SequenceGroup parsing added to annotation file

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

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index a1e99ff..8f1836c 100755 (executable)
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -106,7 +106,7 @@ public class APopupMenu
 \r
     SequenceGroup sg = ap.av.getSelectionGroup();\r
 \r
-    if (sg != null && sg.getSize(false)>0)\r
+    if (sg != null && sg.getSize()>0)\r
     {\r
       showText.setState(sg.getDisplayText());\r
       showColourText.setState(sg.getColourText());\r
@@ -307,7 +307,7 @@ public class APopupMenu
       }\r
 \r
       ChangeCaseCommand caseCommand = new ChangeCaseCommand(\r
-          description, sg.getSequencesAsArray(true), startEnd, caseChange\r
+          description, sg.getSequencesAsArray(ap.av.hiddenRepSequences), startEnd, caseChange\r
           );\r
 \r
       ap.alignFrame.addHistoryItem(caseCommand);\r
@@ -326,22 +326,6 @@ public class APopupMenu
   void outputText(ActionEvent e)\r
   {\r
     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);\r
-    Vector vseqs = new Vector();\r
-\r
-      String [] selection = ap.av.getViewAsString(true);\r
-      SequenceI [] seqs = ap.av.getSelectionAsNewSequence();\r
-      if (selection != null)\r
-      {\r
-        for (int i = 0; i < selection.length; i++)\r
-        {\r
-          Sequence seq = new Sequence(\r
-              seqs[i].getName(),\r
-              selection[i],\r
-              seqs[i].getStart(), seqs[i].getEnd());\r
-          seq.setDescription(seqs[i].getDescription());\r
-          vseqs.addElement( seq );\r
-      }\r
-    }\r
 \r
     Frame frame = new Frame();\r
     frame.add(cap);\r
@@ -351,7 +335,7 @@ public class APopupMenu
 \r
     cap.setText(new jalview.io.AppletFormatAdapter().formatSequences(\r
         e.getActionCommand(),\r
-        vseqs,\r
+      new Alignment( ap.av.getSelectionAsNewSequence() ),\r
         ap.av.showJVSuffix));\r
 \r
   }\r
@@ -529,7 +513,8 @@ public class APopupMenu
   protected void clustalColour_actionPerformed()\r
   {\r
     SequenceGroup sg = getGroup();\r
-    sg.cs = new ClustalxColourScheme(sg.getSequences(true), ap.av.alignment.getWidth());\r
+    sg.cs = new ClustalxColourScheme(sg.getSequences(ap.av.hiddenRepSequences),\r
+                                     ap.av.alignment.getWidth());\r
     refresh();\r
   }\r
 \r
@@ -589,7 +574,7 @@ public class APopupMenu
 \r
     if (abovePIDColour.getState())\r
     {\r
-      sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,\r
+      sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.hiddenRepSequences), 0,\r
                                                ap.av.alignment.getWidth()));\r
       int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,\r
           getGroup().getName());\r
@@ -617,7 +602,7 @@ public class APopupMenu
   {\r
     SequenceGroup sg = getGroup();\r
     sg.cs = new PIDColourScheme();\r
-    sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,\r
+    sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.hiddenRepSequences), 0,\r
                                              ap.av.alignment.getWidth()));\r
     refresh();\r
   }\r
@@ -628,7 +613,7 @@ public class APopupMenu
 \r
     sg.cs = new Blosum62ColourScheme();\r
 \r
-    sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,\r
+    sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.hiddenRepSequences), 0,\r
                                              ap.av.alignment.getWidth()));\r
 \r
     refresh();\r
@@ -651,7 +636,7 @@ public class APopupMenu
 \r
       Conservation c = new Conservation("Group",\r
                                         ResidueProperties.propHash, 3,\r
-                                        sg.getSequences(true), 0,\r
+                                        sg.getSequences(ap.av.hiddenRepSequences), 0,\r
                                         ap.av.alignment.getWidth());\r
 \r
       c.calculate();\r
@@ -711,34 +696,33 @@ public class APopupMenu
   void hideSequences(boolean representGroup)\r
   {\r
     SequenceGroup sg = ap.av.getSelectionGroup();\r
-    if(sg==null || sg.getSize(false)<1)\r
+    if(sg==null || sg.getSize()<1)\r
     {\r
       ap.av.hideSequence(new SequenceI[]{seq});\r
       return;\r
     }\r
 \r
-    int gsize = sg.getSize(false);\r
-    SequenceI [] hseqs;\r
+    ap.av.setSelectionGroup(null);\r
 \r
-    hseqs = new SequenceI[ representGroup ? gsize-1 : gsize ];\r
+    if (representGroup)\r
+    {\r
+      ap.av.hideRepSequences(seq, sg);\r
 \r
-      int index = 0;\r
-      for(int i=0; i<gsize; i++)\r
-      {\r
-        if(representGroup && sg.getSequenceAt(i)!=seq)\r
-        {\r
-          seq.addHiddenSequence(sg.getSequenceAt(i));\r
-          hseqs[index++] = sg.getSequenceAt(i);\r
-        }\r
-        else if(!representGroup)\r
-        {\r
-          hseqs[index++] = sg.getSequenceAt(i);\r
-        }\r
-        }\r
+      return;\r
+    }\r
 \r
-      ap.av.hideSequence(hseqs);\r
+    int gsize = sg.getSize();\r
+    SequenceI[] hseqs;\r
+\r
+    hseqs = new SequenceI[gsize];\r
+\r
+    int index = 0;\r
+    for (int i = 0; i < gsize; i++)\r
+    {\r
+      hseqs[index++] = sg.getSequenceAt(i);\r
+    }\r
 \r
-      ap.av.setSelectionGroup(null);\r
+    ap.av.hideSequence(hseqs);\r
     }\r
 \r
 }\r