X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAnnotationSorter.java;fp=src%2Fjalview%2Fanalysis%2FAnnotationSorter.java;h=fa9c1a83f82ca41bfeda16ca30d5de61f758f3c3;hb=eaf9092bfa74b5162589c8775f68a19dd79dbb1d;hp=289544c4d71d6fd86dd3aff56057c002740fea5a;hpb=d305e02d8b425bb501141ad32142aeb8572adc57;p=jalview.git

diff --git a/src/jalview/analysis/AnnotationSorter.java b/src/jalview/analysis/AnnotationSorter.java
index 289544c..fa9c1a8 100644
--- a/src/jalview/analysis/AnnotationSorter.java
+++ b/src/jalview/analysis/AnnotationSorter.java
@@ -17,16 +17,27 @@ import java.util.Comparator;
 public class AnnotationSorter
 {
 
-  public enum SortOrder
+  public enum SequenceAnnotationOrder
   {
-    SEQUENCE_AND_TYPE, TYPE_AND_SEQUENCE
+    SEQUENCE_AND_LABEL, LABEL_AND_SEQUENCE, NONE
   }
   
   private final AlignmentI alignment;
 
-  public AnnotationSorter(AlignmentI alignmentI)
+  private boolean showAutocalcAbove;
+
+  /**
+   * Constructor given an alignment and the location (top or bottom) of
+   * Consensus and similar.
+   * 
+   * @param alignmentI
+   * @param showAutocalculatedAbove
+   */
+  public AnnotationSorter(AlignmentI alignmentI,
+          boolean showAutocalculatedAbove)
   {
     this.alignment = alignmentI;
+    this.showAutocalcAbove = showAutocalculatedAbove;
   }
 
   /**
@@ -39,7 +50,7 @@ public class AnnotationSorter
    * <li>within the same sequence ref, sort by label (non-case-sensitive)</li>
    * </ul>
    */
-  private final Comparator<? super AlignmentAnnotation> bySequenceAndType = new Comparator<AlignmentAnnotation>()
+  private final Comparator<? super AlignmentAnnotation> bySequenceAndLabel = new Comparator<AlignmentAnnotation>()
   {
     @Override
     public int compare(AlignmentAnnotation o1, AlignmentAnnotation o2)
@@ -79,7 +90,7 @@ public class AnnotationSorter
    * <li>within the same label, sort by order of the related sequences</li>
    * </ul>
    */
-  private final Comparator<? super AlignmentAnnotation> byTypeAndSequence = new Comparator<AlignmentAnnotation>()
+  private final Comparator<? super AlignmentAnnotation> byLabelAndSequence = new Comparator<AlignmentAnnotation>()
   {
     @Override
     public int compare(AlignmentAnnotation o1, AlignmentAnnotation o2)
@@ -107,39 +118,66 @@ public class AnnotationSorter
       }
 
       /*
-       * Sort non-sequence-related after sequence-related.
+       * Sort non-sequence-related before or after sequence-related.
        */
       if (o1.sequenceRef == null)
       {
-        return 1;
+        return showAutocalcAbove ? -1 : 1;
       }
       if (o2.sequenceRef == null)
       {
-        return -1;
+        return showAutocalcAbove ? 1 : -1;
       }
       int labelOrder = compareLabels(o1, o2);
       return labelOrder == 0 ? compareSequences(o1, o2) : labelOrder;
     }
   };
 
-  private final Comparator<? super AlignmentAnnotation> DEFAULT_COMPARATOR = bySequenceAndType;
+  /**
+   * noSort leaves sort order unchanged, within sequence- and
+   * non-sequence-related annotations, but may switch the ordering of these
+   * groups. Note this is guaranteed (at least in Java 7) as Arrays.sort() is
+   * guaranteed to be 'stable' (not change ordering of equal items).
+   */
+  private Comparator<? super AlignmentAnnotation> noSort = new Comparator<AlignmentAnnotation>()
+  {
+    @Override
+    public int compare(AlignmentAnnotation o1, AlignmentAnnotation o2)
+    {
+      if (o1 != null && o2 != null)
+      {
+        if (o1.sequenceRef == null && o2.sequenceRef != null)
+        {
+          return showAutocalcAbove ? -1 : 1;
+        }
+        if (o1.sequenceRef != null && o2.sequenceRef == null)
+        {
+          return showAutocalcAbove ? 1 : -1;
+        }
+      }
+      return 0;
+    }
+  };
   
   /**
-   * Sort by the specified order.
+   * Sort by the specified ordering of sequence-specific annotations.
    * 
    * @param alignmentAnnotations
    * @param order
    */
   public void sort(AlignmentAnnotation[] alignmentAnnotations,
-          SortOrder order)
+          SequenceAnnotationOrder order)
   {
-    Comparator<? super AlignmentAnnotation> comparator = getComparator(order);
-
-    if (alignmentAnnotations != null)
+    if (order != SequenceAnnotationOrder.NONE)
     {
-      synchronized (alignmentAnnotations)
+      Comparator<? super AlignmentAnnotation> comparator = getComparator(order);
+
+      if (alignmentAnnotations != null)
       {
-        Arrays.sort(alignmentAnnotations, comparator);
+        synchronized (alignmentAnnotations)
+        {
+          Arrays.sort(alignmentAnnotations, comparator);
+        }
       }
     }
   }
@@ -151,18 +189,20 @@ public class AnnotationSorter
    * @return
    */
   private Comparator<? super AlignmentAnnotation> getComparator(
-          SortOrder order)
+          SequenceAnnotationOrder order)
   {
     if (order == null)
     {
-      return DEFAULT_COMPARATOR;
+      return noSort;
     }
     switch (order)
     {
-    case SEQUENCE_AND_TYPE:
-      return this.bySequenceAndType;
-    case TYPE_AND_SEQUENCE:
-      return this.byTypeAndSequence;
+    case NONE:
+      return this.noSort;
+    case SEQUENCE_AND_LABEL:
+      return this.bySequenceAndLabel;
+    case LABEL_AND_SEQUENCE:
+      return this.byLabelAndSequence;
     default:
       throw new UnsupportedOperationException(order.toString());
     }
@@ -216,13 +256,16 @@ public class AnnotationSorter
     {
       return 0;
     }
+    /*
+     * Sort non-sequence-related before or after sequence-related.
+     */
     if (seq1 == null)
     {
-      return 1;
+      return showAutocalcAbove ? -1 : 1;
     }
     if (seq2 == null)
     {
-      return -1;
+      return showAutocalcAbove ? 1 : -1;
     }
     // get sequence index - but note -1 means 'at end' so needs special handling
     int index1 = AlignmentUtils.getSequenceIndex(alignment, seq1);