Gethidden sequences

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