package jalview.appletgui;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.datamodel.VisibleContigsIterator;
import jalview.renderer.ScaleRenderer;
import jalview.renderer.ScaleRenderer.ScaleMark;
import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.ViewportListenerI;
+import jalview.viewmodel.ViewportRanges;
import java.awt.Color;
import java.awt.FontMetrics;
import java.awt.Graphics;
import java.awt.Image;
import java.awt.Panel;
+import java.beans.PropertyChangeEvent;
+import java.util.Iterator;
-public class SeqCanvas extends Panel
+public class SeqCanvas extends Panel implements ViewportListenerI
{
FeatureRenderer fr;
sr = new SequenceRenderer(av);
PaintRefresher.Register(this, av.getSequenceSetId());
updateViewport();
+
+ av.getRanges().addPropertyChangeListener(this);
}
int avcharHeight = 0, avcharWidth = 0;
{
if (mstring != null)
{
- g.drawString(mstring, mpos * avcharWidth, ypos
- - (avcharHeight / 2));
+ g.drawString(mstring, mpos * avcharWidth,
+ ypos - (avcharHeight / 2));
}
- g.drawLine((mpos * avcharWidth) + (avcharWidth / 2), (ypos + 2)
- - (avcharHeight / 2), (mpos * avcharWidth)
- + (avcharWidth / 2), ypos - 2);
+ g.drawLine((mpos * avcharWidth) + (avcharWidth / 2),
+ (ypos + 2) - (avcharHeight / 2),
+ (mpos * avcharWidth) + (avcharWidth / 2), ypos - 2);
}
}
}
ypos += avcharHeight;
if (av.hasHiddenColumns())
{
- startx = av.getColumnSelection().adjustForHiddenColumns(startx);
- endx = av.getColumnSelection().adjustForHiddenColumns(endx);
+ startx = av.getAlignment().getHiddenColumns()
+ .visibleToAbsoluteColumn(startx);
+ endx = av.getAlignment().getHiddenColumns()
+ .visibleToAbsoluteColumn(endx);
}
int maxwidth = av.getAlignment().getWidth();
if (av.hasHiddenColumns())
{
- maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+ maxwidth = av.getAlignment().getHiddenColumns()
+ .absoluteToVisibleColumn(maxwidth) - 1;
}
// WEST SCALE
{
int x = LABEL_WEST - fm.stringWidth(String.valueOf(value))
- avcharWidth / 2;
- g.drawString(value + "", x, (ypos + (i * avcharHeight))
- - (avcharHeight / 5));
+ g.drawString(value + "", x,
+ (ypos + (i * avcharHeight)) - (avcharHeight / 5));
}
}
}
if (av.hasHiddenColumns())
{
- endx = av.getColumnSelection().adjustForHiddenColumns(endx);
+ endx = av.getAlignment().getHiddenColumns()
+ .visibleToAbsoluteColumn(endx);
}
SequenceI seq;
if (value != -1)
{
- g.drawString(String.valueOf(value), 0, (ypos + (i * avcharHeight))
- - (avcharHeight / 5));
+ g.drawString(String.valueOf(value), 0,
+ (ypos + (i * avcharHeight)) - (avcharHeight / 5));
}
}
}
return;
}
+ ViewportRanges ranges = av.getRanges();
+
updateViewport();
// Its possible on certain browsers that the call to fastpaint
// is faster than it can paint, so this check here catches
// this possibility
- if (lastsr + horizontal != av.startRes)
+ if (lastsr + horizontal != ranges.getStartRes())
{
- horizontal = av.startRes - lastsr;
+ horizontal = ranges.getStartRes() - lastsr;
}
- lastsr = av.startRes;
+ lastsr = ranges.getStartRes();
fastPaint = true;
- gg.copyArea(horizontal * avcharWidth, vertical * avcharHeight, imgWidth
- - horizontal * avcharWidth,
+ gg.copyArea(horizontal * avcharWidth, vertical * avcharHeight,
+ imgWidth - horizontal * avcharWidth,
imgHeight - vertical * avcharHeight, -horizontal * avcharWidth,
-vertical * avcharHeight);
- int sr = av.startRes, er = av.endRes, ss = av.startSeq, es = av.endSeq, transX = 0, transY = 0;
+ int sr = ranges.getStartRes(), er = ranges.getEndRes(),
+ ss = ranges.getStartSeq(), es = ranges.getEndSeq(), transX = 0,
+ transY = 0;
if (horizontal > 0) // scrollbar pulled right, image to the left
{
else if (vertical > 0) // scroll down
{
ss = es - vertical;
- if (ss < av.startSeq) // ie scrolling too fast, more than a page at a time
+ if (ss < ranges.getStartSeq()) // ie scrolling too fast, more than a page
+ // at a
+ // time
{
- ss = av.startSeq;
+ ss = ranges.getStartSeq();
}
else
{
- transY = imgHeight - vertical * avcharHeight;
+ transY = imgHeight - ((vertical + 1) * avcharHeight);
}
}
else if (vertical < 0)
{
es = ss - vertical;
- if (es > av.endSeq)
+ if (es > ranges.getEndSeq())
{
- es = av.endSeq;
+ es = ranges.getEndSeq();
}
}
{
if (img != null
- && (fastPaint || (getSize().width != g.getClipBounds().width) || (getSize().height != g
- .getClipBounds().height)))
+ && (fastPaint || (getSize().width != g.getClipBounds().width)
+ || (getSize().height != g.getClipBounds().height)))
{
g.drawImage(img, 0, 0, this);
fastPaint = false;
gg.setColor(Color.white);
gg.fillRect(0, 0, imgWidth, imgHeight);
+ ViewportRanges ranges = av.getRanges();
+
if (av.getWrapAlignment())
{
- drawWrappedPanel(gg, imgWidth, imgHeight, av.startRes);
+ drawWrappedPanel(gg, imgWidth, imgHeight, ranges.getStartRes());
}
else
{
- drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, 0);
+ drawPanel(gg, ranges.getStartRes(), ranges.getEndRes(),
+ ranges.getStartSeq(), ranges.getEndSeq(), 0);
}
g.drawImage(img, 0, 0, this);
int canvasHeight, int startRes)
{
AlignmentI al = av.getAlignment();
-
+
FontMetrics fm = getFontMetrics(av.getFont());
-
+
+ LABEL_EAST = 0;
+ LABEL_WEST = 0;
+
if (av.getScaleRightWrapped())
{
LABEL_EAST = fm.stringWidth(getMask());
}
-
+
if (av.getScaleLeftWrapped())
{
LABEL_WEST = fm.stringWidth(getMask());
}
-
+
int hgap = avcharHeight;
if (av.getScaleAboveWrapped())
{
hgap += avcharHeight;
}
-
+
int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / avcharWidth;
int cHeight = av.getAlignment().getHeight() * avcharHeight;
-
+
av.setWrappedWidth(cWidth);
-
- av.endRes = av.startRes + cWidth;
-
+
+ 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.getColumnSelection().findColumnPosition(maxwidth) - 1;
+ maxwidth = av.getAlignment().getHiddenColumns()
+ .absoluteToVisibleColumn(maxwidth);
}
-
+
while ((ypos <= canvasHeight) && (startRes < maxwidth))
{
endx = startRes + cWidth - 1;
-
+
if (endx > maxwidth)
{
endx = maxwidth;
}
-
+
g.setColor(Color.black);
-
+
if (av.getScaleLeftWrapped())
{
drawWestScale(g, startRes, endx, ypos);
}
-
+
if (av.getScaleRightWrapped())
{
g.translate(canvasWidth - LABEL_EAST, 0);
drawEastScale(g, startRes, endx, ypos);
g.translate(-(canvasWidth - LABEL_EAST), 0);
}
-
+
g.translate(LABEL_WEST, 0);
-
+
if (av.getScaleAboveWrapped())
{
drawNorthScale(g, startRes, endx, ypos);
}
if (av.hasHiddenColumns() && av.getShowHiddenMarkers())
{
+ HiddenColumns hidden = av.getAlignment().getHiddenColumns();
g.setColor(Color.blue);
int res;
- for (int i = 0; i < av.getColumnSelection().getHiddenColumns()
- .size(); i++)
+ Iterator<Integer> it = hidden.getStartRegionIterator(startRes,
+ endx + 1);
+ while (it.hasNext())
{
- res = av.getColumnSelection().findHiddenRegionPosition(i)
- - startRes;
-
- if (res < 0 || res > endx - startRes)
- {
- continue;
- }
-
- gg.fillPolygon(new int[] { res * avcharWidth - avcharHeight / 4,
- res * avcharWidth + avcharHeight / 4, res * avcharWidth },
- new int[] { ypos - (avcharHeight / 2),
- ypos - (avcharHeight / 2),
- ypos - (avcharHeight / 2) + 8 }, 3);
-
+ res = it.next() - startRes;
+ gg.fillPolygon(
+ new int[]
+ { res * avcharWidth - avcharHeight / 4, res * avcharWidth + avcharHeight / 4, res * avcharWidth },
+ new int[]
+ { ypos - (avcharHeight / 2), ypos - (avcharHeight / 2), ypos - (avcharHeight / 2) + 8 }, 3);
}
}
-
+
if (g.getClip() == null)
{
g.setClip(0, 0, cWidth * avcharWidth, canvasHeight);
}
-
- drawPanel(g, startRes, endx, 0, al.getHeight(), ypos);
+
+ drawPanel(g, startRes, endx, 0, al.getHeight() - 1, ypos);
g.setClip(null);
-
+
if (av.isShowAnnotation())
{
g.translate(0, cHeight + ypos + 4);
{
annotations = new AnnotationPanel(av);
}
-
+
annotations.drawComponent(g, startRes, endx + 1);
g.translate(0, -cHeight - ypos - 4);
}
g.translate(-LABEL_WEST, 0);
-
+
ypos += cHeight + getAnnotationHeight() + hgap;
-
+
startRes += cWidth;
}
-
+
}
AnnotationPanel annotations;
return annotations.adjustPanelHeight();
}
- private void drawPanel(Graphics g1, int startRes, int endRes,
- int startSeq, int endSeq, int offset)
+ private void drawPanel(Graphics g1, final int startRes, final int endRes,
+ final int startSeq, final int endSeq, final int offset)
{
if (!av.hasHiddenColumns())
}
else
{
-
int screenY = 0;
- int blockStart = startRes;
- int blockEnd = endRes;
-
- if (av.hasHiddenColumns())
- {
- for (int[] region : av.getColumnSelection().getHiddenColumns())
- {
- int hideStart = region[0];
- int hideEnd = region[1];
-
- if (hideStart <= blockStart)
- {
- blockStart += (hideEnd - hideStart) + 1;
- continue;
- }
-
- blockEnd = hideStart - 1;
+ int blockStart;
+ int blockEnd;
- g1.translate(screenY * avcharWidth, 0);
+ HiddenColumns hidden = av.getAlignment().getHiddenColumns();
+ VisibleContigsIterator regions = (VisibleContigsIterator) hidden
+ .getVisContigsIterator(startRes, endRes + 1, true);
- draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
-
- if (av.getShowHiddenMarkers())
- {
- g1.setColor(Color.blue);
- g1.drawLine((blockEnd - blockStart + 1) * avcharWidth - 1,
- 0 + offset, (blockEnd - blockStart + 1) * avcharWidth
- - 1, (endSeq - startSeq) * avcharHeight
- + offset);
- }
-
- g1.translate(-screenY * avcharWidth, 0);
- screenY += blockEnd - blockStart + 1;
- blockStart = hideEnd + 1;
-
- if (screenY > (endRes - startRes))
- {
- // already rendered last block
- return;
- }
- }
- }
- if (screenY <= (endRes - startRes))
+ while (regions.hasNext())
{
- // remaining visible region to render
- blockEnd = blockStart + (endRes - startRes) - screenY;
+ int[] region = regions.next();
+ blockEnd = region[1];
+ blockStart = region[0];
+
+ /*
+ * draw up to just before the next hidden region, or the end of
+ * the visible region, whichever comes first
+ */
g1.translate(screenY * avcharWidth, 0);
+
draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
+ /*
+ * draw the downline of the hidden column marker (ScalePanel draws the
+ * triangle on top) if we reached it
+ */
+ if (av.getShowHiddenMarkers()
+ && (regions.hasNext() || regions.endsAtHidden()))
+ {
+ g1.setColor(Color.blue);
+ g1.drawLine((blockEnd - blockStart + 1) * avcharWidth - 1,
+ 0 + offset, (blockEnd - blockStart + 1) * avcharWidth - 1,
+ (endSeq - startSeq + 1) * avcharHeight + offset);
+ }
+
g1.translate(-screenY * avcharWidth, 0);
+ screenY += blockEnd - blockStart + 1;
}
}
-
}
// int startRes, int endRes, int startSeq, int endSeq, int x, int y,
// / First draw the sequences
// ///////////////////////////
- for (int i = startSeq; i < endSeq; i++)
+ for (int i = startSeq; i <= endSeq; i++)
{
nextSeq = av.getAlignment().getSequenceAt(i);
if (av.isShowSequenceFeatures())
{
- fr.drawSequence(g, nextSeq, startRes, endRes, offset
- + ((i - startSeq) * avcharHeight));
+ fr.drawSequence(g, nextSeq, startRes, endRes,
+ offset + ((i - startSeq) * avcharHeight), false);
}
// / Highlight search Results once all sequences have been drawn
if (av.hasSearchResults())
{
int[] visibleResults = av.getSearchResults().getResults(nextSeq,
- startRes,
- endRes);
+ startRes, endRes);
if (visibleResults != null)
{
for (int r = 0; r < visibleResults.length; r += 2)
{
sr.drawHighlightedText(nextSeq, visibleResults[r],
- visibleResults[r + 1], (visibleResults[r] - startRes)
- * avcharWidth, offset
- + ((i - startSeq) * avcharHeight));
+ visibleResults[r + 1],
+ (visibleResults[r] - startRes) * avcharWidth,
+ offset + ((i - startSeq) * avcharHeight));
}
}
}
int bottom = -1;
int alHeight = av.getAlignment().getHeight() - 1;
- for (i = startSeq; i < endSeq; i++)
+ for (i = startSeq; i <= endSeq; i++)
{
sx = (group.getStartRes() - startRes) * avcharWidth;
sy = offset + ((i - startSeq) * avcharHeight);
- ex = (((group.getEndRes() + 1) - group.getStartRes()) * avcharWidth) - 1;
+ ex = (((group.getEndRes() + 1) - group.getStartRes())
+ * avcharWidth) - 1;
if (sx + ex < 0 || sx > imgWidth)
{
}
if ((sx <= (endRes - startRes) * avcharWidth)
- && group.getSequences(null).contains(
- av.getAlignment().getSequenceAt(i)))
+ && group.getSequences(null)
+ .contains(av.getAlignment().getSequenceAt(i)))
{
if ((bottom == -1)
- && (i >= alHeight || !group.getSequences(null)
- .contains(
- av.getAlignment().getSequenceAt(i + 1))))
+ && (i >= alHeight || !group.getSequences(null).contains(
+ av.getAlignment().getSequenceAt(i + 1))))
{
bottom = sy + avcharHeight;
}
if (!inGroup)
{
- if (((top == -1) && (i == 0))
- || !group.getSequences(null).contains(
- av.getAlignment().getSequenceAt(i - 1)))
+ if (((top == -1) && (i == 0)) || !group.getSequences(null)
+ .contains(av.getAlignment().getSequenceAt(i - 1)))
{
top = sy;
}
repaint();
}
+ @Override
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ String eventName = evt.getPropertyName();
+
+ if (eventName.equals(SequenceGroup.SEQ_GROUP_CHANGED))
+ {
+ fastPaint = true;
+ repaint();
+ return;
+ }
+ else if (eventName.equals(ViewportRanges.MOVE_VIEWPORT))
+ {
+ fastPaint = false;
+ repaint();
+ return;
+ }
+
+ if (!av.getWrapAlignment())
+ {
+ int scrollX = 0;
+ if (eventName.equals(ViewportRanges.STARTRES)
+ || eventName.equals(ViewportRanges.STARTRESANDSEQ))
+ {
+ // Make sure we're not trying to draw a panel
+ // larger than the visible window
+ if (eventName.equals(ViewportRanges.STARTRES))
+ {
+ scrollX = (int) evt.getNewValue() - (int) evt.getOldValue();
+ }
+ else
+ {
+ scrollX = ((int[]) evt.getNewValue())[0]
+ - ((int[]) evt.getOldValue())[0];
+ }
+ ViewportRanges vpRanges = av.getRanges();
+ 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
+ fastPaint(scrollX, 0);
+ }
+ else if (eventName.equals(ViewportRanges.STARTSEQ))
+ {
+ // scroll
+ fastPaint(0, (int) evt.getNewValue() - (int) evt.getOldValue());
+ }
+ else if (eventName.equals(ViewportRanges.STARTRESANDSEQ))
+ {
+ fastPaint(scrollX, 0);
+ }
+ }
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff