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
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
+ * file.
+ *
+ * @author gmcarstairs
+ *
+ */
public enum SequenceAnnotationOrder
{
- SEQUENCE_AND_LABEL, LABEL_AND_SEQUENCE, NONE
+ // 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;
+ // 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.
return 0;
}
};
-
+
/**
* Sort by the specified ordering of sequence-specific annotations.
*
public void sort(AlignmentAnnotation[] alignmentAnnotations,
SequenceAnnotationOrder order)
{
- if (order != SequenceAnnotationOrder.NONE)
+ if (alignmentAnnotations == null)
{
- Comparator<? super AlignmentAnnotation> comparator = getComparator(order);
+ return;
+ }
+ // cache 'alignment sequence position' for the annotations
+ saveSequenceIndices(alignmentAnnotations);
+
+ Comparator<? super AlignmentAnnotation> comparator = getComparator(order);
- if (alignmentAnnotations != null)
+ if (alignmentAnnotations != null)
+ {
+ synchronized (alignmentAnnotations)
{
- synchronized (alignmentAnnotations)
- {
- Arrays.sort(alignmentAnnotations, comparator);
- }
+ Arrays.sort(alignmentAnnotations, 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
+ */
+ 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);
}
}
}
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;