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.awt.Image;
import java.awt.Panel;
import java.beans.PropertyChangeEvent;
-import java.util.List;
+import java.util.Iterator;
public class SeqCanvas extends Panel implements ViewportListenerI
{
if (av.hasHiddenColumns())
{
startx = av.getAlignment().getHiddenColumns()
- .adjustForHiddenColumns(startx);
+ .visibleToAbsoluteColumn(startx);
endx = av.getAlignment().getHiddenColumns()
- .adjustForHiddenColumns(endx);
+ .visibleToAbsoluteColumn(endx);
}
int maxwidth = av.getAlignment().getWidth();
if (av.hasHiddenColumns())
{
maxwidth = av.getAlignment().getHiddenColumns()
- .findColumnPosition(maxwidth) - 1;
+ .absoluteToVisibleColumn(maxwidth) - 1;
}
// 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);
+ .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);
HiddenColumns hidden = av.getAlignment().getHiddenColumns();
g.setColor(Color.blue);
int res;
- List<Integer> positions = hidden.findHiddenRegionPositions();
- for (int pos : positions)
+ Iterator<Integer> it = hidden.getStartRegionIterator(startRes,
+ endx + 1);
+ while (it.hasNext())
{
- res = pos - startRes;
-
- if (res < 0 || res > endx - startRes)
- {
- continue;
- }
-
+ 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;
-
- if (av.hasHiddenColumns())
- {
- HiddenColumns hidden = av.getAlignment().getHiddenColumns();
- for (int[] region : hidden.getHiddenColumnsCopy())
- {
- int hideStart = region[0];
- int hideEnd = region[1];
-
- if (hideStart <= blockStart)
- {
- blockStart += (hideEnd - hideStart) + 1;
- continue;
- }
-
- /*
- * draw up to just before the next hidden region, or the end of
- * the visible region, whichever comes first
- */
- blockEnd = Math.min(hideStart - 1, blockStart + screenYMax
- - screenY);
-
- g1.translate(screenY * avcharWidth, 0);
+ int blockStart;
+ int blockEnd;
- draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
+ HiddenColumns hidden = av.getAlignment().getHiddenColumns();
+ VisibleContigsIterator regions = (VisibleContigsIterator) hidden
+ .getVisContigsIterator(startRes, endRes + 1, true);
- /*
- * draw the downline of the hidden column marker (ScalePanel draws the
- * triangle on top) if we reached it
- */
- if (av.getShowHiddenMarkers() && blockEnd == hideStart - 1)
- {
- 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;
- blockStart = hideEnd + 1;
-
- if (screenY > screenYMax)
- {
- // already rendered last block
- return;
- }
- }
- }
- if (screenY <= screenYMax)
+ 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,
git://source.jalview.org / jalview.git / blobdiff