Its historycvs remove jalview/datamodel/HistoryItem.java

diff --git a/src/jalview/datamodel/HistoryItem.java b/src/jalview/datamodel/HistoryItem.java
deleted file mode 100755 (executable)
index 37e4ce0..0000000
--- a/src/jalview/datamodel/HistoryItem.java
+++ /dev/null
@@ -1,180 +0,0 @@
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 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 jalview.util.ShiftList;
-
-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;
-
-  /** 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;
-  /**
-   * public field - set directly if history involves a frame shift
-   * should contain the <em>inverse</em> frame shift operations.
-   */
-  public ShiftList alColumnChanges=null;
-
-  /**
-   * 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++)
-    {
-      SequenceI seq = al.getSequenceAt(i);
-      sequences.addElement(seq);
-      alignIndex.addElement(i + "");
-      seqAsString.addElement(seq.getStart()
-                             +" "+seq.getEnd()
-                             +" "+seq.getSequence().toString());
-    }
-
-    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;
-  }
-
-  /**
-   * restore state - adjusting gui hiddenColumn view as necessary
-   * @param columnSelection
-   */
-  public void restore(ColumnSelection columnSelection)
-  {
-    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);
-        }
-      }
-      if (alColumnChanges!=null) {
-        columnSelection.compensateForEdits(alColumnChanges);
-      }
-    }
-
-  }
-  /**
-   * note a frame shift that must be compensated for
-   * @param pos start position for shift (in original reference frame)
-   * @param shift length of shift
-   */
-  public void addShift(int pos, int shift) {
-    if (alColumnChanges==null)
-      alColumnChanges = new ShiftList();
-    alColumnChanges.addShift(pos, -shift);
-  }
-}