X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAnnotation.java;h=f6919cd36058cbfdacf9503e3aee84ac2bf516de;hb=ed581b841fe9361bfe80bb006df190a29df264fb;hp=e3588b039fe9ac90d09e1e87d54d85b769954491;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git

diff --git a/src/jalview/datamodel/Annotation.java b/src/jalview/datamodel/Annotation.java
index e3588b0..f6919cd 100755
--- a/src/jalview/datamodel/Annotation.java
+++ b/src/jalview/datamodel/Annotation.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -30,6 +30,12 @@ import java.awt.Color;
  */
 public class Annotation
 {
+  /**
+   * 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 = "";
 
@@ -45,9 +51,11 @@ public class Annotation
    */
   public char secondaryStructure = ' ';
 
-  /** Score for the position - used in histograms, line graphs and for shading */
+  /**
+   * Score for the position - used in histograms, line graphs and for shading
+   */
   public float value;
-  
+
   /** Colour for position */
   public Color colour;
 
@@ -69,7 +77,7 @@ public class Annotation
     description = desc;
     secondaryStructure = ss;
     value = val;
-    
+
   }
 
   /**
@@ -107,9 +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;
@@ -124,15 +136,15 @@ 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
    */
@@ -168,7 +180,7 @@ public class Annotation
     {
       sb.append(",");
     }
-    if (value != Float.NaN)
+    if (!Float.isNaN(value))
     {
       sb.append(value);
     }
@@ -188,4 +200,21 @@ public class Annotation
     }
     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);
+  }
 }