alignmentProperties added

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

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 3ad05ea..04eab48 100755 (executable)
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -57,12 +57,12 @@ public class AlignmentAnnotation
   /**
    * Score associated with label and description.
    */
-  public float score;
+  public float score= Float.NaN;
   /**
    * flag indicating if annotation has a score.
    */
   public boolean hasScore=false;
-  
+
   public GraphLine threshold;
 
   // Graphical hints and tips
@@ -96,6 +96,8 @@ public class AlignmentAnnotation
 
   public static final int LINE_GRAPH = 2;
 
+  public boolean belowAlignment = true;
+
 
   public static int getGraphValueFromString(String string)
   {
@@ -118,7 +120,8 @@ public class AlignmentAnnotation
    *
    * @param label DOCUMENT ME!
    * @param description DOCUMENT ME!
-   * @param annotations DOCUMENT ME!
+   * @param annotations DOCUMENT ME!about:blank
+Loading...
    */
   public AlignmentAnnotation(String label, String description,
                              Annotation[] annotations)
@@ -223,11 +226,13 @@ public class AlignmentAnnotation
    * if appropriate.
    */
   private void validateRangeAndDisplay() {
+
     if (annotations==null)
     {
       visible=false; // try to prevent renderer from displaying.
       return; // this is a non-annotation row annotation - ie a sequence score.
     }
+
     int graphType = graph;
     float min = graphMin;
     float max = graphMax;
@@ -617,7 +622,7 @@ public class AlignmentAnnotation
     this.score = score;
   }
   /**
-   * 
+   *
    * @return true if annotation has an associated score
    */
   public boolean hasScore()