X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAnnotation.java;h=f6919cd36058cbfdacf9503e3aee84ac2bf516de;hb=bb5d9c75833e2d0b9ef8f66b8fcd7d5649a3271f;hp=b371bc3e0e1f53ed289acd092c5355645f3e1eeb;hpb=c5677e9860106a821a3e6e0429b20ede7b9a732a;p=jalview.git

diff --git a/src/jalview/datamodel/Annotation.java b/src/jalview/datamodel/Annotation.java
index b371bc3..f6919cd 100755
--- a/src/jalview/datamodel/Annotation.java
+++ b/src/jalview/datamodel/Annotation.java
@@ -1,52 +1,62 @@
 /*
- * 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
+ * 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.
- * 
+ * 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/>.
+ * You should have received a copy of the GNU General Public License
+ * 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.util.ArrayList;
-
-import fr.orsay.lri.varna.models.rna.RNA;
+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!! */
+  /**
+   * the empty annotation - proxy for null entries in annotation row
+   */
+  public static final Annotation EMPTY_ANNOTATION = new Annotation("", "",
+          ' ', 0f);
+
+  /** 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, E and S(?)
+  /**
+   * 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;
 
   /**
@@ -67,7 +77,7 @@ public class Annotation
     description = desc;
     secondaryStructure = ss;
     value = val;
-    
+
   }
 
   /**
@@ -105,9 +115,13 @@ 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;
@@ -122,10 +136,85 @@ public class Annotation
    */
   public Annotation(float val)
   {
-    this(null, null, ' ', val,null);
+    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();
+  }
+
+  /**
+   * @return true if annot is 'whitespace' annotation (zero score, whitespace or
+   *         zero length display character, label, description
+   */
+  public boolean isWhitespace()
+  {
+    return ((value == 0f)
+            && ((description == null) || (description.trim().length() == 0))
+            && ((displayCharacter == null)
+                    || (displayCharacter.trim().length() == 0)
+                    || (displayCharacter.equals(" ."))) // RNA Stockholm blank
+                                                        // displayCharacter can
+                                                        // end up like this
+            && (secondaryStructure == '\0' || (secondaryStructure == ' '))
+            && colour == null);
   }
-  
-  
-  
-  
 }