Dont add pdb format here

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

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 8f6e49f..3401cc4 100755 (executable)
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -82,11 +82,16 @@ public class APopupMenu
 \r
     SequenceGroup sg = ap.av.getSelectionGroup();\r
 \r
-    if (sg != null && sg.getSize()>0)\r
+    if (sg != null && sg.getSize(false)>0)\r
     {\r
       showText.setState(sg.getDisplayText());\r
       showColourText.setState(sg.getColourText());\r
       showBoxes.setState(sg.getDisplayBoxes());\r
+      if (!ap.av.alignment.getGroups().contains(sg))\r
+      {\r
+        groupMenu.remove(unGroupMenuItem);\r
+      }\r
+\r
     }\r
     else\r
     {\r
@@ -94,12 +99,7 @@ public class APopupMenu
       remove(editMenu);\r
     }\r
 \r
-    if (!ap.av.alignment.getGroups().contains(sg))\r
-    {\r
-      groupMenu.remove(unGroupMenuItem);\r
-    }\r
-\r
-    if (seq != null && links!=null)\r
+    if (links!=null)\r
     {\r
       Menu linkMenu = new Menu("Link");\r
       MenuItem item;\r
@@ -109,13 +109,22 @@ 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
-               + id +\r
-               link.substring(link.indexOf("$SEQUENCE_ID$") + 13);\r
+        final String url;\r
+\r
+        if (link.indexOf("$SEQUENCE_ID$") > -1)\r
+        {\r
+          String id = seq.getName();\r
+          if (id.indexOf("|") > -1)\r
+            id = id.substring(id.lastIndexOf("|") + 1);\r
+\r
+          url = link.substring(link.indexOf("|") + 1,\r
+                               link.indexOf("$SEQUENCE_ID$"))\r
+              + id +\r
+              link.substring(link.indexOf("$SEQUENCE_ID$") + 13);\r
+        }\r
+        else\r
+          url = link.substring(link.lastIndexOf("|")+1);\r
 \r
            item.addActionListener(new java.awt.event.ActionListener()\r
            {\r
@@ -128,18 +137,19 @@ public class APopupMenu
       }\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
+      if(seq!=null)\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
@@ -199,12 +209,14 @@ public class APopupMenu
       SequenceGroup sg = ap.av.getSelectionGroup();\r
       if (sg != null)\r
       {\r
-        for (int g = 0; g < sg.getSize(); g++)\r
+        for (int g = 0; g < sg.getSize(true); g++)\r
         {\r
           if (source == toggleCase)\r
-            sg.getSequenceAt(g).toggleCase(sg.getStartRes(), sg.getEndRes() + 1);\r
+           ((SequenceI) sg.getSequences(true).elementAt(g))\r
+          .toggleCase(sg.getStartRes(), sg.getEndRes() + 1);\r
           else\r
-            sg.getSequenceAt(g).changeCase(source == toUpper, sg.getStartRes(),\r
+            ((SequenceI) sg.getSequences(true).elementAt(g))\r
+                .changeCase(source == toUpper, sg.getStartRes(),\r
                                            sg.getEndRes() + 1);\r
         }\r
         ap.seqPanel.seqCanvas.repaint();\r
@@ -323,7 +335,7 @@ public class APopupMenu
   protected void clustalColour_actionPerformed()\r
   {\r
     SequenceGroup sg = getGroup();\r
-    sg.cs = new ClustalxColourScheme(sg.sequences, ap.av.alignment.getWidth());\r
+    sg.cs = new ClustalxColourScheme(sg.getSequences(true), ap.av.alignment.getWidth());\r
     refresh();\r
   }\r
 \r
@@ -383,7 +395,7 @@ public class APopupMenu
 \r
     if (abovePIDColour.getState())\r
     {\r
-      sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
+      sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,\r
                                                ap.av.alignment.getWidth()));\r
       int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,\r
           getGroup().getName());\r
@@ -411,7 +423,7 @@ public class APopupMenu
   {\r
     SequenceGroup sg = getGroup();\r
     sg.cs = new PIDColourScheme();\r
-    sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
+    sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,\r
                                              ap.av.alignment.getWidth()));\r
     refresh();\r
   }\r
@@ -422,7 +434,7 @@ public class APopupMenu
 \r
     sg.cs = new Blosum62ColourScheme();\r
 \r
-    sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
+    sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,\r
                                              ap.av.alignment.getWidth()));\r
 \r
     refresh();\r
@@ -445,7 +457,7 @@ public class APopupMenu
 \r
       Conservation c = new Conservation("Group",\r
                                         ResidueProperties.propHash, 3,\r
-                                        sg.sequences, 0,\r
+                                        sg.getSequences(true), 0,\r
                                         ap.av.alignment.getWidth());\r
 \r
       c.calculate();\r