JAL-3061 / JAL-3053

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

diff --git a/src/jalview/datamodel/Annotation.java b/src/jalview/datamodel/Annotation.java
index 8e5c490..f6919cd 100755 (executable)
--- a/src/jalview/datamodel/Annotation.java
+++ b/src/jalview/datamodel/Annotation.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * 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 = "";
 
@@ -45,7 +51,9 @@ 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 */
@@ -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;
@@ -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);
+  }
 }