From ad85c28d8fbb6419ff66527d6b4feb1063f26927 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 16 Mar 2006 15:20:31 +0000
Subject: [PATCH] Keeps a record of hidden sequences

---
 src/jalview/datamodel/HiddenSequences.java |  114 ++++++++++++++++++++++++++++
 1 file changed, 114 insertions(+)
 create mode 100755 src/jalview/datamodel/HiddenSequences.java

diff --git a/src/jalview/datamodel/HiddenSequences.java b/src/jalview/datamodel/HiddenSequences.java
new file mode 100755
index 0000000..3a5946c
--- /dev/null
+++ b/src/jalview/datamodel/HiddenSequences.java
@@ -0,0 +1,114 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+
+package jalview.datamodel;
+
+import java.util.*;
+
+public class HiddenSequences
+{
+  Hashtable hiddenSequences;
+  AlignmentI alignment;
+
+  public HiddenSequences(AlignmentI al)
+  {
+    alignment = al;
+  }
+
+  public int getSize()
+  {
+    return hiddenSequences == null ? 0 : hiddenSequences.size();
+  }
+
+  public void hideSequence(SequenceI sequence)
+  {
+    if(hiddenSequences==null)
+      hiddenSequences = new Hashtable();
+
+    int alignmentIndex = alignment.findIndex(sequence);
+    alignmentIndex = adjustForHiddenSeqs(alignmentIndex);
+
+    hiddenSequences.put(new Integer(alignmentIndex), sequence);
+
+    alignment.deleteSequence(sequence);
+  }
+
+  public void showSequence(int alignmentIndex)
+  {
+    SequenceI repSequence = alignment.getSequenceAt(alignmentIndex);
+    if(repSequence.getHiddenSequences()==null && alignmentIndex>0)
+      repSequence = alignment.getSequenceAt(alignmentIndex-1);
+    if(repSequence.getHiddenSequences()==null)
+      repSequence = null;
+
+    int start = adjustForHiddenSeqs(alignmentIndex-1);
+    int end = adjustForHiddenSeqs(alignmentIndex);
+
+    for(int index = end; index > start; index--)
+    {
+      SequenceI seq =  (SequenceI)hiddenSequences.remove(new Integer(
+          index));
+
+      if(seq!=null)
+      {
+        alignment.getSequences().insertElementAt(seq, alignmentIndex);
+        if(repSequence!=null)
+        {
+          repSequence.showHiddenSequence(seq);
+        }
+      }
+    }
+  }
+
+  public SequenceI getHiddenSequence(int alignmentIndex)
+  {
+    return (SequenceI)hiddenSequences.get(new Integer(alignmentIndex));
+  }
+
+  public int findIndexWithoutHiddenSeqs(int alignmentIndex)
+  {
+    int index = 0;
+    int hiddenSeqs = 0;
+    while(index <= alignmentIndex)
+    {
+     if(hiddenSequences.containsKey(new Integer(index)))
+     {
+       hiddenSeqs ++;
+     }
+      index ++;
+    };
+
+    return (alignmentIndex - hiddenSeqs) ;
+  }
+
+  public int adjustForHiddenSeqs(int alignmentIndex)
+  {
+    int index = 0;
+    while(index <= alignmentIndex)
+    {
+     if(hiddenSequences.containsKey(new Integer(index)))
+     {
+       alignmentIndex ++;
+     }
+      index ++;
+    };
+
+    return alignmentIndex ;
+  }
+}
-- 
1.7.10.2