JAL-3081 more efficient algorithm for annotation ordering by sequence

[jalview.git] / src / jalview / analysis / AnnotationSorter.java

diff --git a/src/jalview/analysis/AnnotationSorter.java b/src/jalview/analysis/AnnotationSorter.java
index c1dd6a7..e5e9de4 100644 (file)
--- a/src/jalview/analysis/AnnotationSorter.java
+++ b/src/jalview/analysis/AnnotationSorter.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -50,8 +50,13 @@ public class AnnotationSorter
   public enum SequenceAnnotationOrder
   {
     // Text descriptions surface in the Preferences Sort by... options
-    SEQUENCE_AND_LABEL("Sequence"), LABEL_AND_SEQUENCE("Label"), NONE(
-            "No sort");
+    SEQUENCE_AND_LABEL("Sequence"), LABEL_AND_SEQUENCE("Label"),
+    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
@@ -108,7 +113,8 @@ public class AnnotationSorter
    * <ul>
    * <li>annotations with a reference to a sequence in the alignment are sorted
    * on sequence ordering</li>
-   * <li>other annotations go 'at the end', with their mutual order unchanged</li>
+   * <li>other annotations go 'at the end', with their mutual order
+   * unchanged</li>
    * <li>within the same sequence ref, sort by label (non-case-sensitive)</li>
    * </ul>
    */
@@ -169,7 +175,8 @@ public class AnnotationSorter
    * <ul>
    * <li>annotations with a reference to a sequence in the alignment are sorted
    * on label (non-case-sensitive)</li>
-   * <li>other annotations go 'at the end', with their mutual order unchanged</li>
+   * <li>other annotations go 'at the end', with their mutual order
+   * unchanged</li>
    * <li>within the same label, sort by order of the related sequences</li>
    * </ul>
    */
@@ -271,14 +278,23 @@ 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);
 
-    Comparator<? super AlignmentAnnotation> comparator = getComparator(order);
+    /*
+     * 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);
 
     if (alignmentAnnotations != null)
     {
@@ -300,13 +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);
+        }
       }
     }
   }
@@ -370,7 +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
@@ -385,8 +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)
     {
@@ -396,21 +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());
   }
 }