X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAnnotationSorter.java;h=e5e9de49157dded5a809895b30217cd6426204de;hb=4e52fac08f31a714cb9d706178b10364c8f02d69;hp=2f556f111221d495380873ad990e5422303f3b89;hpb=f4766a7bbcfae845fc95923b01fa14ff83d589ff;p=jalview.git

diff --git a/src/jalview/analysis/AnnotationSorter.java b/src/jalview/analysis/AnnotationSorter.java
index 2f556f1..e5e9de4 100644
--- a/src/jalview/analysis/AnnotationSorter.java
+++ b/src/jalview/analysis/AnnotationSorter.java
@@ -51,7 +51,12 @@ public class AnnotationSorter
   {
     // Text descriptions surface in the Preferences Sort by... options
     SEQUENCE_AND_LABEL("Sequence"), LABEL_AND_SEQUENCE("Label"),
-    NONE("No sort");
+    NONE("No sort"),
+
+    /**
+     * custom is set if user drags to reorder annotations
+     */
+    CUSTOM("Customised");
 
     private String description;
 
@@ -86,7 +91,7 @@ public class AnnotationSorter
   private boolean showAutocalcAbove;
 
   // working map of sequence index in alignment
-  private final Map<SequenceI, Integer> sequenceIndices = new HashMap<SequenceI, Integer>();
+  private final Map<SequenceI, Integer> sequenceIndices = new HashMap<>();
 
   /**
    * Constructor given an alignment and the location (top or bottom) of
@@ -273,12 +278,20 @@ public class AnnotationSorter
   public void sort(AlignmentAnnotation[] alignmentAnnotations,
           SequenceAnnotationOrder order)
   {
-    if (alignmentAnnotations == null)
+    if (alignmentAnnotations == null
+            || order == SequenceAnnotationOrder.CUSTOM)
     {
       return;
     }
-    // cache 'alignment sequence position' for the annotations
-    saveSequenceIndices(alignmentAnnotations);
+
+    /*
+     * cache 'alignment sequence positions' if required for sorting
+     */
+    if (order == SequenceAnnotationOrder.SEQUENCE_AND_LABEL
+            || order == SequenceAnnotationOrder.LABEL_AND_SEQUENCE)
+    {
+      saveSequenceIndices(alignmentAnnotations);
+    }
 
     Comparator<? super AlignmentAnnotation> comparator = getComparator(
             order);
@@ -303,13 +316,19 @@ public class AnnotationSorter
           AlignmentAnnotation[] alignmentAnnotations)
   {
     sequenceIndices.clear();
+
+    Map<SequenceI, Integer> seqPositions = alignment.getSequencePositions();
+
     for (AlignmentAnnotation ann : alignmentAnnotations)
     {
       SequenceI seq = ann.sequenceRef;
       if (seq != null)
       {
-        int index = AlignmentUtils.getSequenceIndex(alignment, seq);
-        sequenceIndices.put(seq, index);
+        Integer index = seqPositions.get(seq);
+        if (index != null)
+        {
+          sequenceIndices.put(seq, index);
+        }
       }
     }
   }
@@ -373,7 +392,7 @@ public class AnnotationSorter
 
   /**
    * Comparison based on position of associated sequence (if any) in the
-   * alignment. Returns zero if either argument is null.
+   * alignment
    * 
    * @param o1
    * @param o2
@@ -388,8 +407,9 @@ public class AnnotationSorter
     {
       return 0;
     }
+
     /*
-     * Sort non-sequence-related before or after sequence-related.
+     * Sort non-sequence-related before or after sequence-related
      */
     if (seq1 == null)
     {
@@ -399,21 +419,20 @@ public class AnnotationSorter
     {
       return showAutocalcAbove ? 1 : -1;
     }
-    // get sequence index - but note -1 means 'at end' so needs special handling
-    int index1 = sequenceIndices.get(seq1);
-    int index2 = sequenceIndices.get(seq2);
-    if (index1 == index2)
-    {
-      return 0;
-    }
-    if (index1 == -1)
+
+    /*
+     * else sort by associated sequence position
+     */
+    Integer index1 = sequenceIndices.get(seq1);
+    Integer index2 = sequenceIndices.get(seq2);
+    if (index1 == null)
     {
-      return -1;
+      return index2 == null ? 0 : -1;
     }
-    if (index2 == -1)
+    if (index2 == null)
     {
       return 1;
     }
-    return Integer.compare(index1, index2);
+    return Integer.compare(index1.intValue(), index2.intValue());
   }
 }