X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=311f1e7ee60d0b461b839c1b3a4c661f0a5d327a;hb=54f6fe32b978af0932428981a56c9960b0df44a7;hp=9d4447987b010d3b423eb2e15506098da0c2d4a7;hpb=f4766a7bbcfae845fc95923b01fa14ff83d589ff;p=jalview.git
diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 9d44479..311f1e7 100644
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -20,6 +20,25 @@
*/
package jalview.appletgui;
+import java.awt.CheckboxMenuItem;
+import java.awt.Frame;
+import java.awt.Menu;
+import java.awt.MenuItem;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.SortedMap;
+import java.util.TreeMap;
+import java.util.Vector;
+
import jalview.analysis.AAFrequency;
import jalview.analysis.AlignmentAnnotationUtils;
import jalview.analysis.AlignmentUtils;
@@ -57,25 +76,6 @@ import jalview.schemes.ZappoColourScheme;
import jalview.util.MessageManager;
import jalview.util.UrlLink;
-import java.awt.CheckboxMenuItem;
-import java.awt.Frame;
-import java.awt.Menu;
-import java.awt.MenuItem;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.ItemEvent;
-import java.awt.event.ItemListener;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.SortedMap;
-import java.util.TreeMap;
-import java.util.Vector;
-
public class APopupMenu extends java.awt.PopupMenu
implements ActionListener, ItemListener
{
@@ -383,7 +383,7 @@ public class APopupMenu extends java.awt.PopupMenu
void addFeatureLinks(final SequenceI seq, List links)
{
Menu linkMenu = new Menu(MessageManager.getString("action.link"));
- Map> linkset = new LinkedHashMap>();
+ Map> linkset = new LinkedHashMap<>();
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.
*/
- SortedMap tipEntries = new TreeMap();
- final Map> candidates = new LinkedHashMap>();
+ SortedMap tipEntries = new TreeMap<>();
+ final Map> candidates = new LinkedHashMap<>();
AlignmentI al = this.ap.av.getAlignment();
AlignmentUtils.findAddableReferenceAnnotations(forSequences, tipEntries,
candidates, al);
@@ -773,8 +773,7 @@ public class APopupMenu extends java.awt.PopupMenu
ap.alignFrame.addHistoryItem(editCommand);
- ap.av.firePropertyChange("alignment", null,
- ap.av.getAlignment().getSequences());
+ ap.av.notifyAlignment();
}
}
}
@@ -811,8 +810,7 @@ public class APopupMenu extends java.awt.PopupMenu
ap.alignFrame.addHistoryItem(caseCommand);
- ap.av.firePropertyChange("alignment", null,
- ap.av.getAlignment().getSequences());
+ ap.av.notifyAlignment();
}
}
@@ -825,8 +823,8 @@ public class APopupMenu extends java.awt.PopupMenu
}
int gSize = sg.getSize();
- List seqs = new ArrayList();
- List features = new ArrayList();
+ List seqs = new ArrayList<>();
+ List features = new ArrayList<>();
for (int i = 0; i < gSize; i++)
{
@@ -900,11 +898,8 @@ public class APopupMenu extends java.awt.PopupMenu
contents.append(MessageManager
.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);
+ new SequenceAnnotationReport(false).createSequenceAnnotationReport(
+ contents, seq, true, true, ap.seqPanel.seqCanvas.fr);
contents.append("
");
}
Frame frame = new Frame();
@@ -930,7 +925,7 @@ public class APopupMenu extends java.awt.PopupMenu
{
seq.setName(dialog.getName());
seq.setDescription(dialog.getDescription());
- ap.paintAlignment(false);
+ ap.paintAlignment(false, false);
}
}
@@ -948,7 +943,7 @@ public class APopupMenu extends java.awt.PopupMenu
}
else
{
- new MCview.AppletPDBViewer(entry, new SequenceI[] { seq }, null, ap,
+ new mc_view.AppletPDBViewer(entry, new SequenceI[] { seq }, null, ap,
DataSourceType.URL);
}
@@ -1163,7 +1158,7 @@ public class APopupMenu extends java.awt.PopupMenu
void refresh()
{
- ap.paintAlignment(true);
+ ap.paintAlignment(true, true);
}
protected void clustalColour_actionPerformed()
@@ -1339,7 +1334,7 @@ public class APopupMenu extends java.awt.PopupMenu
SequenceGroup sg = ap.av.getSelectionGroup();
ap.av.getAlignment().deleteGroup(sg);
ap.av.setSelectionGroup(null);
- ap.paintAlignment(true);
+ ap.paintAlignment(true, true);
}
void createGroupMenuItem_actionPerformed()
@@ -1440,8 +1435,8 @@ public class APopupMenu extends java.awt.PopupMenu
* the insertion order, which is the order of the annotations on the
* alignment.
*/
- Map>> shownTypes = new LinkedHashMap>>();
- Map>> hiddenTypes = new LinkedHashMap>>();
+ Map>> shownTypes = new LinkedHashMap<>();
+ Map>> hiddenTypes = new LinkedHashMap<>();
AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
AlignmentAnnotationUtils.asList(annotations), forSequences);