package jalview.appletgui;
import jalview.datamodel.SequenceI;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
import jalview.viewmodel.OverviewDimensions;
import java.awt.Color;
sr.forOverview = true;
fr = new FeatureRenderer(av);
- od = new OverviewDimensions(av.getPosProps(), av.isShowAnnotation());
+ od = new OverviewDimensions(av.getRanges(),
+ (av.isShowAnnotation() && av.getSequenceConsensusHash() != null));
setSize(new Dimension(od.getWidth(), od.getHeight()));
addComponentListener(new ComponentAdapter()
{
od.updateViewportFromMouse(evt.getX(), evt.getY(), av.getAlignment()
.getHiddenSequences(), av.getColumnSelection(), av
- .getPosProps());
+ .getRanges());
ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
ap.paintAlignment(false);
}
resizing = true;
- if ((getWidth() > 0) && (getHeight() > 0))
+ if ((getSize().width > 0) && (getSize().height > 0))
{
- od.setWidth(getWidth());
- od.setHeight(getHeight());
+ od.setWidth(getSize().width);
+ od.setHeight(getSize().height);
}
setSize(new Dimension(od.getWidth(), od.getHeight()));
if (getSize().width > 0 && getSize().height > 0)
{
od.setWidth(getSize().width);
- od.setHeight(getSize().height - od.getGraphHeight());
+ od.setHeight(getSize().height);
}
setSize(new Dimension(od.getWidth(), od.getHeight()));
buildImage(sampleRow, sampleCol, mg);
- if (av.isShowAnnotation())
+ // check for conservation annotation to make sure overview works for DNA too
+ if (av.isShowAnnotation()
+ && (av.getAlignmentConservationAnnotation() != null))
{
for (int col = 0; col < od.getWidth() && !resizeAgain; col++)
{
int sameCol = 0;
SequenceI seq = null;
+ FeatureColourFinder finder = new FeatureColourFinder(fr);
final boolean hasHiddenCols = av.hasHiddenColumns();
boolean hiddenRow = false;
lastcol = (int) (col * sampleCol);
color = getColumnColourFromSequence(seq, hiddenRow,
- hasHiddenCols, lastcol);
+ hasHiddenCols, lastcol, finder);
mg.setColor(color);
if (sameCol == 1 && sameRow == 1)
*/
private Color getColumnColourFromSequence(
jalview.datamodel.SequenceI seq, boolean hiddenRow,
- boolean hasHiddenCols, int lastcol)
+ boolean hasHiddenCols, int lastcol, FeatureColourFinder finder)
{
- Color color;
+ Color color = Color.white;
if (seq.getLength() > lastcol)
{
- color = sr.getResidueBoxColour(seq, lastcol);
-
- if (av.isShowSequenceFeatures())
- {
- color = fr.findFeatureColour(color, seq, lastcol);
- }
- }
- else
- {
- color = Color.white;
+ color = sr.getResidueColour(seq, lastcol, finder);
}
if (hiddenRow
public void setBoxPosition()
{
od.setBoxPosition(av.getAlignment()
- .getHiddenSequences(), av.getColumnSelection(), av.getPosProps());
+ .getHiddenSequences(), av.getColumnSelection(), av.getRanges());
repaint();
}