X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAnnotationSorter.java;h=83f3adf238bce0f8a64c5476a875330e7666e8a5;hb=a2032664d7eb6954072d43b424e11d219f28df62;hp=a5d2164b655b4a9b1ef9c00595d07070a518b1e5;hpb=76139ef711627a3176736af47272ff55be62e720;p=jalview.git

diff --git a/src/jalview/analysis/AnnotationSorter.java b/src/jalview/analysis/AnnotationSorter.java
index a5d2164..83f3adf 100644
--- a/src/jalview/analysis/AnnotationSorter.java
+++ b/src/jalview/analysis/AnnotationSorter.java
@@ -1,5 +1,26 @@
+/*
+ * 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 jalview.api.AlignViewportI;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
@@ -18,7 +39,6 @@ import java.util.Map;
  */
 public class AnnotationSorter
 {
-
   /**
    * enum for annotation sort options. The text description is used in the
    * Preferences drop-down options. The enum name is saved in the preferences
@@ -30,8 +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;
 
@@ -46,7 +71,8 @@ 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))
@@ -58,27 +84,35 @@ public class AnnotationSorter
     }
   }
 
-  // the alignment with respect to which annotations are sorted
+  /*
+   * the alignment with respect to which annotations are sorted
+   */
   private final AlignmentI alignment;
 
-  // user preference for placement of non-sequence annotations
+  /*
+   * if true, autocalculated are sorted first, if false, last
+   */
   private boolean showAutocalcAbove;
 
-  // working map of sequence index in alignment
-  private final Map<SequenceI, Integer> sequenceIndices = new HashMap<SequenceI, Integer>();
+  /*
+   * working map of sequence index in alignment
+   */
+  private final Map<SequenceI, Integer> sequenceIndices = new HashMap<>();
+
+  /*
+   * if true, sort only repositions auto-calculated annotation (to top or bottom)
+   */
+  private boolean autocalcOnly;
 
   /**
-   * Constructor given an alignment and the location (top or bottom) of
-   * Consensus and similar.
+   * Constructor
    * 
-   * @param alignmentI
-   * @param showAutocalculatedAbove
+   * @param av
    */
-  public AnnotationSorter(AlignmentI alignmentI,
-          boolean showAutocalculatedAbove)
+  public AnnotationSorter(AlignViewportI av)
   {
-    this.alignment = alignmentI;
-    this.showAutocalcAbove = showAutocalculatedAbove;
+    this.alignment = av.getAlignment();
+    this.showAutocalcAbove = av.isShowAutocalculatedAbove();
   }
 
   /**
@@ -87,7 +121,8 @@ 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>
    */
@@ -109,17 +144,42 @@ 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;
+      }
+      if (autocalcOnly)
+      {
+        return 0; // don't reorder other annotations
+      }
       int sequenceOrder = compareSequences(o1, o2);
       return sequenceOrder == 0 ? compareLabels(o1, o2) : sequenceOrder;
     }
+
+    @Override
+    public String toString()
+    {
+      return "Sort by sequence and label";
+    }
   };
 
   /**
@@ -127,7 +187,8 @@ 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>
    */
@@ -149,96 +210,142 @@ 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;
       }
+      if (autocalcOnly)
+      {
+        return 0; // don't reorder other annotations
+      }
       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";
+    }
   };
 
   /**
-   * Sort by the specified ordering of sequence-specific annotations.
+   * Sorts by the specified ordering. If order is {@code CUSTOM}, meaning
+   * annotations have been manually ordered by the user, no sort is performed.
    * 
-   * @param alignmentAnnotations
-   * @param order
+   * @param sortBy
+   *          the sort order to apply
+   * @param autoCalcOnly
+   *          if true, only autocalculated annotations are repositioned (to top
+   *          or bottom), others are left in their current order
    */
-  public void sort(AlignmentAnnotation[] alignmentAnnotations,
-          SequenceAnnotationOrder order)
+  public void sort(SequenceAnnotationOrder sortBy, boolean autoCalcOnly)
   {
-    // cache 'alignment sequence position' for the annotations
-    saveSequenceIndices(alignmentAnnotations);
+    if (sortBy == null || sortBy == SequenceAnnotationOrder.CUSTOM)
+    {
+      return;
+    }
 
-    Comparator<? super AlignmentAnnotation> comparator = getComparator(order);
+    this.autocalcOnly = autoCalcOnly;
 
-    if (alignmentAnnotations != null)
+    /*
+     * cache 'alignment sequence positions' if required for sorting
+     */
+    if (sortBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL
+            || sortBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE)
     {
-      synchronized (alignmentAnnotations)
-      {
-        Arrays.sort(alignmentAnnotations, comparator);
-      }
+      saveSequenceIndices();
+    }
+
+    Comparator<? super AlignmentAnnotation> comparator = getComparator(
+            sortBy);
+
+    AlignmentAnnotation[] annotations = alignment.getAlignmentAnnotation();
+    synchronized (annotations)
+    {
+      Arrays.sort(annotations, comparator);
     }
   }
 
   /**
-   * 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
+   * Calculates and saves in a temporary map the position of each annotation's
+   * associated sequence (if it has one) in the alignment. Faster to do this
+   * once than for every annotation comparison.
    */
-  private void saveSequenceIndices(
-          AlignmentAnnotation[] alignmentAnnotations)
+  private void saveSequenceIndices()
   {
     sequenceIndices.clear();
-    for (AlignmentAnnotation ann : alignmentAnnotations) {
+
+    Map<SequenceI, Integer> seqPositions = alignment.getSequencePositions();
+
+    AlignmentAnnotation[] alignmentAnnotations = alignment
+            .getAlignmentAnnotation();
+    for (AlignmentAnnotation ann : alignmentAnnotations)
+    {
       SequenceI seq = ann.sequenceRef;
-      if (seq != null) {
-        int index = AlignmentUtils.getSequenceIndex(alignment, seq);
-        sequenceIndices.put(seq, index);
+      if (seq != null)
+      {
+        Integer index = seqPositions.get(seq);
+        if (index != null)
+        {
+          sequenceIndices.put(seq, index);
+        }
       }
     }
   }
@@ -302,7 +409,7 @@ 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
@@ -317,8 +424,9 @@ 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)
     {
@@ -328,21 +436,20 @@ 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());
   }
 }