/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
* Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
* DOCUMENT ME!
*
* @author $author$
- * @version $Revision$
+ * @version $Revision: 1.130 $
*/
public class SeqPanel extends JPanel implements MouseListener,
MouseMotionListener, MouseWheelListener, SequenceListener,
addMouseMotionListener(this);
addMouseListener(this);
addMouseWheelListener(this);
- ssm = StructureSelectionManager.getStructureSelectionManager();
+ ssm = StructureSelectionManager.getStructureSelectionManager(Desktop.instance);
ssm.addStructureViewerListener(this);
ssm.addSelectionListener(this);
}
}
else
{
+ if (x>seqCanvas.getWidth()+seqCanvas.getWidth())
+ {
+ // make sure we calculate relative to visible alignment, rather than right-hand gutter
+ x = seqCanvas.getX()+seqCanvas.getWidth();
+ }
res = (x / av.getCharWidth()) + av.getStartRes();
}
y -= hgap;
- seq = Math.min((y % cHeight) / av.getCharHeight(), av.alignment
- .getHeight() - 1);
+ seq = Math.min((y % cHeight) / av.getCharHeight(),
+ av.alignment.getHeight() - 1);
}
else
{
if (lastMessage == null || !lastMessage.equals(tmp))
{
// System.err.println("mouseOver Sequence: "+tmp);
- ssm.mouseOverSequence(sequence, index, pos);
+ ssm.mouseOverSequence(sequence, index, pos, av);
}
lastMessage = tmp;
}
{
if (av.followHighlight)
{
- ap.scrollToPosition(results, false);
+ if (ap.scrollToPosition(results, false))
+ {
+ seqCanvas.revalidate();
+ }
}
seqCanvas.highlightSearchResults(results);
}
if (av.showSequenceFeatures)
{
int rpos;
- SequenceFeature[] features = findFeaturesAtRes(sequence
- .getDatasetSequence(), rpos = sequence.findPosition(res));
+ SequenceFeature[] features = findFeaturesAtRes(
+ sequence.getDatasetSequence(),
+ rpos = sequence.findPosition(res));
appendFeatures(tooltipText, linkImageURL.toString(), rpos, features,
this.ap.seqPanel.seqCanvas.fr.minmax);
}
// Which is bigger, left-right or up-down?
if (Math.abs(evt.getY() - lastMousePress.getY()) > Math.abs(evt
- .getX()
- - lastMousePress.getX()))
+ .getX() - lastMousePress.getX()))
{
int fontSize = av.font.getSize();
fontSize = 1;
}
- av
- .setFont(new Font(av.font.getName(), av.font.getStyle(),
- fontSize));
+ av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
av.charWidth = oldWidth;
ap.fontChanged();
}
av.setSelectionGroup(null);
}
- SequenceFeature[] features = findFeaturesAtRes(sequence
- .getDatasetSequence(), sequence.findPosition(findRes(evt)));
+ SequenceFeature[] features = findFeaturesAtRes(
+ sequence.getDatasetSequence(),
+ sequence.findPosition(findRes(evt)));
if (features != null && features.length > 0)
{
SearchResults highlight = new SearchResults();
- highlight.addResult(sequence, features[0].getBegin(), features[0]
- .getEnd());
+ highlight.addResult(sequence, features[0].getBegin(),
+ features[0].getEnd());
seqCanvas.highlightSearchResults(highlight);
}
if (features != null && features.length > 0)
if (javax.swing.SwingUtilities.isRightMouseButton(evt))
{
- SequenceFeature[] allFeatures = findFeaturesAtRes(sequence
- .getDatasetSequence(), sequence.findPosition(res));
+ SequenceFeature[] allFeatures = findFeaturesAtRes(
+ sequence.getDatasetSequence(), sequence.findPosition(res));
Vector links = new Vector();
for (int i = 0; i < allFeatures.length; i++)
{
{
if (stretchGroup.cs instanceof ClustalxColourScheme)
{
- ((ClustalxColourScheme) stretchGroup.cs).resetClustalX(stretchGroup
- .getSequences(av.hiddenRepSequences), stretchGroup
- .getWidth());
+ ((ClustalxColourScheme) stretchGroup.cs).resetClustalX(
+ stretchGroup.getSequences(av.hiddenRepSequences),
+ stretchGroup.getWidth());
}
if (stretchGroup.cs.conservationApplied())
{
- SliderPanel.setConservationSlider(ap, stretchGroup.cs, stretchGroup
- .getName());
+ SliderPanel.setConservationSlider(ap, stretchGroup.cs,
+ stretchGroup.getName());
}
else
{
- SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup
- .getName());
+ SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
+ stretchGroup.getName());
}
}
PaintRefresher.Refresh(this, av.getSequenceSetId());
// shared between viewports.
if (av == source
|| !av.followSelection
+ || (av.isSelectionGroupChanged(false) || av.isColSelChanged(false))
|| (source instanceof AlignViewport && ((AlignViewport) source)
.getSequenceSetId().equals(av.getSequenceSetId())))
{
}
// do we want to thread this ? (contention with seqsel and colsel locks, I
// suspect)
- boolean repaint = false;
- if (av.selectionGroup == null || !av.isSelectionGroupChanged())
+ // rules are: colsel is copied if there is a real intersection between
+ // sequence selection
+ boolean repaint = false, copycolsel = true;
+ // if (!av.isSelectionGroupChanged(false))
{
SequenceGroup sgroup = null;
- if (seqsel != null)
+ if (seqsel != null && seqsel.getSize()>0)
{
if (av.alignment == null)
{
}
sgroup = seqsel.intersect(av.alignment,
(av.hasHiddenRows) ? av.hiddenRepSequences : null);
+ if ((sgroup == null || sgroup.getSize() == 0)
+ || (colsel == null || colsel.size() == 0))
+ {
+ // don't copy columns if the region didn't intersect.
+ copycolsel = false;
+ }
}
if (sgroup != null && sgroup.getSize() > 0)
{
{
av.setSelectionGroup(null);
}
- repaint = av.isSelectionGroupChanged();
+ av.isSelectionGroupChanged(true);
+ repaint = true;
}
- if (av.colSel == null || !av.isColSelChanged())
+ if (copycolsel)
{
// the current selection is unset or from a previous message
// so import the new colsel.
if (av.colSel != null)
{
av.colSel.clear();
+ repaint=true;
}
}
else
{
+ // TODO: shift colSel according to the intersecting sequences
if (av.colSel == null)
{
av.colSel = new ColumnSelection(colsel);
av.colSel.setElementsFrom(colsel);
}
}
- repaint |= av.isColSelChanged();
+ av.isColSelChanged(true);
+ repaint = true;
}
- if (av.hasHiddenColumns
+ if (copycolsel && av.hasHiddenColumns
&& (av.colSel == null || av.colSel.getHiddenColumns() == null))
{
System.err.println("Bad things");
git://source.jalview.org / jalview.git / blobdiff