JAL-2360 ColourSchemes holds configured schemes, AlignFrame colour menu

[jalview.git] / src / jalview / appletgui / APopupMenu.java

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index d625f78..2f5ac3a 100644 (file)
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -24,7 +24,7 @@ import jalview.analysis.AAFrequency;
 import jalview.analysis.AlignmentAnnotationUtils;
 import jalview.analysis.AlignmentUtils;
 import jalview.analysis.Conservation;
-import jalview.bin.Cache;
+import jalview.bin.JalviewLite;
 import jalview.commands.ChangeCaseCommand;
 import jalview.commands.EditCommand;
 import jalview.commands.EditCommand.Action;
@@ -35,6 +35,8 @@ import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.io.AppletFormatAdapter;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
 import jalview.io.SequenceAnnotationReport;
 import jalview.schemes.Blosum62ColourScheme;
 import jalview.schemes.BuriedColourScheme;
@@ -43,6 +45,7 @@ import jalview.schemes.HelixColourScheme;
 import jalview.schemes.HydrophobicColourScheme;
 import jalview.schemes.NucleotideColourScheme;
 import jalview.schemes.PIDColourScheme;
+import jalview.schemes.PurinePyrimidineColourScheme;
 import jalview.schemes.StrandColourScheme;
 import jalview.schemes.TaylorColourScheme;
 import jalview.schemes.TurnColourScheme;
@@ -64,6 +67,7 @@ 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;
 
@@ -110,6 +114,8 @@ public class APopupMenu extends java.awt.PopupMenu implements
 
   MenuItem nucleotideMenuItem = new MenuItem();
 
+  MenuItem purinePyrimidineMenuItem = new MenuItem();
+
   Menu colourMenu = new Menu();
 
   CheckboxMenuItem showBoxes = new CheckboxMenuItem();
@@ -214,10 +220,9 @@ public class APopupMenu extends java.awt.PopupMenu implements
       e.printStackTrace();
     }
 
-    for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
+    for (String ff : FileFormat.getWritableFormats(true))
     {
-      MenuItem item = new MenuItem(
-              jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
+      MenuItem item = new MenuItem(ff);
 
       item.addActionListener(this);
       outputmenu.add(item);
@@ -320,13 +325,14 @@ public class APopupMenu extends java.awt.PopupMenu implements
         urlLink = new UrlLink(link);
       } catch (Exception foo)
       {
-        Cache.log.error("Exception for URLLink '" + link + "'", foo);
+        System.err.println("Exception for URLLink '" + link + "': "
+                + foo.getMessage());
         continue;
       }
 
       if (!urlLink.isValid())
       {
-        Cache.log.error(urlLink.getInvalidMessage());
+        System.err.println(urlLink.getInvalidMessage());
         continue;
       }
 
@@ -335,17 +341,25 @@ public class APopupMenu extends java.awt.PopupMenu implements
 
     addshowLinks(linkMenu, linkset.values());
 
+    // disable link menu if there are no valid entries
     if (linkMenu.getItemCount() > 0)
     {
-      if (seq != null)
-      {
-        seqMenu.add(linkMenu);
-      }
-      else
-      {
-        add(linkMenu);
-      }
+      linkMenu.setEnabled(true);
+    }
+    else
+    {
+      linkMenu.setEnabled(false);
+    }
+
+    if (seq != null)
+    {
+      seqMenu.add(linkMenu);
+    }
+    else
+    {
+      add(linkMenu);
     }
+
   }
 
   private void addshowLinks(Menu linkMenu, Collection<List<String>> linkset)
@@ -402,7 +416,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
      * 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,
@@ -552,6 +566,10 @@ public class APopupMenu extends java.awt.PopupMenu implements
     {
       nucleotideMenuItem_actionPerformed();
     }
+    else if (source == purinePyrimidineMenuItem)
+    {
+      purinePyrimidineColour_actionPerformed();
+    }
 
     else if (source == userDefinedColour)
     {
@@ -767,15 +785,16 @@ public class APopupMenu extends java.awt.PopupMenu implements
 
     Frame frame = new Frame();
     frame.add(cap);
-    jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
+    JalviewLite.addFrame(frame, MessageManager.formatMessage(
             "label.selection_output_command",
             new Object[] { e.getActionCommand() }), 600, 500);
     // JBPNote: getSelectionAsNewSequence behaviour has changed - this method
     // now returns a full copy of sequence data
     // TODO consider using getSequenceSelection instead here
 
-    cap.setText(new jalview.io.AppletFormatAdapter().formatSequences(
-            e.getActionCommand(), ap.av.getShowJVSuffix(), ap, true));
+    FileFormat fileFormat = FileFormat.valueOf(e.getActionCommand());
+    cap.setText(new AppletFormatAdapter().formatSequences(fileFormat,
+            ap.av.getShowJVSuffix(), ap, true));
 
   }
 
@@ -794,7 +813,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
 
     CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame);
 
-    StringBuffer contents = new StringBuffer();
+    StringBuilder contents = new StringBuilder(128);
     for (SequenceI seq : sequences)
     {
       contents.append(MessageManager.formatMessage(
@@ -805,7 +824,6 @@ public class APopupMenu extends java.awt.PopupMenu implements
               seq,
               true,
               true,
-              false,
               (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr
                       .getMinMax() : null);
       contents.append("</p>");
@@ -836,19 +854,20 @@ public class APopupMenu extends java.awt.PopupMenu implements
 
   void addPDB()
   {
-    if (seq.getAllPDBEntries() != null)
+    Vector<PDBEntry> pdbs = seq.getAllPDBEntries();
+    if (pdbs != null&& !pdbs.isEmpty())
     {
-      PDBEntry entry = seq.getAllPDBEntries().firstElement();
+      PDBEntry entry = pdbs.firstElement();
 
       if (ap.av.applet.jmolAvailable)
       {
         new jalview.appletgui.AppletJmol(entry, new SequenceI[] { seq },
-                null, ap, AppletFormatAdapter.URL);
+                null, ap, DataSourceType.URL);
       }
       else
       {
         new MCview.AppletPDBViewer(entry, new SequenceI[] { seq }, null,
-                ap, AppletFormatAdapter.URL);
+                ap, DataSourceType.URL);
       }
 
     }
@@ -879,11 +898,6 @@ public class APopupMenu extends java.awt.PopupMenu implements
             .getString("action.create_group"));
     createGroupMenuItem.addActionListener(this);
 
-    nucleotideMenuItem.setLabel(MessageManager
-            .getString("label.nucleotide"));
-    nucleotideMenuItem.addActionListener(this);
-    conservationMenuItem.addItemListener(this);
-    abovePIDColour.addItemListener(this);
     colourMenu.setLabel(MessageManager.getString("label.group_colour"));
     showBoxes.setLabel(MessageManager.getString("action.boxes"));
     showBoxes.setState(true);
@@ -892,7 +906,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
     sequenceDetails.addActionListener(this);
     selSeqDetails.addActionListener(this);
     displayNonconserved.setLabel(MessageManager
-            .getString("label.show_non_conversed"));
+            .getString("label.show_non_conserved"));
     displayNonconserved.setState(false);
     displayNonconserved.addItemListener(this);
     showText.setLabel(MessageManager.getString("action.text"));
@@ -936,6 +950,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
     colourMenu.add(turnColour);
     colourMenu.add(buriedColour);
     colourMenu.add(nucleotideMenuItem);
+    colourMenu.add(purinePyrimidineMenuItem);
     colourMenu.add(userDefinedColour);
     colourMenu.addSeparator();
     colourMenu.add(abovePIDColour);
@@ -945,38 +960,51 @@ public class APopupMenu extends java.awt.PopupMenu implements
     noColourmenuItem.addActionListener(this);
 
     clustalColour.setLabel(MessageManager
-            .getString("label.clustalx_colours"));
+            .getString("label.colourScheme_clustal"));
     clustalColour.addActionListener(this);
-    zappoColour.setLabel(MessageManager.getString("label.zappo"));
+    zappoColour.setLabel(MessageManager
+            .getString("label.colourScheme_zappo"));
     zappoColour.addActionListener(this);
-    taylorColour.setLabel(MessageManager.getString("label.taylor"));
+    taylorColour.setLabel(MessageManager
+            .getString("label.colourScheme_taylor"));
     taylorColour.addActionListener(this);
     hydrophobicityColour.setLabel(MessageManager
-            .getString("label.hydrophobicity"));
+            .getString("label.colourScheme_hydrophobic"));
     hydrophobicityColour.addActionListener(this);
-    helixColour
-            .setLabel(MessageManager.getString("label.helix_propensity"));
+    helixColour.setLabel(MessageManager
+            .getString("label.colourScheme_helix_propensity"));
     helixColour.addActionListener(this);
     strandColour.setLabel(MessageManager
-            .getString("label.strand_propensity"));
+            .getString("label.colourScheme_strand_propensity"));
     strandColour.addActionListener(this);
-    turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
+    turnColour.setLabel(MessageManager
+            .getString("label.colourScheme_turn_propensity"));
     turnColour.addActionListener(this);
-    buriedColour.setLabel(MessageManager.getString("label.buried_index"));
+    buriedColour.setLabel(MessageManager
+            .getString("label.colourScheme_buried_index"));
     buriedColour.addActionListener(this);
     abovePIDColour.setLabel(MessageManager
-            .getString("label.above_identity_percentage"));
+            .getString("label.above_identity_threshold"));
 
     userDefinedColour.setLabel(MessageManager
             .getString("action.user_defined"));
     userDefinedColour.addActionListener(this);
     PIDColour.setLabel(MessageManager
-            .getString("label.percentage_identity"));
+            .getString("label.colourScheme_%_identity"));
     PIDColour.addActionListener(this);
-    BLOSUM62Colour.setLabel("BLOSUM62");
+    BLOSUM62Colour.setLabel(MessageManager
+            .getString("label.colourScheme_blosum62"));
     BLOSUM62Colour.addActionListener(this);
     conservationMenuItem.setLabel(MessageManager
             .getString("label.conservation"));
+    nucleotideMenuItem.setLabel(MessageManager
+            .getString("label.colourScheme_nucleotide"));
+    nucleotideMenuItem.addActionListener(this);
+    purinePyrimidineMenuItem.setLabel(MessageManager
+            .getString("label.colourScheme_purine/pyrimidine"));
+    purinePyrimidineMenuItem.addActionListener(this);
+    conservationMenuItem.addItemListener(this);
+    abovePIDColour.addItemListener(this);
 
     editMenu.add(copy);
     copy.addActionListener(this);
@@ -1078,6 +1106,12 @@ public class APopupMenu extends java.awt.PopupMenu implements
     refresh();
   }
 
+  public void purinePyrimidineColour_actionPerformed()
+  {
+    getGroup().cs = new PurinePyrimidineColourScheme();
+    refresh();
+  }
+
   protected void abovePIDColour_itemStateChanged()
   {
     SequenceGroup sg = getGroup();