X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=8488dd8ba6e955589e17f9970880494476aff8c2;hb=17fb03228f2fee0369a03b82d9bec86e80e71bf5;hp=858770a35ec187ca5849712d7b189fa046e988c6;hpb=29f89f52f3fc99e904a55e426c53a830290408cc;p=jalview.git

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 858770a..8488dd8 100755
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -46,7 +46,7 @@ public class APopupMenu
   MenuItem noColourmenuItem = new MenuItem();
   protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
 
-  AlignmentPanel ap;
+  final AlignmentPanel ap;
   MenuItem unGroupMenuItem = new MenuItem();
   MenuItem nucleotideMenuItem = new MenuItem();
   Menu colourMenu = new Menu();
@@ -54,7 +54,7 @@ public class APopupMenu
   CheckboxMenuItem showText = new CheckboxMenuItem();
   CheckboxMenuItem showColourText = new CheckboxMenuItem();
 
-  public APopupMenu(AlignmentPanel ap, Sequence seq, Vector links)
+  public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links)
   {
     ///////////////////////////////////////////////////////////
     // If this is activated from the sequence panel, the user may want to
@@ -63,7 +63,7 @@ public class APopupMenu
     // If from the IDPanel, we must display the sequence menu
     //////////////////////////////////////////////////////////
 
-    this.ap = ap;
+    this.ap = apanel;
 
     try
     {
@@ -97,23 +97,50 @@ public class APopupMenu
         link = links.elementAt(i).toString();
         final String target = link.substring(0, link.indexOf("|"));
         item = new MenuItem(target);
+        String id = seq.getName();
+        if(id.indexOf("|")>-1)
+             id = id.substring(id.lastIndexOf("|")+1);
+
         final String url = link.substring(link.indexOf("|")+1, link.indexOf("$SEQUENCE_ID$"))
-               + seq.getName() +
+               + id +
                link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
 
            item.addActionListener(new java.awt.event.ActionListener()
            {
                public void actionPerformed(ActionEvent e)
                {
-                  jalview.bin.JalviewLite.showURL(url, target);
+                  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()
       throws Exception
   {
@@ -319,6 +346,8 @@ public class APopupMenu
       }
         }
     ap.seqPanel.seqCanvas.repaint();
+    if(ap.overviewPanel!=null)
+      ap.overviewPanel.updateOverviewImage();
   }
 
   protected void clustalColour_actionPerformed(ActionEvent e)
@@ -379,29 +408,24 @@ 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();
@@ -443,6 +467,8 @@ public class APopupMenu
   protected void conservationMenuItem_itemStateChanged(ItemEvent ie)
   {
     SequenceGroup sg = getGroup();
+    if(sg.cs==null)
+          return;
 
     if (conservationMenuItem.getState())
     {
@@ -454,42 +480,20 @@ 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()
   {