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Merge remote-tracking branch 'origin/develop' into bug/JAL-2491
[jalview.git]
/
src
/
jalview
/
gui
/
PopupMenu.java
diff --git
a/src/jalview/gui/PopupMenu.java
b/src/jalview/gui/PopupMenu.java
index
660c651
..
09e3263
100644
(file)
--- a/
src/jalview/gui/PopupMenu.java
+++ b/
src/jalview/gui/PopupMenu.java
@@
-31,8
+31,8
@@
import jalview.commands.EditCommand.Action;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
-import jalview.datamodel.ColumnSelection;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
@@
-55,6
+55,7
@@
import jalview.util.UrlLink;
import java.awt.Color;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.Color;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
+import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
@@
-1445,13
+1446,21
@@
public class PopupMenu extends JPopupMenu implements ColourChangeListener
{
if (sequence != null)
{
{
if (sequence != null)
{
- ColumnSelection cs = ap.av.getColumnSelection();
- if (cs == null)
+ /* ColumnSelection cs = ap.av.getColumnSelection();
+ if (cs == null)
+ {
+ cs = new ColumnSelection();
+ }
+ cs.hideInsertionsFor(sequence);
+ ap.av.setColumnSelection(cs);*/
+
+ HiddenColumns hidden = ap.av.getAlignment().getHiddenColumns();
+ if (hidden == null)
{
{
- cs = new ColumnSelection();
+ hidden = new HiddenColumns();
}
}
- cs.hideInsertionsFor(sequence);
- ap.av.setColumnSelection(cs);
+ hidden.hideInsertionsFor(sequence);
+ ap.av.getAlignment().setHiddenColumns(hidden);
}
refresh();
}
}
refresh();
}
@@
-1880,30
+1889,28
@@
public class PopupMenu extends JPopupMenu implements ColourChangeListener
return;
}
return;
}
- int rsize = 0, gSize = sg.getSize();
- SequenceI[] rseqs, seqs = new SequenceI[gSize];
- SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
+ List<SequenceI> seqs = new ArrayList<SequenceI>();
+ List<SequenceFeature> features = new ArrayList<SequenceFeature>();
+ /*
+ * assemble dataset sequences, and template new sequence features,
+ * for the amend features dialog
+ */
+ int gSize = sg.getSize();
for (int i = 0; i < gSize; i++)
{
int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
int end = sg.findEndRes(sg.getSequenceAt(i));
if (start <= end)
{
for (int i = 0; i < gSize; i++)
{
int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
int end = sg.findEndRes(sg.getSequenceAt(i));
if (start <= end)
{
- seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence();
- features[rsize] = new SequenceFeature(null, null, null, start, end,
- "Jalview");
- rsize++;
+ seqs.add(sg.getSequenceAt(i).getDatasetSequence());
+ features.add(new SequenceFeature(null, null, null, start, end,
+ "Jalview"));
}
}
}
}
- rseqs = new SequenceI[rsize];
- tfeatures = new SequenceFeature[rsize];
- System.arraycopy(seqs, 0, rseqs, 0, rsize);
- System.arraycopy(features, 0, tfeatures, 0, rsize);
- features = tfeatures;
- seqs = rseqs;
+
if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs,
if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs,
- features, true, ap))
+ features, true, ap, null))
{
ap.alignFrame.setShowSeqFeatures(true);
ap.highlightSearchResults(null);
{
ap.alignFrame.setShowSeqFeatures(true);
ap.highlightSearchResults(null);