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 java.beans.PropertyChangeEvent;
import java.util.Iterator;
+@SuppressWarnings("serial")
public class SeqCanvas extends Panel implements ViewportListenerI
{
FeatureRenderer fr;
if (av.hasHiddenColumns())
{
startx = av.getAlignment().getHiddenColumns()
- .adjustForHiddenColumns(startx);
+ .visibleToAbsoluteColumn(startx);
endx = av.getAlignment().getHiddenColumns()
- .adjustForHiddenColumns(endx);
- }
-
- int maxwidth = av.getAlignment().getWidth();
- if (av.hasHiddenColumns())
- {
- maxwidth = av.getAlignment().getHiddenColumns()
- .findColumnPosition(maxwidth) - 1;
+ .visibleToAbsoluteColumn(endx);
}
// WEST SCALE
if (av.hasHiddenColumns())
{
endx = av.getAlignment().getHiddenColumns()
- .adjustForHiddenColumns(endx);
+ .visibleToAbsoluteColumn(endx);
}
SequenceI seq;
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.getRanges().setViewportStartAndWidth(startRes, cWidth);
-
+
int endx;
int ypos = hgap;
-
- int maxwidth = av.getAlignment().getWidth();
-
- if (av.hasHiddenColumns())
- {
- maxwidth = av.getAlignment().getHiddenColumns()
- .findColumnPosition(maxwidth);
- }
-
+
+ int maxwidth = av.getAlignment().getVisibleWidth();
+
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);
HiddenColumns hidden = av.getAlignment().getHiddenColumns();
g.setColor(Color.blue);
int res;
- Iterator<Integer> it = hidden.getBoundedStartIterator(startRes,
+ Iterator<Integer> it = hidden.getStartRegionIterator(startRes,
endx + 1);
while (it.hasNext())
{
res = it.next() - startRes;
gg.fillPolygon(
new int[]
- { res * avcharWidth - avcharHeight / 4, res * avcharWidth + avcharHeight / 4, res * avcharWidth },
+ { res * avcharWidth - avcharHeight / 4,
+ res * avcharWidth + avcharHeight / 4,
+ res * avcharWidth },
new int[]
- { ypos - (avcharHeight / 2), ypos - (avcharHeight / 2), ypos - (avcharHeight / 2) + 8 }, 3);
+ { 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() - 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;
else
{
int screenY = 0;
- final int screenYMax = endRes - startRes;
- int blockStart = startRes;
- int blockEnd = endRes; // equals blockStart + screenYMax - screenY;
+ int blockStart;
+ int blockEnd;
HiddenColumns hidden = av.getAlignment().getHiddenColumns();
- Iterator<int[]> regions = hidden.iterator();
+ VisibleContigsIterator regions = hidden
+ .getVisContigsIterator(startRes, endRes + 1, true);
+
while (regions.hasNext())
{
int[] region = regions.next();
- int hideStart = region[0];
- int hideEnd = region[1];
-
- if (hideStart <= blockStart)
- {
- blockStart += (hideEnd - hideStart) + 1;
- blockEnd += (hideEnd - hideStart) + 1;
- continue;
- }
+ 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
*/
- blockEnd = Math.min(blockEnd, hideStart - 1);
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() && blockEnd == hideStart - 1)
+ if (av.getShowHiddenMarkers()
+ && (regions.hasNext() || regions.endsAtHidden()))
{
g1.setColor(Color.blue);
g1.drawLine((blockEnd - blockStart + 1) * avcharWidth - 1,
g1.translate(-screenY * avcharWidth, 0);
screenY += blockEnd - blockStart + 1;
- blockStart = hideEnd + 1;
- blockEnd = blockStart + screenYMax - screenY;
-
- if (screenY > screenYMax)
- {
- // already rendered last block
- return;
- }
- }
-
- if (screenY <= screenYMax)
- {
- // remaining visible region to render
- g1.translate(screenY * avcharWidth, 0);
- draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
- g1.translate(-screenY * avcharWidth, 0);
}
}
}
if (av.cursorMode && cursorY == i && cursorX >= startRes
&& cursorX <= endRes)
{
- sr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * avcharWidth,
+ char s = nextSeq.getCharAt(cursorX);
+
+ sr.drawCursor(g,s, (cursorX - startRes) * avcharWidth,
offset + ((i - startSeq) * avcharHeight));
}
}
{
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))
+ 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();
- scrollX = (int) evt.getNewValue() - (int) evt.getOldValue();
int range = vpRanges.getEndRes() - vpRanges.getStartRes();
if (scrollX > range)
{
// scroll
fastPaint(0, (int) evt.getNewValue() - (int) evt.getOldValue());
}
+ else if (eventName.equals(ViewportRanges.STARTRESANDSEQ))
+ {
+ fastPaint(scrollX, 0);
+ }
}
}
+ /**
+ * Ensure that a full paint is done next, for whatever reason. This was
+ * necessary for JavaScript; apparently in Java the timing is just right on
+ * multiple threads (EventQueue-0, Consensus, Conservation) that we can get
+ * away with one fast paint before the others, but this ensures that in the
+ * end we get a full paint. Problem arose in relation to copy/paste, where the
+ * paste was not finalized with a full paint.
+ *
+ * @author hansonr 2019.04.17
+ */
+ public void clearFastPaint()
+ {
+ fastPaint = false;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff