debugged mappings and translated sequence recovery

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

diff --git a/src/jalview/datamodel/Annotation.java b/src/jalview/datamodel/Annotation.java
index 6179cfa..9fc69bb 100755 (executable)
--- a/src/jalview/datamodel/Annotation.java
+++ b/src/jalview/datamodel/Annotation.java
@@ -1,16 +1,58 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 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;
@@ -18,4 +60,47 @@ public class Annotation
     secondaryStructure = ss;
     value = val;
   }
+
+  /**
+   * 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);
+  }
 }