startx = av.getAlignment().getHiddenColumns()
- .adjustForHiddenColumns(startx);
- endx = av.getAlignment().getHiddenColumns()
- .adjustForHiddenColumns(endx);
- }
-
- int maxwidth = av.getAlignment().getWidth();
- if (av.hasHiddenColumns())
- {
- maxwidth = av.getAlignment().getHiddenColumns()
- .findColumnPosition(maxwidth) - 1;
+ HiddenColumns hiddenColumns = av.getAlignment().getHiddenColumns();
+ startx = hiddenColumns.adjustForHiddenColumns(startx);
+ endx = hiddenColumns.adjustForHiddenColumns(endx);
}
+ FontMetrics fm = getFontMetrics(av.getFont());
- // WEST SCALE
for (int i = 0; i < av.getAlignment().getHeight(); i++)
{
SequenceI seq = av.getAlignment().getSequenceAt(i);
- int index = startx;
- int value = -1;
- while (index < endx)
+ /*
+ * find sequence position of first non-gapped position -
+ * to the right if scale left, to the left if scale right
+ */
+ int index = left ? startx : endx;
+ int value = -1;
+ while (index >= startx && index <= endx)
{
- if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
+ if (!Comparison.isGap(seq.getCharAt(index)))
+ {
+ value = seq.findPosition(index);
+ break;
+ }
+ if (left)
{
index++;
-
- continue;
}
-
- value = av.getAlignment().getSequenceAt(i).findPosition(index);
-
- break;
- }
-
- if (value != -1)
- {
- int x = labelWidthWest - fm.stringWidth(String.valueOf(value))
- - charWidth / 2;
- g.drawString(value + "", x, (ypos + (i * charHeight))
- - (charHeight / 5));
- }
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param g
- * DOCUMENT ME!
- * @param startx
- * DOCUMENT ME!
- * @param endx
- * DOCUMENT ME!
- * @param ypos
- * DOCUMENT ME!
- */
- void drawEastScale(Graphics g, int startx, int endx, int ypos)
- {
- ypos += charHeight;
-
- if (av.hasHiddenColumns())
- {
- endx = av.getAlignment().getHiddenColumns()
- .adjustForHiddenColumns(endx);
- }
-
- SequenceI seq;
- // EAST SCALE
- for (int i = 0; i < av.getAlignment().getHeight(); i++)
- {
- seq = av.getAlignment().getSequenceAt(i);
- int index = endx;
- int value = -1;
-
- while (index > startx)
- {
- if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
+ else
{
index--;
-
- continue;
}
-
- value = seq.findPosition(index);
-
- break;
}
if (value != -1)
{
- g.drawString(String.valueOf(value), 0, (ypos + (i * charHeight))
+ /*
+ * draw scale value, justified, with half a character width
+ * separation from the sequence data
+ */
+ int justify = fm.stringWidth(String.valueOf(value)) + charWidth;
+ int xpos = left ? labelWidthWest - justify + charWidth / 2
+ : getWidth() - justify - charWidth / 2;
+
+ g.drawString(String.valueOf(value), xpos, (ypos + (i * charHeight))
- (charHeight / 5));
}
}
}
- boolean fastpainting = false;
-
/**
* need to make this thread safe move alignment rendering in response to
* slider adjustment
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());
if (av.getScaleLeftWrapped())
{
- labelWidthWest = getLabelWidth(fm);
+ labelWidthWest = labelWidthEast > 0 ? labelWidthEast
+ : getLabelWidth(fm);
}
- return (cwidth - labelWidthEast - labelWidthWest) / charWidth;
+ return (canvasWidth - labelWidthEast - labelWidthWest) / charWidth;
}
/**
*/
protected int getLabelWidth(FontMetrics fm)
{
+ /*
+ * find the biggest sequence end position we need to show
+ * (note this is not necessarily the sequence length)
+ */
int maxWidth = 0;
- for (int i = 0; i < av.getAlignment().getHeight(); i++)
+ AlignmentI alignment = av.getAlignment();
+ for (int i = 0; i < alignment.getHeight(); i++)
{
- maxWidth = Math.max(maxWidth, av.getAlignment().getSequenceAt(i)
- .getEnd());
+ maxWidth = Math.max(maxWidth, alignment.getSequenceAt(i).getEnd());
}
int length = 2;
int canvasHeight, int startRes)
{
updateViewport();
- AlignmentI al = av.getAlignment();
-
int labelWidth = 0;
if (av.getScaleRightWrapped() || av.getScaleLeftWrapped())
{
}
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();
+ int sequencesHeight = av.getAlignment().getHeight() * charHeight;
while ((ypos <= canvasHeight) && (startRes < maxwidth))
{
- endx = startRes + cWidth - 1;
+ drawWrappedWidth(g, startRes, canvasHeight, cWidth, maxwidth, ypos);
- if (endx > maxwidth)
- {
- endx = maxwidth;
- }
+ ypos += sequencesHeight + annotationHeight + hgap;
- g.setFont(av.getFont());
- g.setColor(Color.black);
+ startRes += cWidth;
+ }
+ }
- if (av.getScaleLeftWrapped())
- {
- drawWestScale(g, startRes, endx, ypos);
- }
+ /**
+ * @param g
+ * @param startRes
+ * @param canvasHeight
+ * @param canvasWidth
+ * @param maxWidth
+ * @param ypos
+ */
+ protected void drawWrappedWidth(Graphics g, int startRes,
+ int canvasHeight, int canvasWidth, int maxWidth, int ypos)
+ {
+ int endx;
+ endx = startRes + canvasWidth - 1;
- if (av.getScaleRightWrapped())
- {
- g.translate(canvasWidth - labelWidthEast, 0);
- drawEastScale(g, startRes, endx, ypos);
- g.translate(-(canvasWidth - labelWidthEast), 0);
- }
+ if (endx > maxWidth)
+ {
+ endx = maxWidth;
+ }
- g.translate(labelWidthWest, 0);
+ g.setFont(av.getFont());
+ g.setColor(Color.black);
- if (av.getScaleAboveWrapped())
- {
- drawNorthScale(g, startRes, endx, ypos);
- }
+ if (av.getScaleLeftWrapped())
+ {
+ drawVerticalScale(g, startRes, endx, ypos, true);
+ }
- if (av.hasHiddenColumns() && av.getShowHiddenMarkers())
- {
- g.setColor(Color.blue);
- int res;
- HiddenColumns hidden = av.getAlignment().getHiddenColumns();
- List<Integer> positions = hidden.findHiddenRegionPositions();
- for (int pos : positions)
- {
- res = pos - startRes;
+ if (av.getScaleRightWrapped())
+ {
+ drawVerticalScale(g, startRes, endx, ypos, false);
+ }
- if (res < 0 || res > endx - startRes)
- {
- continue;
- }
+ g.translate(labelWidthWest, 0);
+
+ if (av.getScaleAboveWrapped())
+ {
+ drawNorthScale(g, startRes, endx, ypos);
+ }
- gg.fillPolygon(
- new int[] { res * charWidth - charHeight / 4,
- res * charWidth + charHeight / 4, res * charWidth },
- new int[] { ypos - (charHeight / 2),
- ypos - (charHeight / 2), ypos - (charHeight / 2) + 8 },
- 3);
+ if (av.hasHiddenColumns() && av.getShowHiddenMarkers())
+ {
+ g.setColor(Color.blue);
+ HiddenColumns hidden = av.getAlignment().getHiddenColumns();
+ List<Integer> positions = hidden.findHiddenRegionPositions();
+ for (int pos : positions)
+ {
+ int res = pos - startRes;
+ if (res < 0 || res > endx - startRes)
+ {
+ continue;
}
- }
- // When printing we have an extra clipped region,
- // the Printable page which we need to account for here
- Shape clip = g.getClip();
+ gg.fillPolygon(new int[] { res * charWidth - charHeight / 4,
+ res * charWidth + charHeight / 4, res * charWidth }, new int[] {
+ ypos - (charHeight / 2), ypos - (charHeight / 2),
+ ypos - (charHeight / 2) + 8 }, 3);
- if (clip == null)
- {
- g.setClip(0, 0, cWidth * charWidth, canvasHeight);
- }
- else
- {
- g.setClip(0, (int) clip.getBounds().getY(), cWidth * charWidth,
- (int) clip.getBounds().getHeight());
}
+ }
- drawPanel(g, startRes, endx, 0, al.getHeight() - 1, ypos);
+ // When printing we have an extra clipped region,
+ // the Printable page which we need to account for here
+ Shape clip = g.getClip();
- if (av.isShowAnnotation())
- {
- g.translate(0, cHeight + ypos + 3);
- if (annotations == null)
- {
- annotations = new AnnotationPanel(av);
- }
+ if (clip == null)
+ {
+ g.setClip(0, 0, canvasWidth * charWidth, canvasHeight);
+ }
+ else
+ {
+ g.setClip(0, (int) clip.getBounds().getY(), canvasWidth * charWidth,
+ (int) clip.getBounds().getHeight());
+ }
- annotations.renderer.drawComponent(annotations, av, g, -1,
- startRes, endx + 1);
- g.translate(0, -cHeight - ypos - 3);
- }
- g.setClip(clip);
- g.translate(-labelWidthWest, 0);
+ drawPanel(g, startRes, endx, 0, av.getAlignment().getHeight() - 1, ypos);
- ypos += cHeight + annotationHeight + hgap;
+ int cHeight = av.getAlignment().getHeight() * charHeight;
- startRes += cWidth;
+ if (av.isShowAnnotation())
+ {
+ g.translate(0, cHeight + ypos + 3);
+ if (annotations == null)
+ {
+ annotations = new AnnotationPanel(av);
+ }
+
+ annotations.renderer.drawComponent(annotations, av, g, -1, startRes,
+ endx + 1);
+ g.translate(0, -cHeight - ypos - 3);
}
+ g.setClip(clip);
+ g.translate(-labelWidthWest, 0);
}
AnnotationPanel annotations;
* 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 boolean highlightSearchResults(SearchResultsI results)
+ public boolean highlightSearchResults(SearchResultsI results,
+ boolean noFastPaint)
{
- updateViewport();
-
- /*
- * for now, don't attempt fastpaint if wrapped format
- */
- boolean wrapped = av.getWrapAlignment();
- if (wrapped)
+ if (fastpainting)
{
- // drawWrappedMappedPositions(results);
- // 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
boolean drawn = false;
if (wrapped)
{
- redrawn = drawWrappedMappedPositions(previous);
- drawn = drawWrappedMappedPositions(results);
+ redrawn = drawMappedPositionsWrapped(previous);
+ drawn = drawMappedPositionsWrapped(results);
redrawn |= drawn;
}
else
{
fastpainting = false;
}
-
}
/**
@Override
public void propertyChange(PropertyChangeEvent evt)
{
- if (!av.getWrapAlignment())
+ String eventName = evt.getPropertyName();
+
+ if (true/*!av.getWrapAlignment()*/)
{
- if (evt.getPropertyName().equals("startres")
- || evt.getPropertyName().equals("endres"))
+ 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;
}
- fastPaint(scrollX, 0);
}
- else if (evt.getPropertyName().equals("startseq")
- || evt.getPropertyName().equals("endseq"))
+
+ // 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);
+ }
+ else
+ {
+ fastPaint(scrollX, 0);
+ }
+ }
+ 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. 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.
+ * 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) > 0 /*av.getRanges().getViewportWidth()*/)
+ {
+ /*
+ * shift of more than one view width is too much
+ * to handle in this method
+ */
+ fastPaint = false;
+ repaint();
+ return;
+ }
+
+ fastPaint = true;
+ shiftWrappedAlignment(-scrollX);
+
+ // add new columns (scale above, sequence, annotation)
+ // at top left if scrollX < 0 or bottom right if scrollX > 0
+
+ repaint();
+ }
+
+ /**
+ * 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 widthToCopy = (ranges.getViewportWidth() - Math.abs(positions))
+ * charWidth;
+ int visibleWidths = getHeight() / repeatHeight;
+ if (getHeight() % repeatHeight > 0)
+ {
+ visibleWidths++;
+ }
+ int viewportWidth = ranges.getViewportWidth();
+
+ 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 = getHeight() / repeatHeight * repeatHeight;
+ int copyFromLeftStart = labelWidthWest;
+ int copyFromRightStart = copyFromLeftStart + widthToCopy;
+
+ while (y >= 0)
+ {
+ // todo limit repeatHeight for a last part height width
+ 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, y, true);
+ }
+ if (av.getScaleRightWrapped())
+ {
+ // drawVerticalScale(gg, xpos, xpos + viewportWidth, y, 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 < getHeight())
+ {
+ // todo limit repeatHeight for a last part height width
+ gg.copyArea(copyFromRightStart, y, widthToCopy, repeatHeight,
+ positions * charWidth, 0);
+ if (y + repeatHeight < getHeight())
+ {
+ gg.copyArea(labelWidthWest, y + repeatHeight, -positions
+ * charWidth, repeatHeight, widthToCopy, -repeatHeight);
+ }
+
+ if (av.getScaleLeftWrapped())
+ {
+ // drawVerticalScale(gg, xpos, xpos + viewportWidth, y, true);
+ }
+ if (av.getScaleRightWrapped())
+ {
+ // drawVerticalScale(gg, xpos, xpos + viewportWidth, y, false);
+ }
+
+ y += repeatHeight;
+ xpos += ranges.getViewportWidth();
+ }
+ }
+ }
+
+ /**
+ * 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 drawWrappedMappedPositions(SearchResultsI results)
+ protected boolean drawMappedPositionsWrapped(SearchResultsI results)
{
if (results == null)
{
}
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
- */
+
+ int wrappedWidth = av.getWrappedWidth();
+ int wrappedHeight = getRepeatHeightWrapped();
+
ViewportRanges ranges = av.getRanges();
- int firstVisibleColumn = ranges.getStartRes() - 6;
- int lastVisibleColumn = ranges.getEndRes() + 6;
+ 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())
{
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();
+
+ int gapHeight = charHeight * (av.getScaleAboveWrapped() ? 2 : 1);
for (int seqNo = ranges.getStartSeq(); seqNo <= ranges
.getEndSeq(); seqNo++)
* transY: offset from top edge of canvas to residue position
*/
int transY = gapHeight;
- transY += (displayColumn / wrappedWidth) * wrappedHeight;
+ transY += (displayColumn - ranges.getStartRes())
+ / wrappedWidth * wrappedHeight;
transY += (seqNo - ranges.getStartSeq()) * av.getCharHeight();
/*
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