X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FHistoryItem.java;h=09e87f320bd3a4448a95bd245435e90ccbf337ab;hb=d6e1bbede5adc04f34c969213ac6a4c6d9e5d34a;hp=bb18b661d40fb840c958b20c75febe8c44e5349e;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git

diff --git a/src/jalview/datamodel/HistoryItem.java b/src/jalview/datamodel/HistoryItem.java
index bb18b66..09e87f3 100755
--- a/src/jalview/datamodel/HistoryItem.java
+++ b/src/jalview/datamodel/HistoryItem.java
@@ -16,56 +16,144 @@
 * 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.*;
 
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
 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;
-  public static final int PASTE= 3;
+
+  /** DOCUMENT ME!! */
+  public static final int PASTE = 3;
 
   final int type;
+
+  AlignmentI alignment;
+  String description;
+
   Vector sequences;
+  Vector seqAsString;
   Vector alignIndex;
-  String description;
+
   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();
-    hiddenSeqs = new Vector();
+    seqAsString = new Vector();
 
     for (int i = 0; i < al.getHeight(); i++)
     {
       SequenceI seq = al.getSequenceAt(i);
       sequences.addElement(seq);
       alignIndex.addElement(i + "");
-      hiddenSeqs.addElement(seq.getSequence().toString());
+      seqAsString.addElement(seq.getStart()
+                             +" "+seq.getEnd()
+                             +" "+seq.getSequence().toString());
     }
-  }
 
-  public int getType()
-  {return type;}
-
-  public Vector getSequences()
-  {return sequences;}
+    if(alignment.getHiddenSequences()!=null
+       && alignment.getHiddenSequences().getSize()>0)
+    {
+      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; }
+  {
+    return description;
+  }
 
-  public Vector getHidden()
-  { return hiddenSeqs; }
 
-  public int getAlignIndex(int seq)
+  public void restore()
   {
-    return Integer.parseInt(alignIndex.elementAt(seq).toString());
-  }
+    if (type == HistoryItem.SORT)
+    {
+      for (int i = 0; i < sequences.size(); i++)
+      {
+        alignment.getSequences().setElementAt(sequences.elementAt(i), i);
+      }
+    }
+    else
+    {
+      StringTokenizer st;
+      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
+          alignment.getSequences().insertElementAt(restore,
+              Integer.parseInt(alignIndex.elementAt(i).toString()));
+        }
+
+        st = new StringTokenizer(seqAsString.elementAt(i).toString());
+        restore.setStart(Integer.parseInt(st.nextToken()));
+        restore.setEnd(Integer.parseInt(st.nextToken()));
+        restore.setSequence(st.nextToken());
+      }
+
+      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);
+        }
+      }
+    }
+
+  }
 }