X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAnnotationSorter.java;h=92ed9bec374645afb0f6099c73e4688e7f6f852a;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=28fa1f8a2667bb42a37b0f8e6e75bf32e90de2c1;hpb=7c5e7c1c51a48eab1b217a221df82748c35b76b1;p=jalview.git

diff --git a/src/jalview/analysis/AnnotationSorter.java b/src/jalview/analysis/AnnotationSorter.java
index 28fa1f8..92ed9be 100644
--- a/src/jalview/analysis/AnnotationSorter.java
+++ b/src/jalview/analysis/AnnotationSorter.java
@@ -1,11 +1,35 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.analysis;
 
+import java.util.Locale;
+
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
 
 import java.util.Arrays;
 import java.util.Comparator;
+import java.util.HashMap;
+import java.util.Map;
 
 /**
  * A helper class to sort all annotations associated with an alignment in
@@ -28,8 +52,8 @@ 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");
 
     private String description;
 
@@ -44,7 +68,8 @@ public class AnnotationSorter
       return description;
     }
 
-    public static SequenceAnnotationOrder forDescription(String d) {
+    public static SequenceAnnotationOrder forDescription(String d)
+    {
       for (SequenceAnnotationOrder order : values())
       {
         if (order.toString().equals(d))
@@ -56,10 +81,15 @@ public class AnnotationSorter
     }
   }
 
+  // the alignment with respect to which annotations are sorted
   private final AlignmentI alignment;
 
+  // user preference for placement of non-sequence annotations
   private boolean showAutocalcAbove;
 
+  // working map of sequence index in alignment
+  private final Map<SequenceI, Integer> sequenceIndices = new HashMap<SequenceI, Integer>();
+
   /**
    * Constructor given an alignment and the location (top or bottom) of
    * Consensus and similar.
@@ -80,7 +110,8 @@ 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>
    */
@@ -102,17 +133,38 @@ public class AnnotationSorter
         return 1;
       }
 
+      // TODO how to treat sequence-related autocalculated annotation
+      boolean o1auto = o1.autoCalculated && o1.sequenceRef == null;
+      boolean o2auto = o2.autoCalculated && o2.sequenceRef == null;
       /*
        * Ignore label (keep existing ordering) for
        * Conservation/Quality/Consensus etc
        */
-      if (o1.sequenceRef == null && o2.sequenceRef == null)
+      if (o1auto && o2auto)
       {
         return 0;
       }
+
+      /*
+       * Sort autocalculated before or after sequence-related.
+       */
+      if (o1auto)
+      {
+        return showAutocalcAbove ? -1 : 1;
+      }
+      if (o2auto)
+      {
+        return showAutocalcAbove ? 1 : -1;
+      }
       int sequenceOrder = compareSequences(o1, o2);
       return sequenceOrder == 0 ? compareLabels(o1, o2) : sequenceOrder;
     }
+
+    @Override
+    public String toString()
+    {
+      return "Sort by sequence and label";
+    }
   };
 
   /**
@@ -120,7 +172,8 @@ 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>
    */
@@ -142,55 +195,75 @@ public class AnnotationSorter
         return 1;
       }
 
+      // TODO how to treat sequence-related autocalculated annotation
+      boolean o1auto = o1.autoCalculated && o1.sequenceRef == null;
+      boolean o2auto = o2.autoCalculated && o2.sequenceRef == null;
       /*
        * Ignore label (keep existing ordering) for
        * Conservation/Quality/Consensus etc
        */
-      if (o1.sequenceRef == null && o2.sequenceRef == null)
+      if (o1auto && o2auto)
       {
         return 0;
       }
 
       /*
-       * Sort non-sequence-related before or after sequence-related.
+       * Sort autocalculated before or after sequence-related.
        */
-      if (o1.sequenceRef == null)
+      if (o1auto)
       {
         return showAutocalcAbove ? -1 : 1;
       }
-      if (o2.sequenceRef == null)
+      if (o2auto)
       {
         return showAutocalcAbove ? 1 : -1;
       }
       int labelOrder = compareLabels(o1, o2);
       return labelOrder == 0 ? compareSequences(o1, o2) : labelOrder;
     }
+
+    @Override
+    public String toString()
+    {
+      return "Sort by label and sequence";
+    }
   };
 
   /**
-   * 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).
+   * noSort leaves sort order unchanged, within sequence- and autocalculated
+   * 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)
     {
+      // TODO how to treat sequence-related autocalculated annotation
+      boolean o1auto = o1.autoCalculated && o1.sequenceRef == null;
+      boolean o2auto = o2.autoCalculated && o2.sequenceRef == null;
+      // TODO skip this test to allow customised ordering of all annotations
+      // - needs a third option: place autocalculated first / last / none
       if (o1 != null && o2 != null)
       {
-        if (o1.sequenceRef == null && o2.sequenceRef != null)
+        if (o1auto && !o2auto)
         {
           return showAutocalcAbove ? -1 : 1;
         }
-        if (o1.sequenceRef != null && o2.sequenceRef == null)
+        if (!o1auto && o2auto)
         {
           return showAutocalcAbove ? 1 : -1;
         }
       }
       return 0;
     }
+
+    @Override
+    public String toString()
+    {
+      return "No sort";
+    }
   };
 
   /**
@@ -202,7 +275,15 @@ public class AnnotationSorter
   public void sort(AlignmentAnnotation[] alignmentAnnotations,
           SequenceAnnotationOrder order)
   {
-    Comparator<? super AlignmentAnnotation> comparator = getComparator(order);
+    if (alignmentAnnotations == null)
+    {
+      return;
+    }
+    // cache 'alignment sequence position' for the annotations
+    saveSequenceIndices(alignmentAnnotations);
+
+    Comparator<? super AlignmentAnnotation> comparator = getComparator(
+            order);
 
     if (alignmentAnnotations != null)
     {
@@ -214,6 +295,28 @@ public class AnnotationSorter
   }
 
   /**
+   * Calculate and save in a temporary map the position of each annotation's
+   * sequence (if it has one) in the alignment. Faster to do this once than for
+   * every annotation comparison.
+   * 
+   * @param alignmentAnnotations
+   */
+  private void saveSequenceIndices(
+          AlignmentAnnotation[] alignmentAnnotations)
+  {
+    sequenceIndices.clear();
+    for (AlignmentAnnotation ann : alignmentAnnotations)
+    {
+      SequenceI seq = ann.sequenceRef;
+      if (seq != null)
+      {
+        int index = AlignmentUtils.getSequenceIndex(alignment, seq);
+        sequenceIndices.put(seq, index);
+      }
+    }
+  }
+
+  /**
    * Get the comparator for the specified sort order.
    * 
    * @param order
@@ -267,7 +370,8 @@ public class AnnotationSorter
     {
       return 1;
     }
-    return label1.toUpperCase().compareTo(label2.toUpperCase());
+    return label1.toUpperCase(Locale.ROOT)
+            .compareTo(label2.toUpperCase(Locale.ROOT));
   }
 
   /**
@@ -299,8 +403,8 @@ public class AnnotationSorter
       return showAutocalcAbove ? 1 : -1;
     }
     // get sequence index - but note -1 means 'at end' so needs special handling
-    int index1 = AlignmentUtils.getSequenceIndex(alignment, seq1);
-    int index2 = AlignmentUtils.getSequenceIndex(alignment, seq2);
+    int index1 = sequenceIndices.get(seq1);
+    int index2 = sequenceIndices.get(seq2);
     if (index1 == index2)
     {
       return 0;