JAL-1645 source formatting and organise imports

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

diff --git a/src/jalview/analysis/AnnotationSorter.java b/src/jalview/analysis/AnnotationSorter.java
index a5d2164..b0cfe20 100644 (file)
--- a/src/jalview/analysis/AnnotationSorter.java
+++ b/src/jalview/analysis/AnnotationSorter.java
@@ -46,7 +46,8 @@ 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))
@@ -109,17 +110,38 @@ 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";
+    }
   };
 
   /**
@@ -149,55 +171,75 @@ 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";
+    }
   };
 
   /**
@@ -209,6 +251,10 @@ public class AnnotationSorter
   public void sort(AlignmentAnnotation[] alignmentAnnotations,
           SequenceAnnotationOrder order)
   {
+    if (alignmentAnnotations == null)
+    {
+      return;
+    }
     // cache 'alignment sequence position' for the annotations
     saveSequenceIndices(alignmentAnnotations);
 
@@ -234,9 +280,11 @@ public class AnnotationSorter
           AlignmentAnnotation[] alignmentAnnotations)
   {
     sequenceIndices.clear();
-    for (AlignmentAnnotation ann : alignmentAnnotations) {
+    for (AlignmentAnnotation ann : alignmentAnnotations)
+    {
       SequenceI seq = ann.sequenceRef;
-      if (seq != null) {
+      if (seq != null)
+      {
         int index = AlignmentUtils.getSequenceIndex(alignment, seq);
         sequenceIndices.put(seq, index);
       }