Feature Groups added

[jalview.git] / src / jalview / datamodel / HistoryItem.java

diff --git a/src/jalview/datamodel/HistoryItem.java b/src/jalview/datamodel/HistoryItem.java
index 3a5b180..eb4979d 100755 (executable)
--- a/src/jalview/datamodel/HistoryItem.java
+++ b/src/jalview/datamodel/HistoryItem.java
@@ -1,52 +1,124 @@
+/*\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
-  public static final int EDIT = 0;\r
-  public static final int SORT = 1;\r
-  public static final int HIDE = 2;\r
-  public static final int PASTE= 3;\r
-\r
-  final int type;\r
-  Vector sequences;\r
-  Vector alignIndex;\r
-  String description;\r
-  Vector hiddenSeqs;\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
-\r
-    for (int i = 0; i < al.getHeight(); i++)\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
-      SequenceI seq = al.getSequenceAt(i);\r
-      sequences.addElement(seq);\r
-      alignIndex.addElement(i + "");\r
-      hiddenSeqs.addElement(seq.getSequence().toString());\r
-    }\r
-  }\r
+        this.type = type;\r
+        this.description = description;\r
+        sequences = new Vector();\r
+        alignIndex = new Vector();\r
+        hiddenSeqs = new Vector();\r
 \r
-  public int getType()\r
-  {return type;}\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
 \r
-  public Vector getSequences()\r
-  {return sequences;}\r
+    /**\r
+     * DOCUMENT ME!\r
+     *\r
+     * @return DOCUMENT ME!\r
+     */\r
+    public int getType()\r
+    {\r
+        return type;\r
+    }\r
 \r
-  public String getDescription()\r
-  {return description; }\r
+    /**\r
+     * DOCUMENT ME!\r
+     *\r
+     * @return DOCUMENT ME!\r
+     */\r
+    public Vector getSequences()\r
+    {\r
+        return sequences;\r
+    }\r
 \r
-  public Vector getHidden()\r
-  { return hiddenSeqs; }\r
+    /**\r
+     * DOCUMENT ME!\r
+     *\r
+     * @return DOCUMENT ME!\r
+     */\r
+    public String getDescription()\r
+    {\r
+        return description;\r
+    }\r
 \r
-  public int getAlignIndex(int seq)\r
-  {\r
-    return Integer.parseInt(alignIndex.elementAt(seq).toString());\r
-  }\r
+    /**\r
+     * DOCUMENT ME!\r
+     *\r
+     * @return DOCUMENT ME!\r
+     */\r
+    public Vector getHidden()\r
+    {\r
+        return hiddenSeqs;\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
+    {\r
+        return Integer.parseInt(alignIndex.elementAt(seq).toString());\r
+    }\r
 }\r