X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=f46bd4e03807c86517b2de8d93dd9c198469f7cb;hb=5ea5764f835390ab631afbf54c2de40f63aa8f31;hp=8a37952d68e363dea01d81db84cf8b9f2574d854;hpb=0b573ed90b14079f7326281f50c0c9cffdace586;p=jalview.git
diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 8a37952..f46bd4e 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -20,6 +20,35 @@
*/
package jalview.gui;
+import java.awt.BorderLayout;
+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.BitSet;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.Hashtable;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Objects;
+import java.util.SortedMap;
+import java.util.TreeMap;
+import java.util.Vector;
+
+import javax.swing.ButtonGroup;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JInternalFrame;
+import javax.swing.JLabel;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JPanel;
+import javax.swing.JPopupMenu;
+import javax.swing.JRadioButtonMenuItem;
+import javax.swing.JScrollPane;
+
import jalview.analysis.AAFrequency;
import jalview.analysis.AlignmentAnnotationUtils;
import jalview.analysis.AlignmentUtils;
@@ -35,11 +64,13 @@ import jalview.datamodel.DBRefEntry;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.MappedFeatures;
import jalview.datamodel.PDBEntry;
+import jalview.datamodel.ResidueCount;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.gui.ColourMenuHelper.ColourChangeListener;
import jalview.gui.JalviewColourChooser.ColourChooserListener;
+import jalview.io.CountReader;
import jalview.io.FileFormatI;
import jalview.io.FileFormats;
import jalview.io.FormatAdapter;
@@ -58,34 +89,8 @@ import jalview.util.StringUtils;
import jalview.util.UrlLink;
import jalview.viewmodel.seqfeatures.FeatureRendererModel;
-import java.awt.BorderLayout;
-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.BitSet;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.Hashtable;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Objects;
-import java.util.SortedMap;
-import java.util.TreeMap;
-import java.util.Vector;
-
-import javax.swing.ButtonGroup;
-import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JInternalFrame;
-import javax.swing.JLabel;
-import javax.swing.JMenu;
-import javax.swing.JMenuItem;
-import javax.swing.JPanel;
-import javax.swing.JPopupMenu;
-import javax.swing.JRadioButtonMenuItem;
-import javax.swing.JScrollPane;
+import java.io.IOException;
+import java.net.MalformedURLException;
/**
* The popup menu that is displayed on right-click on a sequence id, or in the
@@ -94,6 +99,11 @@ import javax.swing.JScrollPane;
public class PopupMenu extends JPopupMenu implements ColourChangeListener
{
/*
+ * maximum length of feature description to include in popup menu item text
+ */
+ private static final int FEATURE_DESC_MAX = 40;
+
+ /*
* true for ID Panel menu, false for alignment panel menu
*/
private final boolean forIdPanel;
@@ -296,7 +306,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
jalview.util.BrowserLauncher.openURL(url);
} catch (Exception ex)
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
MessageManager.getString("label.web_browser_not_found_unix"),
MessageManager.getString("label.web_browser_not_found"),
JvOptionPane.WARNING_MESSAGE);
@@ -540,6 +550,36 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
}
}
+ if (seq.hasHMMProfile())
+ {
+ menuItem = new JMenuItem(MessageManager
+ .getString("action.add_background_frequencies"));
+ menuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ try
+ {
+ ResidueCount counts = CountReader.getBackgroundFrequencies(ap,
+ seq);
+ if (counts != null)
+ {
+ seq.getHMM().setBackgroundFrequencies(counts);
+ ap.alignFrame.buildColourMenu();
+ }
+ } catch (MalformedURLException e1)
+ {
+ e1.printStackTrace();
+ } catch (IOException e1)
+ {
+ e1.printStackTrace();
+ }
+ }
+ });
+ add(menuItem);
+ }
+
menuItem = new JMenuItem(
MessageManager.getString("action.hide_sequences"));
menuItem.addActionListener(new ActionListener()
@@ -664,7 +704,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
buildGroupURLMenu(sg, groupLinks);
}
// Add a 'show all structures' for the current selection
- Hashtable
" + calcId + "/" + tipEntries.get(calcId));
+ tooltip.append("
" + calcId + "/" + tipEntries.get(calcId));
}
String tooltipText = JvSwingUtils.wrapTooltip(true,
tooltip.toString());
@@ -1789,7 +1844,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
"label.create_sequence_details_report_annotation_for",
new Object[]
{ seq.getDisplayId(true) }) + "
"); - new SequenceAnnotationReport(null).createSequenceAnnotationReport( + new SequenceAnnotationReport(false).createSequenceAnnotationReport( contents, seq, true, true, ap.getSeqPanel().seqCanvas.fr); contents.append("
"); } @@ -2021,8 +2076,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener ap.paintAlignment(false, false); } sequence.setDescription(dialog.getDescription()); - ap.av.firePropertyChange("alignment", null, - ap.av.getAlignment().getSequences()); + ap.av.notifyAlignment(); } }); } @@ -2064,7 +2118,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener refresh(); } }; - JalviewColourChooser.showColourChooser(Desktop.getDesktop(), + JalviewColourChooser.showColourChooser(Desktop.getDesktopPane(), title, Color.BLUE, listener); } @@ -2153,9 +2207,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener startEnd, caseChange); ap.alignFrame.addHistoryItem(caseCommand); + ap.av.notifyAlignment(); - ap.av.firePropertyChange("alignment", null, - ap.av.getAlignment().getSequences()); } } @@ -2262,8 +2315,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment()); ap.alignFrame.addHistoryItem(editCommand); - ap.av.firePropertyChange("alignment", null, - ap.av.getAlignment().getSequences()); + ap.av.notifyAlignment(); } }); }