JAL-2344 FileFormats singleton for formats, FileFormatI simplified

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

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 45e39cc..8f7a15b 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;
@@ -34,6 +35,9 @@ import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.io.AppletFormatAdapter;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
 import jalview.io.SequenceAnnotationReport;
 import jalview.schemes.Blosum62ColourScheme;
 import jalview.schemes.BuriedColourScheme;
@@ -213,10 +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 : FileFormats.getInstance().getWritableFormats(true))
     {
-      MenuItem item = new MenuItem(
-              jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
+      MenuItem item = new MenuItem(ff);
 
       item.addActionListener(this);
       outputmenu.add(item);
@@ -242,8 +245,12 @@ public class APopupMenu extends java.awt.PopupMenu implements
       {
         menu1.setLabel(MessageManager.getString("action.edit_group"));
         groupMenu.remove(createGroupMenuItem);
+        if (sg.cs != null)
+        {
+          abovePIDColour.setState(sg.cs.getThreshold() > 0);
+          conservationMenuItem.setState(sg.cs.conservationApplied());
+        }
       }
-
     }
     else
     {
@@ -498,23 +505,28 @@ public class APopupMenu extends java.awt.PopupMenu implements
   @Override
   public void itemStateChanged(ItemEvent evt)
   {
-    if (evt.getSource() == abovePIDColour)
+    Object source = evt.getSource();
+    if (source == abovePIDColour)
     {
       abovePIDColour_itemStateChanged();
     }
-    else if (evt.getSource() == showColourText)
+    else if (source == conservationMenuItem)
+    {
+      conservationMenuItem_itemStateChanged();
+    }
+    else if (source == showColourText)
     {
       showColourText_itemStateChanged();
     }
-    else if (evt.getSource() == showText)
+    else if (source == showText)
     {
       showText_itemStateChanged();
     }
-    else if (evt.getSource() == showBoxes)
+    else if (source == showBoxes)
     {
       showBoxes_itemStateChanged();
     }
-    else if (evt.getSource() == displayNonconserved)
+    else if (source == displayNonconserved)
     {
       this.showNonconserved_itemStateChanged();
     }
@@ -577,10 +589,6 @@ public class APopupMenu extends java.awt.PopupMenu implements
     {
       noColourmenuItem_actionPerformed();
     }
-    else if (source == conservationMenuItem)
-    {
-      conservationMenuItem_itemStateChanged();
-    }
     else if (source == unGroupMenuItem)
     {
       unGroupMenuItem_actionPerformed();
@@ -775,15 +783,17 @@ 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));
+    FileFormatI fileFormat = FileFormats.getInstance().forName(
+            e.getActionCommand());
+    cap.setText(new AppletFormatAdapter().formatSequences(fileFormat,
+            ap.av.getShowJVSuffix(), ap, true));
 
   }
 
@@ -802,7 +812,7 @@ 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(
@@ -813,7 +823,6 @@ 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>");
@@ -844,19 +853,20 @@ 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);
       }
 
     }