X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAnnotation.java;h=71ebbb3f87daff70034c35427fc428fa7dd1e7fc;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=348c9a4b4bc9a8c3e418ceeb83a752d7de4188e3;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git

diff --git a/src/jalview/datamodel/Annotation.java b/src/jalview/datamodel/Annotation.java
index 348c9a4..71ebbb3 100755
--- a/src/jalview/datamodel/Annotation.java
+++ b/src/jalview/datamodel/Annotation.java
@@ -1,61 +1,67 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
- * 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 file is part of Jalview.
  * 
- * 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 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 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!! */
+  /** Colour for position */
   public Color colour;
 
   /**
    * Creates a new Annotation object.
    * 
    * @param displayChar
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param desc
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param ss
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param val
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public Annotation(String displayChar, String desc, char ss, float val)
   {
@@ -63,21 +69,22 @@ public class Annotation
     description = desc;
     secondaryStructure = ss;
     value = val;
+
   }
 
   /**
    * Creates a new Annotation object.
    * 
    * @param displayChar
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param desc
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param ss
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param val
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param colour
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public Annotation(String displayChar, String desc, char ss, float val,
           Color colour)
@@ -91,7 +98,7 @@ public class Annotation
    * attributes as the given template
    * 
    * @param that
-   *                template annotation
+   *          template annotation
    */
   public Annotation(Annotation that)
   {
@@ -100,22 +107,89 @@ public class Annotation
       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
+   *          value at this annotation position
    */
   public Annotation(float val)
   {
-    this(null, null, ' ', 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 (!Float.isNaN(value))
+    {
+      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();
   }
 }