X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAnnotation.java;h=6b22cade9cd4f262abe1b727795b1b49c45771b4;hb=a822fc744dcc06e6a8d2399218da0d0dfd56cf2b;hp=16ede508eeb13439a9c2b605d3e31c23b08dd754;hpb=59a81cfb8e64c68d882182601663d82016f1a866;p=jalview.git

diff --git a/src/jalview/datamodel/Annotation.java b/src/jalview/datamodel/Annotation.java
index 16ede50..6b22cad 100755
--- a/src/jalview/datamodel/Annotation.java
+++ b/src/jalview/datamodel/Annotation.java
@@ -1,16 +1,61 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview 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 3 of the License, or (at your option) any later version.
+ * 
+ * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ */
 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, E and S(?)
+
+  /** 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;
@@ -18,8 +63,58 @@ 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);
+  }
 }