added shiftList to record changes in alignment column positions.

diff --git a/src/jalview/datamodel/HistoryItem.java b/src/jalview/datamodel/HistoryItem.java
index 09e87f3..7ce0803 100755 (executable)
--- a/src/jalview/datamodel/HistoryItem.java
+++ b/src/jalview/datamodel/HistoryItem.java
@@ -1,159 +1,180 @@
-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
-*/\r
-package jalview.datamodel;\r
-\r
-import java.util.*;\r
-\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class HistoryItem\r
-{\r
-  /** DOCUMENT ME!! */\r
-  public static final int EDIT = 0;\r
-\r
-  /** DOCUMENT ME!! */\r
-  public static final int SORT = 1;\r
-\r
-  /** DOCUMENT ME!! */\r
-  public static final int HIDE = 2;\r
-\r
-  /** DOCUMENT ME!! */\r
-  public static final int PASTE = 3;\r
-\r
-  final int type;\r
-\r
-  AlignmentI alignment;\r
-  String description;\r
-\r
-  Vector sequences;\r
-  Vector seqAsString;\r
-  Vector alignIndex;\r
-\r
-  Vector hiddenSeqs;\r
-  Vector hiddenSeqsAsString;\r
-\r
-\r
-  /**\r
-   * Creates a new HistoryItem object.\r
-   *\r
-   * @param description DOCUMENT ME!\r
-   * @param al DOCUMENT ME!\r
-   * @param type DOCUMENT ME!\r
-   */\r
-  public HistoryItem(String description, AlignmentI al, int type)\r
-  {\r
-    alignment = al;\r
-    this.type = type;\r
-    this.description = description;\r
-    sequences = new Vector();\r
-    alignIndex = new Vector();\r
-    seqAsString = new Vector();\r
-\r
-    for (int i = 0; i < al.getHeight(); i++)\r
-    {\r
-      SequenceI seq = al.getSequenceAt(i);\r
-      sequences.addElement(seq);\r
-      alignIndex.addElement(i + "");\r
-      seqAsString.addElement(seq.getStart()\r
-                             +" "+seq.getEnd()\r
-                             +" "+seq.getSequence().toString());\r
-    }\r
-\r
-    if(alignment.getHiddenSequences()!=null\r
-       && alignment.getHiddenSequences().getSize()>0)\r
-    {\r
-      hiddenSeqs = new Vector();\r
-      hiddenSeqsAsString = new Vector();\r
-      Enumeration en = alignment.getHiddenSequences().hiddenSequences.elements();\r
-      while (en.hasMoreElements())\r
-      {\r
-        SequenceI key = (SequenceI) en.nextElement();\r
-        hiddenSeqs.addElement(key);\r
-        hiddenSeqsAsString.addElement(key.getSequence().toString());\r
-      }\r
-    }\r
-  }\r
-\r
-  /**\r
-   * DOCUMENT ME!\r
-   *\r
-   * @return DOCUMENT ME!\r
-   */\r
-  public String getDescription()\r
-  {\r
-    return description;\r
-  }\r
-\r
-\r
-  public void restore()\r
-  {\r
-    if (type == HistoryItem.SORT)\r
-    {\r
-      for (int i = 0; i < sequences.size(); i++)\r
-      {\r
-        alignment.getSequences().setElementAt(sequences.elementAt(i), i);\r
-      }\r
-    }\r
-    else\r
-    {\r
-      StringTokenizer st;\r
-      for (int i = 0; i < sequences.size(); i++)\r
-      {\r
-        SequenceI restore = (SequenceI) sequences.elementAt(i);\r
-\r
-\r
-        if (restore.getLength() == 0)\r
-        {\r
-          //This is for edits which remove all residues in a sequence\r
-          alignment.getSequences().insertElementAt(restore,\r
-              Integer.parseInt(alignIndex.elementAt(i).toString()));\r
-        }\r
-\r
-        st = new StringTokenizer(seqAsString.elementAt(i).toString());\r
-        restore.setStart(Integer.parseInt(st.nextToken()));\r
-        restore.setEnd(Integer.parseInt(st.nextToken()));\r
-        restore.setSequence(st.nextToken());\r
-      }\r
-\r
-      if(hiddenSeqs!=null)\r
-      {\r
-        for(int hs=0; hs<hiddenSeqs.size(); hs++)\r
-        {\r
-          SequenceI key = (SequenceI) hiddenSeqs.elementAt(hs);\r
-          key.setSequence(hiddenSeqsAsString.elementAt(hs).toString());\r
-        }\r
-      }\r
-\r
-      if (type == HistoryItem.PASTE)\r
-      {\r
-        for (int i = alignment.getHeight() - 1;\r
-             i > (sequences.size() - 1); i--)\r
-        {\r
-          alignment.deleteSequence(i);\r
-        }\r
-      }\r
-    }\r
-\r
-  }\r
-}\r
+/*
+* 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 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);
+  }
+}