X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=803f323d480811fd8f53bea6cf75af3e5de1b38e;hb=83f6c6309e9705037a0853a26da74821c9d4fd12;hp=a103073895c00f6a88aedbec6eeec04a872f140d;hpb=890bd0eac47a4b0f55bd062a359c16a43c3780a0;p=jalview.git

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index a103073..803f323 100755
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -28,6 +28,7 @@ import jalview.analysis.*;
 import jalview.commands.*;
 import jalview.datamodel.*;
 import jalview.schemes.*;
+import jalview.io.AppletFormatAdapter;
 
 public class APopupMenu
     extends java.awt.PopupMenu implements ActionListener, ItemListener
@@ -68,6 +69,8 @@ public class APopupMenu
   MenuItem hideSeqs = new MenuItem();
   MenuItem repGroup = new MenuItem();
   MenuItem sequenceName = new MenuItem("Edit Name/Description");
+  MenuItem sequenceFeature = new MenuItem("Create Sequence Feature");
+  MenuItem editSequence = new MenuItem("Edit Sequence");
 
   Sequence seq;
   MenuItem revealAll = new MenuItem();
@@ -302,12 +305,12 @@ public class APopupMenu
           getGroup().getDescription(),
           "       Group Name",
           "Group Description",
-          ap,
-          "Edit Group Name / Description");
+          ap.alignFrame,
+          "Edit Group Name / Description",
+          500,100, true);
 
       if (dialog.accept)
       {
-
         getGroup().setName(dialog.getName().replace(' ', '_'));
         getGroup().setDescription(dialog.getDescription());
       }
@@ -321,6 +324,42 @@ public class APopupMenu
     {
       ap.alignFrame.cut_actionPerformed();
     }
+    else if(source == editSequence)
+    {
+      SequenceGroup sg = ap.av.getSelectionGroup();
+
+      if(sg!=null)
+      {
+        if (seq == null)
+          seq = (Sequence) sg.getSequenceAt(0);
+
+        EditNameDialog dialog = new EditNameDialog(seq.getSequenceAsString(
+            sg.getStartRes(),
+            sg.getEndRes() + 1),
+                                                   null,
+                                                   "Edit Sequence ",
+                                                   null,
+
+                                                   ap.alignFrame,
+                                                   "Edit Sequence",
+                                                   500, 100, true);
+
+        if (dialog.accept)
+        {
+          EditCommand editCommand = new EditCommand(
+              "Edit Sequences", EditCommand.REPLACE,
+              dialog.getName().replace(' ', ap.av.getGapCharacter()),
+              sg.getSequencesAsArray(ap.av.hiddenRepSequences),
+              sg.getStartRes(), sg.getEndRes()+1, ap.av.alignment
+              );
+
+          ap.alignFrame.addHistoryItem(editCommand);
+
+          ap.av.firePropertyChange("alignment", null,
+                                 ap.av.getAlignment().getSequences());
+        }
+      }
+    }
     else if (source == toUpper || source == toLower || source == toggleCase)
     {
       SequenceGroup sg = ap.av.getSelectionGroup();
@@ -398,6 +437,35 @@ public class APopupMenu
 
       }
     }
+    else if(source == sequenceFeature)
+    {
+      SequenceGroup sg = ap.av.getSelectionGroup();
+      if (sg == null)
+      {
+        return;
+      }
+
+      int gSize = sg.getSize();
+      SequenceI[] seqs = new SequenceI[gSize];
+      SequenceFeature[] features = new SequenceFeature[gSize];
+
+      for (int i = 0; i < gSize; i++)
+      {
+        seqs[i] = sg.getSequenceAt(i);
+        int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
+        int end = sg.findEndRes(sg.getSequenceAt(i));
+        features[i] = new SequenceFeature(null, null, null, start, end,
+                                          "Jalview");
+      }
+
+      if (ap.seqPanel.seqCanvas.getFeatureRenderer()
+          .amendFeatures(seqs, features, true, ap))
+      {
+        ap.alignFrame.sequenceFeatures.setState(true);
+        ap.av.showSequenceFeatures(true);
+        ap.highlightSearchResults(null);
+      }
+    }
     else
     {
       outputText(evt);
@@ -429,8 +497,9 @@ public class APopupMenu
         seq.getDescription(),
         "       Sequence Name",
         "Sequence Description",
-        ap,
-        "Edit Sequence Name / Description");
+        ap.alignFrame,
+        "Edit Sequence Name / Description",
+        500,100, true);
 
     if (dialog.accept)
     {
@@ -442,12 +511,33 @@ public class APopupMenu
 
   void addPDB()
   {
-    CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
-    cap.setText("Paste your PDB file here.");
-    cap.setPDBImport(seq);
-    Frame frame = new Frame();
-    frame.add(cap);
-    jalview.bin.JalviewLite.addFrame(frame, "Paste PDB file ", 400, 300);
+    if(seq.getPDBId()!=null)
+    {
+      PDBEntry entry = (PDBEntry)seq.getPDBId().firstElement();
+
+      if ( ap.av.applet.jmolAvailable )
+       new jalview.appletgui.AppletJmol(entry,
+                                        new Sequence[]{seq},
+                                        null,
+                                        ap,
+                                        AppletFormatAdapter.URL);
+     else
+       new MCview.AppletPDBViewer(entry,
+                                  new Sequence[]{seq},
+                                  null,
+                                  ap,
+                                  AppletFormatAdapter.URL);
+
+    }
+    else
+    {
+      CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
+      cap.setText("Paste your PDB file here.");
+      cap.setPDBImport(seq);
+      Frame frame = new Frame();
+      frame.add(cap);
+      jalview.bin.JalviewLite.addFrame(frame, "Paste PDB file ", 400, 300);
+    }
   }
 
   private void jbInit()
@@ -455,6 +545,7 @@ public class APopupMenu
   {
     groupMenu.setLabel("Group");
     groupMenu.setLabel("Selection");
+    sequenceFeature.addActionListener(this);
 
     editGroupName.addActionListener(this);
     unGroupMenuItem.setLabel("Remove Group");
@@ -488,7 +579,9 @@ public class APopupMenu
     groupMenu.add(editGroupName);
     groupMenu.add(editMenu);
     groupMenu.add(outputmenu);
+    groupMenu.add(sequenceFeature);
     groupMenu.add(menu1);
+
     colourMenu.add(noColourmenuItem);
     colourMenu.add(clustalColour);
     colourMenu.add(BLOSUM62Colour);
@@ -539,6 +632,10 @@ public class APopupMenu
     copy.addActionListener(this);
     editMenu.add(cut);
     cut.addActionListener(this);
+
+    editMenu.add(editSequence);
+    editSequence.addActionListener(this);
+
     editMenu.add(toUpper);
     toUpper.addActionListener(this);
     editMenu.add(toLower);