PDBViewer available if necessary

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

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 1df8041..888dba1 100755 (executable)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -84,8 +84,9 @@ public class PopupMenu
   JMenu jMenu1 = new JMenu();\r
   JMenu structureMenu = new JMenu();\r
   JMenu viewStructureMenu = new JMenu();\r
-  JMenu colStructureMenu = new JMenu();\r
+ // JMenu colStructureMenu = new JMenu();\r
   JMenuItem editSequence = new JMenuItem();\r
+ // JMenuItem annotationMenuItem = new JMenuItem();\r
 \r
   /**\r
    * Creates a new PopupMenu object.\r
@@ -149,7 +150,8 @@ public class PopupMenu
       sequenceMenu.setText(sequence.getName());\r
 \r
       JMenuItem menuItem;\r
-      if (seq.getDatasetSequence().getPDBId() != null)\r
+      if (seq.getDatasetSequence().getPDBId() != null\r
+          && seq.getDatasetSequence().getPDBId().size()>0)\r
       {\r
         java.util.Enumeration e = seq.getDatasetSequence().getPDBId().\r
             elements();\r
@@ -187,12 +189,13 @@ public class PopupMenu
               SequenceI [] seqs2 = new SequenceI[seqs.size()];\r
               seqs.toArray(seqs2);\r
 \r
-              new AppJMol(pdb, seqs2, ap);\r
+              new AppJmol(pdb, seqs2, null, ap);\r
+              //  new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE);\r
             }\r
           });\r
           viewStructureMenu.add(menuItem);\r
 \r
-          menuItem = new JMenuItem();\r
+       /*   menuItem = new JMenuItem();\r
           menuItem.setText(pdb.getId());\r
           menuItem.addActionListener(new java.awt.event.ActionListener()\r
           {\r
@@ -201,9 +204,14 @@ public class PopupMenu
               colourByStructure(pdb.getId());\r
             }\r
           });\r
-          colStructureMenu.add(menuItem);\r
+          colStructureMenu.add(menuItem);*/\r
         }\r
       }\r
+      else\r
+      {\r
+        structureMenu.remove(viewStructureMenu);\r
+       // structureMenu.remove(colStructureMenu);\r
+      }\r
 \r
       menuItem = new JMenuItem("Hide Sequences");\r
       menuItem.addActionListener(new java.awt.event.ActionListener()\r
@@ -566,7 +574,7 @@ public class PopupMenu
     jMenu1.setText("Group");\r
     structureMenu.setText("Structure");\r
     viewStructureMenu.setText("View Structure");\r
-    colStructureMenu.setText("Colour By Structure");\r
+  //  colStructureMenu.setText("Colour By Structure");\r
     editSequence.setText("Edit Sequence...");\r
     editSequence.addActionListener(new ActionListener()\r
     {\r
@@ -575,6 +583,14 @@ public class PopupMenu
         editSequence_actionPerformed(actionEvent);\r
       }\r
     });\r
+   /* annotationMenuItem.setText("By Annotation");\r
+    annotationMenuItem.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent actionEvent)\r
+      {\r
+        annotationMenuItem_actionPerformed(actionEvent);\r
+      }\r
+    });*/\r
 \r
     add(groupMenu);\r
 \r
@@ -623,6 +639,7 @@ public class PopupMenu
     colourMenu.addSeparator();\r
     colourMenu.add(abovePIDColour);\r
     colourMenu.add(conservationMenuItem);\r
+    //colourMenu.add(annotationMenuItem);\r
     editMenu.add(copy);\r
     editMenu.add(cut);\r
     editMenu.add(editSequence);\r
@@ -641,7 +658,7 @@ public class PopupMenu
     jMenu1.add(outline);\r
     structureMenu.add(pdbMenu);\r
     structureMenu.add(viewStructureMenu);\r
-    structureMenu.add(colStructureMenu);\r
+   // structureMenu.add(colStructureMenu);\r
     noColourmenuItem.setText("None");\r
     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
     {\r
@@ -1009,6 +1026,23 @@ public class PopupMenu
     refresh();\r
   }\r
 \r
+  public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)\r
+  {\r
+    SequenceGroup sg = getGroup();\r
+    if (sg == null)\r
+    {\r
+      return;\r
+    }\r
+\r
+    AnnotationColourGradient acg = new AnnotationColourGradient(\r
+        sequence.getAnnotation()[0], null, AnnotationColourGradient.NO_THRESHOLD);\r
+\r
+    acg.predefinedColours = true;\r
+    sg.cs = acg;\r
+\r
+    refresh();\r
+  }\r
+\r
   /**\r
    * DOCUMENT ME!\r
    *\r
@@ -1340,7 +1374,7 @@ public class PopupMenu
     if (id != null && id.length() > 0)\r
     {\r
       PDBEntry entry = new PDBEntry();\r
-      entry.setId(id);\r
+      entry.setId(id.toUpperCase());\r
       sequence.getDatasetSequence()\r
           .addPDBId(entry);\r
     }\r
@@ -1436,7 +1470,7 @@ public class PopupMenu
         {\r
           EditCommand editCommand = new EditCommand(\r
               "Edit Sequences", EditCommand.REPLACE,\r
-              dialog.getName(),\r
+              dialog.getName().replace(' ', ap.av.getGapCharacter()),\r
               sg.getSequencesAsArray(ap.av.hiddenRepSequences),\r
               sg.getStartRes(), sg.getEndRes() + 1, ap.av.alignment\r
               );\r
@@ -1448,4 +1482,6 @@ public class PopupMenu
         }\r
       }\r
   }\r
+\r
+\r
 }\r