X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAnnotationSorter.java;h=92ed9bec374645afb0f6099c73e4688e7f6f852a;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=289544c4d71d6fd86dd3aff56057c002740fea5a;hpb=d305e02d8b425bb501141ad32142aeb8572adc57;p=jalview.git

diff --git a/src/jalview/analysis/AnnotationSorter.java b/src/jalview/analysis/AnnotationSorter.java
index 289544c..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
@@ -17,16 +41,67 @@ import java.util.Comparator;
 public class AnnotationSorter
 {
 
-  public enum SortOrder
+  /**
+   * enum for annotation sort options. The text description is used in the
+   * Preferences drop-down options. The enum name is saved in the preferences
+   * file.
+   * 
+   * @author gmcarstairs
+   *
+   */
+  public enum SequenceAnnotationOrder
   {
-    SEQUENCE_AND_TYPE, TYPE_AND_SEQUENCE
+    // Text descriptions surface in the Preferences Sort by... options
+    SEQUENCE_AND_LABEL("Sequence"), LABEL_AND_SEQUENCE("Label"),
+    NONE("No sort");
+
+    private String description;
+
+    private SequenceAnnotationOrder(String s)
+    {
+      description = s;
+    }
+
+    @Override
+    public String toString()
+    {
+      return description;
+    }
+
+    public static SequenceAnnotationOrder forDescription(String d)
+    {
+      for (SequenceAnnotationOrder order : values())
+      {
+        if (order.toString().equals(d))
+        {
+          return order;
+        }
+      }
+      return null;
+    }
   }
-  
+
+  // the alignment with respect to which annotations are sorted
   private final AlignmentI alignment;
 
-  public AnnotationSorter(AlignmentI alignmentI)
+  // 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.
+   * 
+   * @param alignmentI
+   * @param showAutocalculatedAbove
+   */
+  public AnnotationSorter(AlignmentI alignmentI,
+          boolean showAutocalculatedAbove)
   {
     this.alignment = alignmentI;
+    this.showAutocalcAbove = showAutocalculatedAbove;
   }
 
   /**
@@ -35,11 +110,12 @@ 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>
    */
-  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)
@@ -57,17 +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";
+    }
   };
 
   /**
@@ -75,11 +172,12 @@ 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>
    */
-  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)
@@ -97,43 +195,95 @@ 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 after sequence-related.
+       * Sort autocalculated before or after sequence-related.
        */
-      if (o1.sequenceRef == null)
+      if (o1auto)
       {
-        return 1;
+        return showAutocalcAbove ? -1 : 1;
       }
-      if (o2.sequenceRef == null)
+      if (o2auto)
       {
-        return -1;
+        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 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 (o1auto && !o2auto)
+        {
+          return showAutocalcAbove ? -1 : 1;
+        }
+        if (!o1auto && o2auto)
+        {
+          return showAutocalcAbove ? 1 : -1;
+        }
+      }
+      return 0;
+    }
+
+    @Override
+    public String toString()
+    {
+      return "No sort";
+    }
   };
 
-  private final Comparator<? super AlignmentAnnotation> DEFAULT_COMPARATOR = bySequenceAndType;
-  
   /**
-   * 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)
+    {
+      return;
+    }
+    // cache 'alignment sequence position' for the annotations
+    saveSequenceIndices(alignmentAnnotations);
+
+    Comparator<? super AlignmentAnnotation> comparator = getComparator(
+            order);
 
     if (alignmentAnnotations != null)
     {
@@ -145,24 +295,48 @@ 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
    * @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());
     }
@@ -196,7 +370,8 @@ public class AnnotationSorter
     {
       return 1;
     }
-    return label1.toUpperCase().compareTo(label2.toUpperCase());
+    return label1.toUpperCase(Locale.ROOT)
+            .compareTo(label2.toUpperCase(Locale.ROOT));
   }
 
   /**
@@ -216,17 +391,20 @@ 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);
-    int index2 = AlignmentUtils.getSequenceIndex(alignment, seq2);
+    int index1 = sequenceIndices.get(seq1);
+    int index2 = sequenceIndices.get(seq2);
     if (index1 == index2)
     {
       return 0;