From 19e35813ebb5102a69682857bd25f46955f17cbb Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 16 Mar 2006 15:21:58 +0000
Subject: [PATCH] Gethidden sequences

---
 src/jalview/datamodel/HistoryItem.java |  190 +++++++++++++++++++-------------
 1 file changed, 111 insertions(+), 79 deletions(-)

diff --git a/src/jalview/datamodel/HistoryItem.java b/src/jalview/datamodel/HistoryItem.java
index eb4979d..0520bc0 100755
--- a/src/jalview/datamodel/HistoryItem.java
+++ b/src/jalview/datamodel/HistoryItem.java
@@ -29,96 +29,128 @@ import java.util.*;
  */
 public class HistoryItem
 {
-    /** DOCUMENT ME!! */
-    public static final int EDIT = 0;
-
-    /** DOCUMENT ME!! */
-    public static final int SORT = 1;
-
-    /** DOCUMENT ME!! */
-    public static final int HIDE = 2;
-
-    /** DOCUMENT ME!! */
-    public static final int PASTE = 3;
-    final int type;
-    Vector sequences;
-    Vector alignIndex;
-    String description;
-    Vector hiddenSeqs;
-
-    /**
-     * Creates a new HistoryItem object.
-     *
-     * @param description DOCUMENT ME!
-     * @param al DOCUMENT ME!
-     * @param type DOCUMENT ME!
-     */
-    public HistoryItem(String description, AlignmentI al, int type)
-    {
-        this.type = type;
-        this.description = description;
-        sequences = new Vector();
-        alignIndex = new Vector();
-        hiddenSeqs = new Vector();
+  /** DOCUMENT ME!! */
+  public static final int EDIT = 0;
 
-        for (int i = 0; i < al.getHeight(); i++)
-        {
-            SequenceI seq = al.getSequenceAt(i);
-            sequences.addElement(seq);
-            alignIndex.addElement(i + "");
-            hiddenSeqs.addElement(seq.getSequence().toString());
-        }
-    }
+  /** DOCUMENT ME!! */
+  public static final int SORT = 1;
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getType()
-    {
-        return type;
-    }
+  /** DOCUMENT ME!! */
+  public static final int HIDE = 2;
+
+  /** DOCUMENT ME!! */
+  public static final int PASTE = 3;
+
+  final int type;
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Vector getSequences()
+  AlignmentI alignment;
+  String description;
+
+  Vector sequences;
+  Vector seqAsString;
+  Vector alignIndex;
+
+  Vector hiddenSeqs;
+  Vector hiddenSeqsAsString;
+
+
+  /**
+   * Creates a new HistoryItem object.
+   *
+   * @param description DOCUMENT ME!
+   * @param al DOCUMENT ME!
+   * @param type DOCUMENT ME!
+   */
+  public HistoryItem(String description, AlignmentI al, int type)
+  {
+    alignment = al;
+    this.type = type;
+    this.description = description;
+    sequences = new Vector();
+    alignIndex = new Vector();
+    seqAsString = new Vector();
+
+    for (int i = 0; i < al.getHeight(); i++)
     {
-        return sequences;
+      SequenceI seq = al.getSequenceAt(i);
+      sequences.addElement(seq);
+      alignIndex.addElement(i + "");
+      seqAsString.addElement(seq.getSequence().toString());
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public String getDescription()
+    if(alignment.getHiddenSequences()!=null
+       && alignment.getHiddenSequences().getSize()>0)
     {
-        return description;
+      hiddenSeqs = new Vector();
+      hiddenSeqsAsString = new Vector();
+      Enumeration en = alignment.getHiddenSequences().hiddenSequences.elements();
+      while (en.hasMoreElements())
+      {
+        SequenceI key = (SequenceI) en.nextElement();
+        hiddenSeqs.addElement(key);
+        hiddenSeqsAsString.addElement(key.getSequence().toString());
+      }
     }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public String getDescription()
+  {
+    return description;
+  }
+
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Vector getHidden()
+  public void restore()
+  {
+    if (type == HistoryItem.SORT)
     {
-        return hiddenSeqs;
+      for (int i = 0; i < sequences.size(); i++)
+      {
+        alignment.getSequences().setElementAt(sequences.elementAt(i), i);
+      }
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param seq DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getAlignIndex(int seq)
+    else
     {
-        return Integer.parseInt(alignIndex.elementAt(seq).toString());
+
+      for (int i = 0; i < sequences.size(); i++)
+      {
+        SequenceI restore = (SequenceI) sequences.elementAt(i);
+
+        if (restore.getLength() == 0)
+        {
+          //This is for edits which remove all residues in a sequence
+          restore.setSequence(seqAsString.elementAt(i).toString());
+          alignment.getSequences().insertElementAt(restore,
+              Integer.parseInt(alignIndex.elementAt(i).toString()));
+        }
+        else
+        {
+          restore.setSequence(seqAsString.elementAt(i).toString());
+        }
+      }
+
+      if(hiddenSeqs!=null)
+      {
+        for(int hs=0; hs<hiddenSeqs.size(); hs++)
+        {
+          SequenceI key = (SequenceI) hiddenSeqs.elementAt(hs);
+          key.setSequence(hiddenSeqsAsString.elementAt(hs).toString());
+        }
+      }
+
+      if (type == HistoryItem.PASTE)
+      {
+        for (int i = alignment.getHeight() - 1;
+             i > (sequences.size() - 1); i--)
+        {
+          alignment.deleteSequence(i);
+        }
+      }
     }
+
+  }
 }
-- 
1.7.10.2