X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAnnotation.java;h=a73ea7a491e47ac40b170c61a7517ab375c5bfb7;hb=4ec235370b49c38ae7e7b3a46f92f926fc430bf1;hp=b99ce9f2cf05205b0a78da5dadee9dab5c2e97a0;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git

diff --git a/src/jalview/datamodel/Annotation.java b/src/jalview/datamodel/Annotation.java
index b99ce9f..a73ea7a 100755
--- a/src/jalview/datamodel/Annotation.java
+++ b/src/jalview/datamodel/Annotation.java
@@ -1,35 +1,62 @@
 /*
-* 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
-*/
-
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+ * Copyright (C) 2009 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 java.awt.*;
 
+/**
+ * DOCUMENT ME!
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
 public class Annotation
 {
-  public String displayCharacter="";
-  public String description="";       // currently used as mouse over
-  public char secondaryStructure=' '; // recognises H and E
+  /** DOCUMENT ME!! */
+  public String displayCharacter = "";
+
+  /** DOCUMENT ME!! */
+  public String description = ""; // currently used as mouse over
+
+  /** DOCUMENT ME!! */
+  public char secondaryStructure = ' '; // recognises H and E
+
+  /** DOCUMENT ME!! */
   public float value;
 
   // add visual cues here
-  public Color colour = Color.black;
 
+  /** DOCUMENT ME!! */
+  public Color colour;
+
+  /**
+   * Creates a new Annotation object.
+   * 
+   * @param displayChar
+   *                DOCUMENT ME!
+   * @param desc
+   *                DOCUMENT ME!
+   * @param ss
+   *                DOCUMENT ME!
+   * @param val
+   *                DOCUMENT ME!
+   */
   public Annotation(String displayChar, String desc, char ss, float val)
   {
     displayCharacter = displayChar;
@@ -37,8 +64,58 @@ public class Annotation
     secondaryStructure = ss;
     value = val;
   }
-  public Annotation(String displayChar, String desc, char ss, float val, Color colour) {
+
+  /**
+   * Creates a new Annotation object.
+   * 
+   * @param displayChar
+   *                DOCUMENT ME!
+   * @param desc
+   *                DOCUMENT ME!
+   * @param ss
+   *                DOCUMENT ME!
+   * @param val
+   *                DOCUMENT ME!
+   * @param colour
+   *                DOCUMENT ME!
+   */
+  public Annotation(String displayChar, String desc, char ss, float val,
+          Color colour)
+  {
     this(displayChar, desc, ss, val);
     this.colour = colour;
   }
+
+  /**
+   * Copy constructor New annotation takes on the same (or duplicated)
+   * attributes as the given template
+   * 
+   * @param that
+   *                template annotation
+   */
+  public Annotation(Annotation that)
+  {
+    if (that == null || this == that)
+    {
+      return;
+    }
+    if (that.displayCharacter != null)
+      displayCharacter = new String(that.displayCharacter);
+    if (that.description != null)
+      description = new String(that.description);
+    secondaryStructure = that.secondaryStructure;
+    value = that.value;
+    colour = that.colour;
+  }
+
+  /**
+   * Value only annotation.
+   * 
+   * @param val
+   *                value at this annotation position
+   */
+  public Annotation(float val)
+  {
+    this(null, null, ' ', val);
+  }
 }