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Merge branch 'develop' into task/JAL-3348_document_cli_memory_settings_when_launching...
[jalview.git]
/
src
/
jalview
/
appletgui
/
APopupMenu.java
diff --git
a/src/jalview/appletgui/APopupMenu.java
b/src/jalview/appletgui/APopupMenu.java
index
6fdb49c
..
76f2705
100644
(file)
--- a/
src/jalview/appletgui/APopupMenu.java
+++ b/
src/jalview/appletgui/APopupMenu.java
@@
-383,7
+383,7
@@
public class APopupMenu extends java.awt.PopupMenu
void addFeatureLinks(final SequenceI seq, List<String> links)
{
Menu linkMenu = new Menu(MessageManager.getString("action.link"));
void addFeatureLinks(final SequenceI seq, List<String> links)
{
Menu linkMenu = new Menu(MessageManager.getString("action.link"));
- Map<String, List<String>> linkset = new LinkedHashMap<String, List<String>>();
+ Map<String, List<String>> linkset = new LinkedHashMap<>();
for (String link : links)
{
for (String link : links)
{
@@
-485,8
+485,8
@@
public class APopupMenu extends java.awt.PopupMenu
* Temporary store to hold distinct calcId / type pairs for the tooltip.
* Using TreeMap means calcIds are shown in alphabetical order.
*/
* Temporary store to hold distinct calcId / type pairs for the tooltip.
* Using TreeMap means calcIds are shown in alphabetical order.
*/
- SortedMap<String, String> tipEntries = new TreeMap<String, String>();
- final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<SequenceI, List<AlignmentAnnotation>>();
+ SortedMap<String, String> tipEntries = new TreeMap<>();
+ final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<>();
AlignmentI al = this.ap.av.getAlignment();
AlignmentUtils.findAddableReferenceAnnotations(forSequences, tipEntries,
candidates, al);
AlignmentI al = this.ap.av.getAlignment();
AlignmentUtils.findAddableReferenceAnnotations(forSequences, tipEntries,
candidates, al);
@@
-825,8
+825,8
@@
public class APopupMenu extends java.awt.PopupMenu
}
int gSize = sg.getSize();
}
int gSize = sg.getSize();
- List<SequenceI> seqs = new ArrayList<SequenceI>();
- List<SequenceFeature> features = new ArrayList<SequenceFeature>();
+ List<SequenceI> seqs = new ArrayList<>();
+ List<SequenceFeature> features = new ArrayList<>();
for (int i = 0; i < gSize; i++)
{
for (int i = 0; i < gSize; i++)
{
@@
-835,7
+835,7
@@
public class APopupMenu extends java.awt.PopupMenu
if (start <= end)
{
seqs.add(sg.getSequenceAt(i));
if (start <= end)
{
seqs.add(sg.getSequenceAt(i));
- features.add(new SequenceFeature(null, null, null, start, end,
+ features.add(new SequenceFeature(null, null, start, end,
"Jalview"));
}
}
"Jalview"));
}
}
@@
-847,7
+847,8
@@
public class APopupMenu extends java.awt.PopupMenu
{
ap.alignFrame.sequenceFeatures.setState(true);
ap.av.setShowSequenceFeatures(true);
{
ap.alignFrame.sequenceFeatures.setState(true);
ap.av.setShowSequenceFeatures(true);
- ap.highlightSearchResults(null);
+ ap.av.setSearchResults(null); // clear highlighting
+ ap.repaint(); // draw new/amended features
}
}
}
}
}
}
@@
-900,10
+901,7
@@
public class APopupMenu extends java.awt.PopupMenu
.formatMessage("label.annotation_for_displayid", new Object[]
{ seq.getDisplayId(true) }));
new SequenceAnnotationReport(null).createSequenceAnnotationReport(
.formatMessage("label.annotation_for_displayid", new Object[]
{ seq.getDisplayId(true) }));
new SequenceAnnotationReport(null).createSequenceAnnotationReport(
- contents, seq, true, true,
- (ap.seqPanel.seqCanvas.fr != null)
- ? ap.seqPanel.seqCanvas.fr.getMinMax()
- : null);
+ contents, seq, true, true, ap.seqPanel.seqCanvas.fr);
contents.append("</p>");
}
Frame frame = new Frame();
contents.append("</p>");
}
Frame frame = new Frame();
@@
-929,7
+927,7
@@
public class APopupMenu extends java.awt.PopupMenu
{
seq.setName(dialog.getName());
seq.setDescription(dialog.getDescription());
{
seq.setName(dialog.getName());
seq.setDescription(dialog.getDescription());
- ap.paintAlignment(false);
+ ap.paintAlignment(false, false);
}
}
}
}
@@
-1162,7
+1160,7
@@
public class APopupMenu extends java.awt.PopupMenu
void refresh()
{
void refresh()
{
- ap.paintAlignment(true);
+ ap.paintAlignment(true, true);
}
protected void clustalColour_actionPerformed()
}
protected void clustalColour_actionPerformed()
@@
-1338,7
+1336,7
@@
public class APopupMenu extends java.awt.PopupMenu
SequenceGroup sg = ap.av.getSelectionGroup();
ap.av.getAlignment().deleteGroup(sg);
ap.av.setSelectionGroup(null);
SequenceGroup sg = ap.av.getSelectionGroup();
ap.av.getAlignment().deleteGroup(sg);
ap.av.setSelectionGroup(null);
- ap.paintAlignment(true);
+ ap.paintAlignment(true, true);
}
void createGroupMenuItem_actionPerformed()
}
void createGroupMenuItem_actionPerformed()
@@
-1439,8
+1437,8
@@
public class APopupMenu extends java.awt.PopupMenu
* the insertion order, which is the order of the annotations on the
* alignment.
*/
* the insertion order, which is the order of the annotations on the
* alignment.
*/
- Map<String, List<List<String>>> shownTypes = new LinkedHashMap<String, List<List<String>>>();
- Map<String, List<List<String>>> hiddenTypes = new LinkedHashMap<String, List<List<String>>>();
+ Map<String, List<List<String>>> shownTypes = new LinkedHashMap<>();
+ Map<String, List<List<String>>> hiddenTypes = new LinkedHashMap<>();
AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
AlignmentAnnotationUtils.asList(annotations), forSequences);
AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
AlignmentAnnotationUtils.asList(annotations), forSequences);