Select revealed seqs

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

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 99d0794..7c46cd9 100755 (executable)
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -775,9 +775,23 @@ public class AlignViewport
 \r
   public void showSequence(int index)\r
   {\r
-    alignment.getHiddenSequences().showSequence(index);\r
+    Vector tmp = alignment.getHiddenSequences().showSequence(index);\r
+    if (tmp.size() > 0)\r
+    {\r
+      if (selectionGroup == null)\r
+      {\r
+        selectionGroup = new SequenceGroup();\r
+        selectionGroup.setEndRes(alignment.getWidth() - 1);\r
+      }\r
 \r
-    if(alignment.getHiddenSequences().getSize()<1)\r
+      for (int t = 0; t < tmp.size(); t++)\r
+      {\r
+        selectionGroup.addSequence(\r
+            (SequenceI) tmp.elementAt(t), false\r
+            );\r
+      }\r
+    }\r
+    if (alignment.getHiddenSequences().getSize() < 1)\r
       hasHiddenRows = false;\r
   }\r
 \r
@@ -798,9 +812,20 @@ public class AlignViewport
   {\r
     if(alignment.getHiddenSequences().getSize()>0)\r
     {\r
-      alignment.getHiddenSequences().showAll();\r
+      if(selectionGroup==null)\r
+      {\r
+        selectionGroup = new SequenceGroup();\r
+        selectionGroup.setEndRes(alignment.getWidth()-1);\r
+      }\r
+      Vector tmp = alignment.getHiddenSequences().showAll();\r
+      for(int t=0; t<tmp.size(); t++)\r
+      {\r
+        selectionGroup.addSequence(\r
+            (SequenceI)tmp.elementAt(t), false\r
+            );\r
+      }\r
       hasHiddenRows = false;\r
-    }\r
+      }\r
   }\r
 \r
   public int adjustForHiddenSeqs(int alignmentIndex)\r