package jalview.gui;
import jalview.api.AlignViewportI;
+import jalview.bin.Cache;
import jalview.commands.EditCommand;
import jalview.commands.EditCommand.Action;
import jalview.commands.EditCommand.Edit;
import java.awt.event.MouseMotionListener;
import java.awt.event.MouseWheelEvent;
import java.awt.event.MouseWheelListener;
+import java.util.ArrayList;
import java.util.List;
-import java.util.Vector;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
+import javax.swing.SwingUtilities;
import javax.swing.ToolTipManager;
/**
void insertNucAtCursor(boolean group, String nuc)
{
+ // TODO not called - delete?
groupEditing = group;
startseq = seqCanvas.cursorY;
lastres = seqCanvas.cursorX;
{
lastMousePress = evt.getPoint();
- if (javax.swing.SwingUtilities.isMiddleMouseButton(evt))
+ if (SwingUtilities.isMiddleMouseButton(evt))
{
mouseWheelPressed = true;
return;
{
for (int j = 0; j < startres - lastres; j++)
{
- if (!jalview.util.Comparison.isGap(groupSeqs[g]
- .getCharAt(fixedRight - j)))
+ if (!Comparison.isGap(groupSeqs[g].getCharAt(fixedRight - j)))
{
blank = false;
break;
continue;
}
- if (!jalview.util.Comparison.isGap(groupSeqs[g].getCharAt(j)))
+ if (!Comparison.isGap(groupSeqs[g].getCharAt(j)))
{
// Not a gap, block edit not valid
endEditing();
for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
{
- if (jalview.util.Comparison.isGap(seq[s].getCharAt(blankColumn)))
+ if (Comparison.isGap(seq[s].getCharAt(blankColumn)))
{
// Theres a space, so break and insert the gap
break;
}
- if (javax.swing.SwingUtilities.isRightMouseButton(evt))
+ if (evt.isPopupTrigger())
{
List<SequenceFeature> allFeatures = ap.getFeatureRenderer()
.findFeaturesAtRes(sequence.getDatasetSequence(),
sequence.findPosition(res));
- Vector links = new Vector();
+ List<String> links = new ArrayList<String>();
for (SequenceFeature sf : allFeatures)
{
if (sf.links != null)
{
- for (int j = 0; j < sf.links.size(); j++)
+ for (String link : sf.links)
{
- links.addElement(sf.links.elementAt(j));
+ links.add(link);
}
}
}
- jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null, links);
+ PopupMenu pop = new PopupMenu(ap, null, links);
pop.show(this, evt.getX(), evt.getY());
return;
}
// do we want to thread this ? (contention with seqsel and colsel locks, I
// suspect)
- // rules are: colsel is copied if there is a real intersection between
- // sequence selection
+ /*
+ * only copy colsel if there is a real intersection between
+ * sequence selection and this panel's alignment
+ */
boolean repaint = false;
- boolean copycolsel = true;
+ boolean copycolsel = false;
SequenceGroup sgroup = null;
if (seqsel != null && seqsel.getSize() > 0)
{
if (av.getAlignment() == null)
{
- jalview.bin.Cache.log.warn("alignviewport av SeqSetId="
+ Cache.log.warn("alignviewport av SeqSetId="
+ av.getSequenceSetId() + " ViewId=" + av.getViewId()
+ " 's alignment is NULL! returning immediately.");
return;
}
sgroup = seqsel.intersect(av.getAlignment(),
(av.hasHiddenRows()) ? av.getHiddenRepSequences() : null);
- if ((sgroup == null || sgroup.getSize() == 0)
- || (colsel == null || colsel.isEmpty()))
+ if ((sgroup != null && sgroup.getSize() > 0))
{
- // don't copy columns if the region didn't intersect.
- copycolsel = false;
+ copycolsel = true;
}
}
if (sgroup != null && sgroup.getSize() > 0)
ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv,
av);
av.setColumnSelection(cs);
- av.isColSelChanged(true);
PaintRefresher.Refresh(this, av.getSequenceSetId());