From f89b132a228ea9b89195f2b1a8cc89e3ae6b772a Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 16 Mar 2006 15:21:24 +0000
Subject: [PATCH] HiddenSequence methods

---
 src/jalview/datamodel/Sequence.java  |   40 ++++++++++++++++++++++++----------
 src/jalview/datamodel/SequenceI.java |   14 +++++-------
 2 files changed, 35 insertions(+), 19 deletions(-)

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 48057b8..87a9306 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -49,6 +49,11 @@ public class Sequence implements SequenceI
     /** DOCUMENT ME!! */
     public SequenceFeature [] sequenceFeatures;
 
+    /** This array holds hidden sequences
+     * of which this sequence is the representitive member of a group
+     */
+    SequenceGroup hiddenSequences;
+
     /**
      * Creates a new Sequence object.
      *
@@ -496,16 +501,6 @@ public class Sequence implements SequenceI
         }
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param i DOCUMENT ME!
-     * @param c DOCUMENT ME!
-     */
-    public void insertCharAt(int i, char c)
-    {
-        insertCharAt(i, c, true);
-    }
 
     /**
      * DOCUMENT ME!
@@ -514,7 +509,7 @@ public class Sequence implements SequenceI
      * @param c DOCUMENT ME!
      * @param chop DOCUMENT ME!
      */
-    public void insertCharAt(int i, char c, boolean chop)
+    public void insertCharAt(int i, char c)
     {
         String tmp = new String(sequence);
 
@@ -612,4 +607,27 @@ public class Sequence implements SequenceI
       this.annotation.addElement( annotation );
     }
 
+    public SequenceGroup getHiddenSequences()
+    {
+      return hiddenSequences;
+    }
+
+    public void addHiddenSequence(SequenceI seq)
+    {
+      if(hiddenSequences==null)
+      {
+        hiddenSequences = new SequenceGroup();
+      }
+      hiddenSequences.addSequence(seq, false);
+    }
+
+    public void showHiddenSequence(SequenceI seq)
+    {
+      hiddenSequences.deleteSequence(seq, false);
+      if (hiddenSequences.getSize() < 1)
+      {
+        hiddenSequences = null;
+      }
+
+    }
 }
diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 089a5f6..1f7a232 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -183,14 +183,6 @@ public interface SequenceI
      */
     public void insertCharAt(int i, char c);
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param i DOCUMENT ME!
-     * @param c DOCUMENT ME!
-     * @param chop DOCUMENT ME!
-     */
-    public void insertCharAt(int i, char c, boolean chop);
 
     /**
      * DOCUMENT ME!
@@ -256,4 +248,10 @@ public interface SequenceI
 
     public void addAlignmentAnnotation(AlignmentAnnotation annotation);
 
+    public SequenceGroup getHiddenSequences();
+
+    public void addHiddenSequence(SequenceI seq);
+
+    public void showHiddenSequence(SequenceI seq);
+
 }
-- 
1.7.10.2