From b169b1a49c078d123feb729db6acb9779f50e7d6 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 15 Aug 2006 10:34:11 +0000
Subject: [PATCH] Select revealed seqs

---
 src/jalview/appletgui/AlignViewport.java   |   33 ++++++++++++++++++++++++----
 src/jalview/datamodel/HiddenSequences.java |   17 +++++++++++---
 src/jalview/gui/AlignViewport.java         |   29 ++++++++++++++++++++++--
 3 files changed, 70 insertions(+), 9 deletions(-)

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 99d0794..7c46cd9 100755
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -775,9 +775,23 @@ public class AlignViewport
 
   public void showSequence(int index)
   {
-    alignment.getHiddenSequences().showSequence(index);
+    Vector tmp = alignment.getHiddenSequences().showSequence(index);
+    if (tmp.size() > 0)
+    {
+      if (selectionGroup == null)
+      {
+        selectionGroup = new SequenceGroup();
+        selectionGroup.setEndRes(alignment.getWidth() - 1);
+      }
 
-    if(alignment.getHiddenSequences().getSize()<1)
+      for (int t = 0; t < tmp.size(); t++)
+      {
+        selectionGroup.addSequence(
+            (SequenceI) tmp.elementAt(t), false
+            );
+      }
+    }
+    if (alignment.getHiddenSequences().getSize() < 1)
       hasHiddenRows = false;
   }
 
@@ -798,9 +812,20 @@ public class AlignViewport
   {
     if(alignment.getHiddenSequences().getSize()>0)
     {
-      alignment.getHiddenSequences().showAll();
+      if(selectionGroup==null)
+      {
+        selectionGroup = new SequenceGroup();
+        selectionGroup.setEndRes(alignment.getWidth()-1);
+      }
+      Vector tmp = alignment.getHiddenSequences().showAll();
+      for(int t=0; t<tmp.size(); t++)
+      {
+        selectionGroup.addSequence(
+            (SequenceI)tmp.elementAt(t), false
+            );
+      }
       hasHiddenRows = false;
-    }
+      }
   }
 
   public int adjustForHiddenSeqs(int alignmentIndex)
diff --git a/src/jalview/datamodel/HiddenSequences.java b/src/jalview/datamodel/HiddenSequences.java
index 36c6498..9a7afd2 100755
--- a/src/jalview/datamodel/HiddenSequences.java
+++ b/src/jalview/datamodel/HiddenSequences.java
@@ -62,14 +62,21 @@ public class HiddenSequences
     alignment.deleteSequence(sequence);
   }
 
-  public void showAll()
+  public Vector showAll()
   {
+   Vector revealedSeqs = new Vector();
    for(int i=0; i<alignment.getHeight()+hiddenSequences.size(); i++)
-     showSequence(i);
+    {
+      Vector tmp = showSequence(i);
+      for(int t=0; t<tmp.size(); t++)
+        revealedSeqs.addElement(tmp.elementAt(t));
+    }
+    return revealedSeqs;
   }
 
-  public void showSequence(int alignmentIndex)
+  public Vector showSequence(int alignmentIndex)
   {
+    Vector revealedSeqs = new Vector();
     SequenceI repSequence = alignment.getSequenceAt(alignmentIndex);
     if(repSequence!=null
        && repSequence.getHiddenSequences()==null
@@ -88,8 +95,10 @@ public class HiddenSequences
       SequenceI seq =  (SequenceI)hiddenSequences.remove(new Integer(
           index));
 
+
       if(seq!=null)
       {
+        revealedSeqs.addElement(seq);
         alignment.getSequences().insertElementAt(seq, alignmentIndex);
         if(repSequence!=null)
         {
@@ -97,6 +106,8 @@ public class HiddenSequences
         }
       }
     }
+
+    return revealedSeqs;
   }
 
   public Hashtable getHiddenSequences()
diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 2dd5fda..bca3589 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -1133,8 +1133,22 @@ public class AlignViewport
 
     public void showSequence(int index)
     {
-      alignment.getHiddenSequences().showSequence(index);
+      Vector tmp = alignment.getHiddenSequences().showSequence(index);
+      if(tmp.size()>0)
+      {
+        if(selectionGroup==null)
+        {
+          selectionGroup = new SequenceGroup();
+          selectionGroup.setEndRes(alignment.getWidth()-1);
+        }
 
+        for (int t = 0; t < tmp.size(); t++)
+        {
+          selectionGroup.addSequence(
+              (SequenceI) tmp.elementAt(t), false
+              );
+        }
+      }
       if(alignment.getHiddenSequences().getSize()<1)
         hasHiddenRows = false;
     }
@@ -1156,7 +1170,18 @@ public class AlignViewport
     {
       if(alignment.getHiddenSequences().getSize()>0)
       {
-        alignment.getHiddenSequences().showAll();
+        if(selectionGroup==null)
+        {
+          selectionGroup = new SequenceGroup();
+          selectionGroup.setEndRes(alignment.getWidth()-1);
+        }
+        Vector tmp = alignment.getHiddenSequences().showAll();
+        for(int t=0; t<tmp.size(); t++)
+        {
+          selectionGroup.addSequence(
+              (SequenceI)tmp.elementAt(t), false
+              );
+        }
         hasHiddenRows = false;
       }
     }
-- 
1.7.10.2