JAL-2361 extract methods to (re-)build colour menu

[jalview.git] / src / jalview / gui / PopupMenu.java

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index aa3cad4..0166e75 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -38,6 +38,8 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.io.FileFormat;
+import jalview.io.FileFormatI;
 import jalview.io.FormatAdapter;
 import jalview.io.SequenceAnnotationReport;
 import jalview.schemes.AnnotationColourGradient;
@@ -69,6 +71,7 @@ import java.util.Hashtable;
 import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
+import java.util.SortedMap;
 import java.util.TreeMap;
 import java.util.Vector;
 
@@ -77,7 +80,6 @@ import javax.swing.JCheckBoxMenuItem;
 import javax.swing.JColorChooser;
 import javax.swing.JMenu;
 import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
 import javax.swing.JPopupMenu;
 import javax.swing.JRadioButtonMenuItem;
 
@@ -254,10 +256,9 @@ public class PopupMenu extends JPopupMenu
     colours.add(purinePyrimidineColour);
     colours.add(RNAInteractionColour);
 
-    for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
+    for (String ff : FileFormat.getWritableFormats(true))
     {
-      JMenuItem item = new JMenuItem(
-              jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
+      JMenuItem item = new JMenuItem(ff);
 
       item.addActionListener(new java.awt.event.ActionListener()
       {
@@ -616,7 +617,7 @@ public class PopupMenu extends JPopupMenu
   void addFeatureLinks(final SequenceI seq, List<String> links)
   {
     JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
-    Map<String, String[]> linkset = new LinkedHashMap<String, String[]>();
+    Map<String, List<String>> linkset = new LinkedHashMap<String, List<String>>();
 
     for (String link : links)
     {
@@ -641,6 +642,16 @@ public class PopupMenu extends JPopupMenu
 
     addshowLinks(linkMenu, linkset.values());
 
+    // disable link menu if there are no valid entries
+    if (linkMenu.getItemCount() > 0)
+    {
+      linkMenu.setEnabled(true);
+    }
+    else
+    {
+      linkMenu.setEnabled(false);
+    }
+
     if (sequence != null)
     {
       sequenceMenu.add(linkMenu);
@@ -649,6 +660,7 @@ public class PopupMenu extends JPopupMenu
     {
       add(linkMenu);
     }
+
   }
 
 
@@ -927,12 +939,12 @@ public class PopupMenu extends JPopupMenu
     }
   }
 
-  private void addshowLinks(JMenu linkMenu, Collection<String[]> linkset)
+  private void addshowLinks(JMenu linkMenu, Collection<List<String>> linkset)
   {
-    for (String[] linkstrset : linkset)
+    for (List<String> linkstrset : linkset)
     {
       // split linkstr into label and url
-      addshowLink(linkMenu, linkstrset[1], linkstrset[3]);
+      addshowLink(linkMenu, linkstrset.get(1), linkstrset.get(3));
     }
   }
 
@@ -1341,19 +1353,16 @@ public class PopupMenu extends JPopupMenu
     colourMenu.add(nucleotideMenuItem);
     if (ap.getAlignment().isNucleotide())
     {
-      // JBPNote - commented since the colourscheme isn't functional
       colourMenu.add(purinePyrimidineColour);
     }
-    colourMenu.add(userDefinedColour);
 
-    if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
+    SortedMap<String, UserColourScheme> userColourSchemes = UserDefinedColours
+            .getUserColourSchemes();
+    if (userColourSchemes != null)
     {
-      java.util.Enumeration userColours = jalview.gui.UserDefinedColours
-              .getUserColourSchemes().keys();
-
-      while (userColours.hasMoreElements())
-      {
-        JMenuItem item = new JMenuItem(userColours.nextElement().toString());
+      for (String userColour : userColourSchemes.keySet())
+    {
+        JMenuItem item = new JMenuItem(userColour);
         item.addActionListener(new ActionListener()
         {
           @Override
@@ -1365,6 +1374,7 @@ public class PopupMenu extends JPopupMenu
         colourMenu.add(item);
       }
     }
+    colourMenu.add(userDefinedColour);
 
     colourMenu.addSeparator();
     colourMenu.add(abovePIDColour);
@@ -1396,8 +1406,7 @@ public class PopupMenu extends JPopupMenu
       }
     });
 
-    clustalColour.setText(MessageManager
-            .getString("label.clustalx_colours"));
+    clustalColour.setText(MessageManager.getString("label.clustalx"));
     clustalColour.addActionListener(new java.awt.event.ActionListener()
     {
       @Override
@@ -1502,7 +1511,8 @@ public class PopupMenu extends JPopupMenu
         PIDColour_actionPerformed();
       }
     });
-    BLOSUM62Colour.setText(MessageManager.getString("label.blosum62"));
+    BLOSUM62Colour
+            .setText(MessageManager.getString("label.blosum62_score"));
     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
     {
       @Override
@@ -1564,7 +1574,7 @@ public class PopupMenu extends JPopupMenu
      * Temporary store to hold distinct calcId / type pairs for the tooltip.
      * Using TreeMap means calcIds are shown in alphabetical order.
      */
-    Map<String, String> tipEntries = new TreeMap<String, String>();
+    SortedMap<String, String> tipEntries = new TreeMap<String, String>();
     final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<SequenceI, List<AlignmentAnnotation>>();
     AlignmentI al = this.ap.av.getAlignment();
     AlignmentUtils.findAddableReferenceAnnotations(forSequences,
@@ -1666,7 +1676,7 @@ public class PopupMenu extends JPopupMenu
   public void createSequenceDetailsReport(SequenceI[] sequences)
   {
     CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
-    StringBuffer contents = new StringBuffer();
+    StringBuilder contents = new StringBuilder(128);
     for (SequenceI seq : sequences)
     {
       contents.append("<p><h2>"
@@ -1681,7 +1691,6 @@ public class PopupMenu extends JPopupMenu
                       seq,
                       true,
                       true,
-                      false,
                       (ap.getSeqPanel().seqCanvas.fr != null) ? ap
                               .getSeqPanel().seqCanvas.fr.getMinMax()
                               : null);
@@ -1885,7 +1894,7 @@ public class PopupMenu extends JPopupMenu
     }
     else
     {
-      UserColourScheme udc = (UserColourScheme) UserDefinedColours
+      UserColourScheme udc = UserDefinedColours
               .getUserColourSchemes().get(e.getActionCommand());
 
       sg.cs = udc;
@@ -1969,7 +1978,7 @@ public class PopupMenu extends JPopupMenu
     if (conservationMenuItem.isSelected())
     {
       // JBPNote: Conservation name shouldn't be i18n translated
-      Conservation c = new Conservation("Group", 3, sg.getSequences(ap.av
+      Conservation c = new Conservation("Group", sg.getSequences(ap.av
               .getHiddenRepSequences()), sg.getStartRes(),
               sg.getEndRes() + 1);
 
@@ -2078,14 +2087,14 @@ public class PopupMenu extends JPopupMenu
     {
       if (dialog.getName().indexOf(" ") > -1)
       {
-        JOptionPane
+        JvOptionPane
                 .showMessageDialog(
                         ap,
                         MessageManager
                                 .getString("label.spaces_converted_to_backslashes"),
                         MessageManager
                                 .getString("label.no_spaces_allowed_sequence_name"),
-                        JOptionPane.WARNING_MESSAGE);
+                        JvOptionPane.WARNING_MESSAGE);
       }
 
       sequence.setName(dialog.getName().replace(' ', '_'));
@@ -2184,10 +2193,10 @@ public class PopupMenu extends JPopupMenu
       jalview.util.BrowserLauncher.openURL(url);
     } catch (Exception ex)
     {
-      JOptionPane.showInternalMessageDialog(Desktop.desktop,
+      JvOptionPane.showInternalMessageDialog(Desktop.desktop,
               MessageManager.getString("label.web_browser_not_found_unix"),
               MessageManager.getString("label.web_browser_not_found"),
-              JOptionPane.WARNING_MESSAGE);
+              JvOptionPane.WARNING_MESSAGE);
 
       ex.printStackTrace();
     }
@@ -2263,8 +2272,8 @@ public class PopupMenu extends JPopupMenu
     // or we simply trust the user wants
     // wysiwig behaviour
 
-    cap.setText(new FormatAdapter(ap).formatSequences(e.getActionCommand(),
-            ap, true));
+    FileFormatI fileFormat = FileFormat.forName(e.getActionCommand());
+    cap.setText(new FormatAdapter(ap).formatSequences(fileFormat, ap, true));
   }
 
   public void sequenceFeature_actionPerformed()