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 bb816cd..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()
       {
@@ -1352,19 +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
@@ -1376,6 +1374,7 @@ public class PopupMenu extends JPopupMenu
         colourMenu.add(item);
       }
     }
+    colourMenu.add(userDefinedColour);
 
     colourMenu.addSeparator();
     colourMenu.add(abovePIDColour);
@@ -1407,8 +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
@@ -1513,7 +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
@@ -1575,7 +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,
@@ -1677,7 +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>"
@@ -1692,7 +1691,6 @@ public class PopupMenu extends JPopupMenu
                       seq,
                       true,
                       true,
-                      false,
                       (ap.getSeqPanel().seqCanvas.fr != null) ? ap
                               .getSeqPanel().seqCanvas.fr.getMinMax()
                               : null);
@@ -1896,7 +1894,7 @@ public class PopupMenu extends JPopupMenu
     }
     else
     {
-      UserColourScheme udc = (UserColourScheme) UserDefinedColours
+      UserColourScheme udc = UserDefinedColours
               .getUserColourSchemes().get(e.getActionCommand());
 
       sg.cs = udc;
@@ -2089,14 +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(' ', '_'));
@@ -2195,10 +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();
     }
@@ -2274,8 +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()