JAL-885; hasRNAStructure method was introduced to AlignmentI and

Alignment; determines if Alignment contains an RNA structure;
Structure conservation row is just added if yes;

Change-Id: I6fa20f14e54cd656c65f82bc6b68f84d1d6f2c64

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 4e279d3..a2392b1 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -43,6 +43,8 @@ public class Alignment implements AlignmentI
   public static final int PROTEIN = 0;
 
   public static final int NUCLEOTIDE = 1;
+  
+  public boolean hasRNAStructure = false;
 
   /** DOCUMENT ME!! */
   public AlignmentAnnotation[] annotations;
@@ -732,6 +734,10 @@ public class Alignment implements AlignmentI
    */
   public void addAnnotation(AlignmentAnnotation aa, int pos)
   {
+    if(aa.getRNAStruc()!= null){
+      hasRNAStructure=true;
+    }
+    
     int aSize = 1;
     if (annotations != null)
     {
@@ -832,6 +838,10 @@ public class Alignment implements AlignmentI
       return false;
     }
   }
+  
+  public boolean hasRNAStructure(){
+    return hasRNAStructure;
+  }
 
   public void setDataset(Alignment data)
   {

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 2e0903d..05d3a10 100755 (executable)
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -204,9 +204,9 @@ public interface AlignmentI
 
   /**
    * Deletes a specific AlignmentAnnotation from the alignment, and removes its
-   * reference from any SequenceI or SequenceGroup object's annotation if and only if aa is
-   * contained within the alignment's annotation vector. Otherwise, it will do
-   * nothing.
+   * reference from any SequenceI or SequenceGroup object's annotation if and
+   * only if aa is contained within the alignment's annotation vector.
+   * Otherwise, it will do nothing.
    * 
    * @param aa
    *          the annotation to delete
@@ -215,15 +215,17 @@ public interface AlignmentI
   public boolean deleteAnnotation(AlignmentAnnotation aa);
 
   /**
-   * Deletes a specific AlignmentAnnotation from the alignment, and optionally removes any
-   * reference from any SequenceI or SequenceGroup object's annotation if and only if aa is
-   * contained within the alignment's annotation vector. Otherwise, it will do
-   * nothing.
+   * Deletes a specific AlignmentAnnotation from the alignment, and optionally
+   * removes any reference from any SequenceI or SequenceGroup object's
+   * annotation if and only if aa is contained within the alignment's annotation
+   * vector. Otherwise, it will do nothing.
    * 
    * @param aa
    *          the annotation to delete
    * @param unhook
-   *          flag indicating if any references should be removed from annotation - use this if you intend to add the annotation back into the alignment
+   *          flag indicating if any references should be removed from
+   *          annotation - use this if you intend to add the annotation back
+   *          into the alignment
    * @return true if annotation was deleted from this alignment.
    */
   public boolean deleteAnnotation(AlignmentAnnotation aa, boolean unhook);
@@ -259,6 +261,13 @@ public interface AlignmentI
   public boolean isNucleotide();
 
   /**
+   * Test if alignment contains RNA structure
+   * 
+   * @return true if RNA structure AligmnentAnnotation was added to alignment
+   */
+  public boolean hasRNAStructure();
+
+  /**
    * Set alignment to be a nucleotide sequence
    * 
    */

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 0a9cad4..b056fec 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -413,7 +413,7 @@ public class AlignViewport implements SelectionSource, VamsasSource
       consensus.hasText = true;
       consensus.autoCalculated = true;
 
-      if (alignment.isNucleotide())
+      if (alignment.isNucleotide() && alignment.hasRNAStructure())
       {
         strucConsensus = new AlignmentAnnotation("StrucConsensus", "PID",
                 new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
@@ -425,7 +425,7 @@ public class AlignViewport implements SelectionSource, VamsasSource
       {
         alignment.addAnnotation(consensus);
         // TODO: Make own if for structure
-        if (alignment.isNucleotide())
+        if (alignment.isNucleotide() && alignment.hasRNAStructure())
         {
           alignment.addAnnotation(strucConsensus);
         }