FileFormatI further tweaks, clean compile

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

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 1d2feb2..1b66e9c 100644 (file)
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -24,6 +24,7 @@ import jalview.analysis.AAFrequency;
 import jalview.analysis.AlignmentAnnotationUtils;
 import jalview.analysis.AlignmentUtils;
 import jalview.analysis.Conservation;
+import jalview.bin.JalviewLite;
 import jalview.commands.ChangeCaseCommand;
 import jalview.commands.EditCommand;
 import jalview.commands.EditCommand.Action;
@@ -35,6 +36,8 @@ 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;
@@ -70,8 +73,6 @@ import java.util.Vector;
 public class APopupMenu extends java.awt.PopupMenu implements
         ActionListener, ItemListener
 {
-  private static final String ALL_ANNOTATIONS = "All";
-
   Menu groupMenu = new Menu();
 
   MenuItem editGroupName = new MenuItem();
@@ -216,10 +217,9 @@ 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())
     {
-      MenuItem item = new MenuItem(
-              jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
+      MenuItem item = new MenuItem(ff);
 
       item.addActionListener(this);
       outputmenu.add(item);
@@ -274,7 +274,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
 
           // collect matching db-refs
           DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
-                  seq.getDBRef(), new String[] { target });
+                  seq.getDBRefs(), new String[] { target });
           // collect id string too
           String id = seq.getName();
           String descr = seq.getDescription();
@@ -537,6 +537,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
     MenuItem item = new MenuItem(label);
     item.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         ap.alignFrame.showURL(url, target);
@@ -545,6 +546,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
     linkMenu.add(item);
   }
 
+  @Override
   public void itemStateChanged(ItemEvent evt)
   {
     if (evt.getSource() == abovePIDColour)
@@ -569,6 +571,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
     }
   }
 
+  @Override
   public void actionPerformed(ActionEvent evt)
   {
     Object source = evt.getSource();
@@ -823,15 +826,16 @@ 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));
 
   }
 
@@ -899,12 +903,12 @@ public class APopupMenu extends java.awt.PopupMenu implements
       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);
       }
 
     }
@@ -963,7 +967,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
             "label.represent_group_with", new Object[] { "" }));
     revealAll.setLabel(MessageManager.getString("action.reveal_all"));
     revealSeq.setLabel(MessageManager.getString("action.reveal_sequences"));
-    menu1.setLabel(MessageManager.getString("label.group") + ":");
+    menu1.setLabel(MessageManager.getString("label.group:"));
     add(groupMenu);
     this.add(seqMenu);
     this.add(hideSeqs);
@@ -1299,35 +1303,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
 
   void hideSequences(boolean representGroup)
   {
-    SequenceGroup sg = ap.av.getSelectionGroup();
-    if (sg == null || sg.getSize() < 1)
-    {
-      ap.av.hideSequence(new SequenceI[] { seq });
-      return;
-    }
-
-    ap.av.setSelectionGroup(null);
-
-    if (representGroup)
-    {
-      ap.av.hideRepSequences(seq, sg);
-
-      return;
-    }
-
-    int gsize = sg.getSize();
-    SequenceI[] hseqs;
-
-    hseqs = new SequenceI[gsize];
-
-    int index = 0;
-    for (int i = 0; i < gsize; i++)
-    {
-      hseqs[index++] = sg.getSequenceAt(i);
-    }
-
-    ap.av.hideSequence(hseqs);
-    ap.av.sendSelection();
+    ap.av.hideSequences(seq, representGroup);
   }
 
   /**
@@ -1351,7 +1327,8 @@ public class APopupMenu extends java.awt.PopupMenu implements
     showMenu.removeAll();
     hideMenu.removeAll();
 
-    final List<String> all = Arrays.asList(ALL_ANNOTATIONS);
+    final List<String> all = Arrays.asList(new String[] { MessageManager
+            .getString("label.all") });
     addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true, true);
     addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
             false);