X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=0435d2576ce62e94e7c842d69b550e728feca1db;hb=4232f0a5699af84c5361e6cea446a97e7bcc788e;hp=42546f956aa5b5a812592f896cdc2a7f3a5a79ef;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 42546f9..0435d25 100755
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -21,6 +21,7 @@ package jalview.appletgui;
 
 import java.awt.*;
 import java.awt.event.*;
+import java.util.Vector;
 
 import jalview.analysis.*;
 import jalview.datamodel.*;
@@ -45,10 +46,7 @@ public class APopupMenu
   MenuItem noColourmenuItem = new MenuItem();
   protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
 
-  AlignmentPanel ap;
-  Menu sequenceMenu = new Menu();
-  MenuItem sequenceName = new MenuItem();
-  Sequence sequence;
+  final AlignmentPanel ap;
   MenuItem unGroupMenuItem = new MenuItem();
   MenuItem nucleotideMenuItem = new MenuItem();
   Menu colourMenu = new Menu();
@@ -56,7 +54,7 @@ public class APopupMenu
   CheckboxMenuItem showText = new CheckboxMenuItem();
   CheckboxMenuItem showColourText = new CheckboxMenuItem();
 
-  public APopupMenu(AlignmentPanel ap, Sequence seq)
+  public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links)
   {
     ///////////////////////////////////////////////////////////
     // If this is activated from the sequence panel, the user may want to
@@ -65,8 +63,7 @@ public class APopupMenu
     // If from the IDPanel, we must display the sequence menu
     //////////////////////////////////////////////////////////
 
-    this.ap = ap;
-    sequence = seq;
+    this.ap = apanel;
 
     try
     {
@@ -90,11 +87,54 @@ public class APopupMenu
       groupMenu.remove(unGroupMenuItem);
     }
 
-    if (seq == null)
+    if (seq != null && links!=null)
     {
-      remove(sequenceMenu);
+      Menu linkMenu = new Menu("Link");
+      MenuItem item;
+      String link;
+      for(int i=0; i<links.size(); i++)
+      {
+        link = links.elementAt(i).toString();
+        final String target = link.substring(0, link.indexOf("|"));
+        item = new MenuItem(target);
+        final String url = link.substring(link.indexOf("|")+1, link.indexOf("$SEQUENCE_ID$"))
+               + seq.getName() +
+               link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
+
+           item.addActionListener(new java.awt.event.ActionListener()
+           {
+               public void actionPerformed(ActionEvent e)
+               {
+                  ap.alignFrame.showURL(url, target);
+               }
+           });
+          linkMenu.add(item);
+      }
+      add(linkMenu);
+
+      item = new MenuItem("Show PDB Structure");
+      item.addActionListener(new java.awt.event.ActionListener()
+           {
+               public void actionPerformed(ActionEvent e)
+               {
+                  addPDB(seq);
+               }
+           });
+
+      add(item);
+
+
     }
+  }
 
+  void addPDB(Sequence seq)
+  {
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame.applet);
+    cap.setText("Paste your PDB file here.");
+    cap.setPDBImport(seq, ap.seqPanel.seqCanvas);
+    Frame frame = new Frame();
+    frame.add(cap);
+    jalview.bin.JalviewLite.addFrame(frame, "Paste PDB file ", 400, 300);
   }
 
   private void jbInit()
@@ -103,8 +143,6 @@ public class APopupMenu
     groupMenu.setLabel("Group");
     groupMenu.setLabel("Define");
 
-    sequenceMenu.setLabel("Sequence");
-    sequenceName.setLabel("Edit name");
     unGroupMenuItem.setLabel("Remove Group");
     unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
@@ -165,14 +203,12 @@ public class APopupMenu
     });
 
     add(groupMenu);
-    this.add(sequenceMenu);
     groupMenu.add(unGroupMenuItem);
     groupMenu.add(colourMenu);
     groupMenu.addSeparator();
     groupMenu.add(showBoxes);
     groupMenu.add(showText);
     groupMenu.add(showColourText);
-    sequenceMenu.add(sequenceName);
     colourMenu.add(noColourmenuItem);
     colourMenu.add(clustalColour);
     colourMenu.add(BLOSUM62Colour);
@@ -296,13 +332,18 @@ public class APopupMenu
   void refresh()
   {
     SequenceGroup sg = getGroup();
-    SuperGroup superG = ap.av.alignment.getSuperGroup(sg);
-    if (superG != null)
+    if(sg!=null)
     {
-      superG.setSuperGroupProperties(sg);
-    }
+      SuperGroup superG = ap.av.alignment.getSuperGroup(sg);
 
+      if (superG != null)
+      {
+        superG.setSuperGroupProperties(sg);
+      }
+        }
     ap.seqPanel.seqCanvas.repaint();
+    if(ap.overviewPanel!=null)
+      ap.overviewPanel.updateOverviewImage();
   }
 
   protected void clustalColour_actionPerformed(ActionEvent e)
@@ -363,29 +404,24 @@ public class APopupMenu
   protected void abovePIDColour_itemStateChanged(ItemEvent ie)
   {
     SequenceGroup sg = getGroup();
+    if(sg.cs==null)
+          return;
+
     if (abovePIDColour.getState())
     {
       sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
                                                ap.av.alignment.getWidth()));
       int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
           getGroup().getName());
-      if (sg.cs instanceof ResidueColourScheme)
-      {
-        ( (ResidueColourScheme) sg.cs).setThreshold(threshold);
-      }
-      else if (sg.cs instanceof ScoreColourScheme)
-      {
-        ( (ScoreColourScheme) sg.cs).setThreshold(threshold);
-      }
+
+      sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
 
       SliderPanel.showPIDSlider();
 
     }
     else // remove PIDColouring
     {
-      ResidueColourScheme rcs = (ResidueColourScheme) sg.cs;
-      rcs.setThreshold(0);
-      sg.cs = rcs;
+      sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
     }
 
     refresh();
@@ -427,6 +463,8 @@ public class APopupMenu
   protected void conservationMenuItem_itemStateChanged(ItemEvent ie)
   {
     SequenceGroup sg = getGroup();
+    if(sg.cs==null)
+          return;
 
     if (conservationMenuItem.getState())
     {
@@ -438,49 +476,28 @@ public class APopupMenu
 
       c.calculate();
       c.verdict(false, ap.av.ConsPercGaps);
-      ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
 
-      sg.cs = ccs;
+      sg.cs.setConservation(c);
 
-      SliderPanel.setConservationSlider(ap, ccs, sg.getName());
+      SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
       SliderPanel.showConservationSlider();
     }
     else // remove ConservationColouring
     {
-      ConservationColourScheme ccs = (ConservationColourScheme) sg.cs;
-      sg.cs = ccs.cs;
+      sg.cs.setConservation(null);
     }
 
     refresh();
   }
 
-  protected void analyze_actionPerformed(ActionEvent e)
-  {
-    CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
-    Frame frame = new Frame();
-    frame.add(cap);
-    jalview.bin.JalviewLite.addFrame(frame, "Analyze this - ", 400, 300);
-    SequenceGroup sg = getGroup();
-    StringBuffer sb = new StringBuffer();
-
-    for (int i = 0; i < sg.sequences.size(); i++)
-    {
-      Sequence tmp = (Sequence) sg.sequences.elementAt(i);
-      sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));
-      sb.append("\n");
-    }
-
-    sb.append("Something amazing will happen soon");
-    cap.setText(sb.toString());
-
-  }
 
   SequenceGroup getGroup()
   {
     SequenceGroup sg = ap.av.getSelectionGroup();
 
     // this method won't add a new group if it already exists
-    ap.av.alignment.addGroup(sg);
+    if(sg!=null)
+      ap.av.alignment.addGroup(sg);
 
     return sg;
   }