Edit and annotate wrapped alignment

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

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index cf854b0..80006c2 100755 (executable)
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -21,6 +21,7 @@ package jalview.appletgui;
 \r
 import java.awt.*;\r
 import java.awt.event.*;\r
+import java.util.Vector;\r
 \r
 import jalview.analysis.*;\r
 import jalview.datamodel.*;\r
@@ -46,9 +47,6 @@ public class APopupMenu
   protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();\r
 \r
   AlignmentPanel ap;\r
-  Menu sequenceMenu = new Menu();\r
-  MenuItem sequenceName = new MenuItem();\r
-  Sequence sequence;\r
   MenuItem unGroupMenuItem = new MenuItem();\r
   MenuItem nucleotideMenuItem = new MenuItem();\r
   Menu colourMenu = new Menu();\r
@@ -56,7 +54,7 @@ public class APopupMenu
   CheckboxMenuItem showText = new CheckboxMenuItem();\r
   CheckboxMenuItem showColourText = new CheckboxMenuItem();\r
 \r
-  public APopupMenu(AlignmentPanel ap, Sequence seq)\r
+  public APopupMenu(AlignmentPanel ap, Sequence seq, Vector links)\r
   {\r
     ///////////////////////////////////////////////////////////\r
     // If this is activated from the sequence panel, the user may want to\r
@@ -66,7 +64,6 @@ public class APopupMenu
     //////////////////////////////////////////////////////////\r
 \r
     this.ap = ap;\r
-    sequence = seq;\r
 \r
     try\r
     {\r
@@ -90,11 +87,31 @@ public class APopupMenu
       groupMenu.remove(unGroupMenuItem);\r
     }\r
 \r
-    if (seq == null)\r
+    if (seq != null && links!=null)\r
     {\r
-      remove(sequenceMenu);\r
+      Menu linkMenu = new Menu("Link");\r
+      MenuItem item;\r
+      String link;\r
+      for(int i=0; i<links.size(); i++)\r
+      {\r
+        link = links.elementAt(i).toString();\r
+        final String target = link.substring(0, link.indexOf("|"));\r
+        item = new MenuItem(target);\r
+        final String url = link.substring(link.indexOf("|")+1, link.indexOf("$SEQUENCE_ID$"))\r
+               + seq.getName() +\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
+               }\r
+           });\r
+          linkMenu.add(item);\r
+      }\r
+      add(linkMenu);\r
     }\r
-\r
   }\r
 \r
   private void jbInit()\r
@@ -103,8 +120,6 @@ public class APopupMenu
     groupMenu.setLabel("Group");\r
     groupMenu.setLabel("Define");\r
 \r
-    sequenceMenu.setLabel("Sequence");\r
-    sequenceName.setLabel("Edit name");\r
     unGroupMenuItem.setLabel("Remove Group");\r
     unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
     {\r
@@ -165,14 +180,12 @@ public class APopupMenu
     });\r
 \r
     add(groupMenu);\r
-    this.add(sequenceMenu);\r
     groupMenu.add(unGroupMenuItem);\r
     groupMenu.add(colourMenu);\r
     groupMenu.addSeparator();\r
     groupMenu.add(showBoxes);\r
     groupMenu.add(showText);\r
     groupMenu.add(showColourText);\r
-    sequenceMenu.add(sequenceName);\r
     colourMenu.add(noColourmenuItem);\r
     colourMenu.add(clustalColour);\r
     colourMenu.add(BLOSUM62Colour);\r
@@ -366,29 +379,24 @@ 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
@@ -430,6 +438,8 @@ 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
@@ -441,17 +451,15 @@ 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