X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAnnotation.java;h=dae81ef4940663b226b9d91ab30c074f42cfb425;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=adb9bc541f37f678bc7977bfeced4d0754a1b72e;hpb=d4b1e4d0c74b1c6d0f3c3556b10be91a6aaea475;p=jalview.git

diff --git a/src/jalview/datamodel/Annotation.java b/src/jalview/datamodel/Annotation.java
index adb9bc5..dae81ef 100755
--- a/src/jalview/datamodel/Annotation.java
+++ b/src/jalview/datamodel/Annotation.java
@@ -1,57 +1,67 @@
 /*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * 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.
- *
- * 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.
- *
+ *  
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.datamodel;
 
-import java.awt.*;
+import java.awt.Color;
 
 /**
- * DOCUMENT ME!
- *
+ * Holds all annotation values for a position in an AlignmentAnnotation row
+ * 
  * @author $author$
  * @version $Revision$
  */
 public class Annotation
 {
-  /** DOCUMENT ME!! */
+  /** Character label - also shown below histogram */
   public String displayCharacter = "";
 
-  /** DOCUMENT ME!! */
-  public String description = ""; // currently used as mouse over
+  /**
+   * Text label for position: shown in mouse over and displayed on secondary
+   * structure glyphs
+   */
+  public String description = "";
 
-  /** DOCUMENT ME!! */
-  public char secondaryStructure = ' '; // recognises H and E
+  /**
+   * Secondary structure symbol: Protein symbols are H, E and S(?), RNA are
+   * WUSS/Vienna plus extended pseudoknot symbols
+   */
+  public char secondaryStructure = ' ';
 
-  /** DOCUMENT ME!! */
+  /** Score for the position - used in histograms, line graphs and for shading */
   public float value;
 
-  // add visual cues here
-
-  /** DOCUMENT ME!! */
-  public Color colour = Color.black;
+  /** Colour for position */
+  public Color colour;
 
   /**
    * Creates a new Annotation object.
-   *
-   * @param displayChar DOCUMENT ME!
-   * @param desc DOCUMENT ME!
-   * @param ss DOCUMENT ME!
-   * @param val DOCUMENT ME!
+   * 
+   * @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)
   {
@@ -59,48 +69,123 @@ public class Annotation
     description = desc;
     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!
+   * 
+   * @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)
+          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
+   * 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)
+  public Annotation(Annotation that)
+  {
+    if (that == null || this == that)
     {
       return;
     }
-    if (that.displayCharacter!=null)
+    if (that.displayCharacter != null)
       displayCharacter = new String(that.displayCharacter);
-    if (that.description!=null)
+    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
+   * 
+   * @param val
+   *          value at this annotation position
    */
   public Annotation(float val)
   {
-    this(null, null, '\0', val);
+    this(null, null, ' ', val, null);
+  }
+
+  /**
+   * human readable representation of an annotation row element.
+   * 
+   * Format is 'display Char','secondary Structure
+   * Char',"description",score,[colourstring]
+   * 
+   * fields may be missing if they are null, whitespace, or equivalent to
+   * Float.NaN
+   */
+  @Override
+  public String toString()
+  {
+    StringBuffer sb = new StringBuffer();
+    if (displayCharacter != null)
+    {
+      sb.append("\'");
+      sb.append(displayCharacter);
+      sb.append("\'");
+    }
+    {
+      sb.append(",");
+    }
+    if (secondaryStructure != 0
+            && !("" + displayCharacter).equals("" + secondaryStructure))
+    {
+      sb.append("\'");
+      sb.append(secondaryStructure);
+      sb.append("\'");
+    }
+    {
+      sb.append(",");
+    }
+    if (description != null && description.length() > 0)
+    {
+      sb.append("\"");
+      sb.append(description);
+      sb.append("\"");
+    }
+    {
+      sb.append(",");
+    }
+    if (value != Float.NaN)
+    {
+      sb.append(value);
+    }
+    if (colour != null)
+    {
+      if (sb.length() > 0)
+      {
+        sb.append(",");
+      }
+      sb.append("[");
+      sb.append(colour.getRed());
+      sb.append(",");
+      sb.append(colour.getGreen());
+      sb.append(",");
+      sb.append(colour.getBlue());
+      sb.append("]");
+    }
+    return sb.toString();
   }
 }