X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FHistoryItem.java;h=09e87f320bd3a4448a95bd245435e90ccbf337ab;hb=621a628afc1f6ee7a2778b9d0ae2729b88fe5bfd;hp=ed119e8d8c649eb6e0dbf1c950e81c955bbd2f7d;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/datamodel/HistoryItem.java b/src/jalview/datamodel/HistoryItem.java
index ed119e8..09e87f3 100755
--- a/src/jalview/datamodel/HistoryItem.java
+++ b/src/jalview/datamodel/HistoryItem.java
@@ -21,49 +21,139 @@ package jalview.datamodel;
 import java.util.*;
 
 
-public class HistoryItem {
-    public static final int EDIT = 0;
-    public static final int SORT = 1;
-    public static final int HIDE = 2;
-    public static final int PASTE = 3;
-    final int type;
-    Vector sequences;
-    Vector alignIndex;
-    String description;
-    Vector hiddenSeqs;
-
-    public HistoryItem(String description, AlignmentI al, int type) {
-        this.type = type;
-        this.description = description;
-        sequences = new Vector();
-        alignIndex = new Vector();
-        hiddenSeqs = 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());
-        }
-    }
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class HistoryItem
+{
+  /** DOCUMENT ME!! */
+  public static final int EDIT = 0;
 
-    public int getType() {
-        return type;
-    }
+  /** 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;
+
+  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();
 
-    public Vector getSequences() {
-        return sequences;
+    for (int i = 0; i < al.getHeight(); i++)
+    {
+      SequenceI seq = al.getSequenceAt(i);
+      sequences.addElement(seq);
+      alignIndex.addElement(i + "");
+      seqAsString.addElement(seq.getStart()
+                             +" "+seq.getEnd()
+                             +" "+seq.getSequence().toString());
     }
 
-    public String getDescription() {
-        return description;
+    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());
+      }
     }
+  }
 
-    public Vector getHidden() {
-        return hiddenSeqs;
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public String getDescription()
+  {
+    return description;
+  }
+
+
+  public void restore()
+  {
+    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()));
+        }
 
-    public int getAlignIndex(int seq) {
-        return Integer.parseInt(alignIndex.elementAt(seq).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);
+        }
+      }
     }
+
+  }
 }