Parse id before showing uniprot link

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

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 858770a..8488dd8 100755 (executable)
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -46,7 +46,7 @@ public class APopupMenu
   MenuItem noColourmenuItem = new MenuItem();\r
   protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();\r
 \r
-  AlignmentPanel ap;\r
+  final AlignmentPanel ap;\r
   MenuItem unGroupMenuItem = new MenuItem();\r
   MenuItem nucleotideMenuItem = new MenuItem();\r
   Menu colourMenu = new Menu();\r
@@ -54,7 +54,7 @@ public class APopupMenu
   CheckboxMenuItem showText = new CheckboxMenuItem();\r
   CheckboxMenuItem showColourText = new CheckboxMenuItem();\r
 \r
-  public APopupMenu(AlignmentPanel ap, Sequence seq, Vector links)\r
+  public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links)\r
   {\r
     ///////////////////////////////////////////////////////////\r
     // If this is activated from the sequence panel, the user may want to\r
@@ -63,7 +63,7 @@ public class APopupMenu
     // If from the IDPanel, we must display the sequence menu\r
     //////////////////////////////////////////////////////////\r
 \r
-    this.ap = ap;\r
+    this.ap = apanel;\r
 \r
     try\r
     {\r
@@ -97,23 +97,50 @@ public class APopupMenu
         link = links.elementAt(i).toString();\r
         final String target = link.substring(0, link.indexOf("|"));\r
         item = new MenuItem(target);\r
+        String id = seq.getName();\r
+        if(id.indexOf("|")>-1)\r
+             id = id.substring(id.lastIndexOf("|")+1);\r
+\r
         final String url = link.substring(link.indexOf("|")+1, link.indexOf("$SEQUENCE_ID$"))\r
-               + seq.getName() +\r
+               + id +\r
                link.substring(link.indexOf("$SEQUENCE_ID$") + 13);\r
 \r
            item.addActionListener(new java.awt.event.ActionListener()\r
            {\r
                public void actionPerformed(ActionEvent e)\r
                {\r
-                  jalview.bin.JalviewLite.showURL(url, target);\r
+                  ap.alignFrame.showURL(url, target);\r
                }\r
            });\r
           linkMenu.add(item);\r
       }\r
       add(linkMenu);\r
+\r
+      item = new MenuItem("Show PDB Structure");\r
+      item.addActionListener(new java.awt.event.ActionListener()\r
+           {\r
+               public void actionPerformed(ActionEvent e)\r
+               {\r
+                  addPDB(seq);\r
+               }\r
+           });\r
+\r
+      add(item);\r
+\r
+\r
     }\r
   }\r
 \r
+  void addPDB(Sequence seq)\r
+  {\r
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame.applet);\r
+    cap.setText("Paste your PDB file here.");\r
+    cap.setPDBImport(seq, ap.seqPanel.seqCanvas);\r
+    Frame frame = new Frame();\r
+    frame.add(cap);\r
+    jalview.bin.JalviewLite.addFrame(frame, "Paste PDB file ", 400, 300);\r
+  }\r
+\r
   private void jbInit()\r
       throws Exception\r
   {\r
@@ -319,6 +346,8 @@ public class APopupMenu
       }\r
         }\r
     ap.seqPanel.seqCanvas.repaint();\r
+    if(ap.overviewPanel!=null)\r
+      ap.overviewPanel.updateOverviewImage();\r
   }\r
 \r
   protected void clustalColour_actionPerformed(ActionEvent e)\r
@@ -379,29 +408,24 @@ public class APopupMenu
   protected void abovePIDColour_itemStateChanged(ItemEvent ie)\r
   {\r
     SequenceGroup sg = getGroup();\r
+    if(sg.cs==null)\r
+          return;\r
+\r
     if (abovePIDColour.getState())\r
     {\r
       sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
                                                ap.av.alignment.getWidth()));\r
       int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,\r
           getGroup().getName());\r
-      if (sg.cs instanceof ResidueColourScheme)\r
-      {\r
-        ( (ResidueColourScheme) sg.cs).setThreshold(threshold);\r
-      }\r
-      else if (sg.cs instanceof ScoreColourScheme)\r
-      {\r
-        ( (ScoreColourScheme) sg.cs).setThreshold(threshold);\r
-      }\r
+\r
+      sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());\r
 \r
       SliderPanel.showPIDSlider();\r
 \r
     }\r
     else // remove PIDColouring\r
     {\r
-      ResidueColourScheme rcs = (ResidueColourScheme) sg.cs;\r
-      rcs.setThreshold(0);\r
-      sg.cs = rcs;\r
+      sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());\r
     }\r
 \r
     refresh();\r
@@ -443,6 +467,8 @@ public class APopupMenu
   protected void conservationMenuItem_itemStateChanged(ItemEvent ie)\r
   {\r
     SequenceGroup sg = getGroup();\r
+    if(sg.cs==null)\r
+          return;\r
 \r
     if (conservationMenuItem.getState())\r
     {\r
@@ -454,42 +480,20 @@ public class APopupMenu
 \r
       c.calculate();\r
       c.verdict(false, ap.av.ConsPercGaps);\r
-      ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
 \r
-      sg.cs = ccs;\r
+      sg.cs.setConservation(c);\r
 \r
-      SliderPanel.setConservationSlider(ap, ccs, sg.getName());\r
+      SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());\r
       SliderPanel.showConservationSlider();\r
     }\r
     else // remove ConservationColouring\r
     {\r
-      ConservationColourScheme ccs = (ConservationColourScheme) sg.cs;\r
-      sg.cs = ccs.cs;\r
+      sg.cs.setConservation(null);\r
     }\r
 \r
     refresh();\r
   }\r
 \r
-  protected void analyze_actionPerformed(ActionEvent e)\r
-  {\r
-    CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
-    Frame frame = new Frame();\r
-    frame.add(cap);\r
-    jalview.bin.JalviewLite.addFrame(frame, "Analyze this - ", 400, 300);\r
-    SequenceGroup sg = getGroup();\r
-    StringBuffer sb = new StringBuffer();\r
-\r
-    for (int i = 0; i < sg.sequences.size(); i++)\r
-    {\r
-      Sequence tmp = (Sequence) sg.sequences.elementAt(i);\r
-      sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));\r
-      sb.append("\n");\r
-    }\r
-\r
-    sb.append("Something amazing will happen soon");\r
-    cap.setText(sb.toString());\r
-\r
-  }\r
 \r
   SequenceGroup getGroup()\r
   {\r