X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=56bfd74e604ae135c1b7ef5b0e9ba07bdd9fbed2;hb=136c0793b90b72b928c4d77dc109dd5c644e00d3;hp=2a89fa1ac0be7630d3a132ee6d6b05101a68aac2;hpb=267f5674a53a735d8e13a2a4c12a4c8d8b0c1f00;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 2a89fa1..56bfd74 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -96,14 +96,13 @@ public class AlignmentAnnotation
    * Updates the _rnasecstr field Determines the positions that base pair and
    * the positions of helices based on secondary structure from a Stockholm file
    * 
-   * @param RNAannot
+   * @param rnaAnnotation
    */
-  private void _updateRnaSecStr(CharSequence RNAannot)
+  private void _updateRnaSecStr(CharSequence rnaAnnotation)
   {
     try
     {
-      bps = Rna.getModeleBP(RNAannot);
-      _rnasecstr = Rna.getBasePairs(bps);
+      _rnasecstr = Rna.getHelixMap(rnaAnnotation);
       invalidrnastruc = -1;
     } catch (WUSSParseException px)
     {
@@ -114,8 +113,6 @@ public class AlignmentAnnotation
     {
       return;
     }
-    Rna.HelixMap(_rnasecstr);
-    // setRNAStruc(RNAannot);
 
     if (_rnasecstr != null && _rnasecstr.length > 0)
     {
@@ -170,10 +167,14 @@ public class AlignmentAnnotation
    */
   private Map<Integer, Annotation> sequenceMapping;
 
-  /** DOCUMENT ME!! */
+  /**
+   * lower range for quantitative data
+   */
   public float graphMin;
 
-  /** DOCUMENT ME!! */
+  /**
+   * Upper range for quantitative data
+   */
   public float graphMax;
 
   /**
@@ -269,12 +270,6 @@ public class AlignmentAnnotation
     }
   }
 
-  // JBPNote: what does this do ?
-  public void ConcenStru(CharSequence RNAannot) throws WUSSParseException
-  {
-    bps = Rna.getModeleBP(RNAannot);
-  }
-
   /**
    * Creates a new AlignmentAnnotation object.
    * 
@@ -863,6 +858,10 @@ public class AlignmentAnnotation
   @Override
   public String toString()
   {
+    if (annotations == null)
+    {
+      return "";
+    }
     StringBuilder buffer = new StringBuilder(256);
 
     for (int i = 0; i < annotations.length; i++)
@@ -1142,14 +1141,14 @@ public class AlignmentAnnotation
    * @param colSel
    */
   public AlignmentAnnotation(AlignmentAnnotation alignmentAnnotation,
-          ColumnSelection colSel)
+          HiddenColumns hidden)
   {
     this(alignmentAnnotation);
     if (annotations == null)
     {
       return;
     }
-    colSel.makeVisibleAnnotation(this);
+    hidden.makeVisibleAnnotation(this);
   }
 
   public void setPadGaps(boolean padgaps, char gapchar)
@@ -1307,8 +1306,7 @@ public class AlignmentAnnotation
    *       already
    */
   public void remap(SequenceI newref, HashMap<Integer, int[]> mapping,
-          int from, int to,
-          int idxoffset)
+          int from, int to, int idxoffset)
   {
     if (mapping != null)
     {
@@ -1487,4 +1485,13 @@ public class AlignmentAnnotation
   {
     return counter++;
   }
+
+  /**
+   * 
+   * @return true for rows that have a range of values in their annotation set
+   */
+  public boolean isQuantitative()
+  {
+    return graphMin < graphMax;
+  }
 }