--- /dev/null
+package jalview.analysis;
+
+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
+ * various ways.
+ *
+ * @author gmcarstairs
+ *
+ */
+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
+ {
+ // 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.
+ *
+ * @param alignmentI
+ * @param showAutocalculatedAbove
+ */
+ public AnnotationSorter(AlignmentI alignmentI,
+ boolean showAutocalculatedAbove)
+ {
+ this.alignment = alignmentI;
+ this.showAutocalcAbove = showAutocalculatedAbove;
+ }
+
+ /**
+ * Default comparator sorts as follows by annotation type within sequence
+ * order:
+ * <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>within the same sequence ref, sort by label (non-case-sensitive)</li>
+ * </ul>
+ */
+ private final Comparator<? super AlignmentAnnotation> bySequenceAndLabel = new Comparator<AlignmentAnnotation>()
+ {
+ @Override
+ public int compare(AlignmentAnnotation o1, AlignmentAnnotation o2)
+ {
+ if (o1 == null && o2 == null)
+ {
+ return 0;
+ }
+ if (o1 == null)
+ {
+ return -1;
+ }
+ if (o2 == null)
+ {
+ return 1;
+ }
+
+ /*
+ * Ignore label (keep existing ordering) for
+ * Conservation/Quality/Consensus etc
+ */
+ if (o1.sequenceRef == null && o2.sequenceRef == null)
+ {
+ return 0;
+ }
+ int sequenceOrder = compareSequences(o1, o2);
+ return sequenceOrder == 0 ? compareLabels(o1, o2) : sequenceOrder;
+ }
+ };
+
+ /**
+ * This comparator sorts as follows by sequence order within annotation type
+ * <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>within the same label, sort by order of the related sequences</li>
+ * </ul>
+ */
+ private final Comparator<? super AlignmentAnnotation> byLabelAndSequence = new Comparator<AlignmentAnnotation>()
+ {
+ @Override
+ public int compare(AlignmentAnnotation o1, AlignmentAnnotation o2)
+ {
+ if (o1 == null && o2 == null)
+ {
+ return 0;
+ }
+ if (o1 == null)
+ {
+ return -1;
+ }
+ if (o2 == null)
+ {
+ return 1;
+ }
+
+ /*
+ * Ignore label (keep existing ordering) for
+ * Conservation/Quality/Consensus etc
+ */
+ if (o1.sequenceRef == null && o2.sequenceRef == null)
+ {
+ return 0;
+ }
+
+ /*
+ * Sort non-sequence-related before or after sequence-related.
+ */
+ if (o1.sequenceRef == null)
+ {
+ return showAutocalcAbove ? -1 : 1;
+ }
+ if (o2.sequenceRef == null)
+ {
+ return showAutocalcAbove ? 1 : -1;
+ }
+ int labelOrder = compareLabels(o1, o2);
+ return labelOrder == 0 ? compareSequences(o1, o2) : labelOrder;
+ }
+ };
+
+ /**
+ * 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).
+ */
+ private Comparator<? super AlignmentAnnotation> noSort = new Comparator<AlignmentAnnotation>()
+ {
+ @Override
+ public int compare(AlignmentAnnotation o1, AlignmentAnnotation o2)
+ {
+ if (o1 != null && o2 != null)
+ {
+ if (o1.sequenceRef == null && o2.sequenceRef != null)
+ {
+ return showAutocalcAbove ? -1 : 1;
+ }
+ if (o1.sequenceRef != null && o2.sequenceRef == null)
+ {
+ return showAutocalcAbove ? 1 : -1;
+ }
+ }
+ return 0;
+ }
+ };
+
+ /**
+ * Sort by the specified ordering of sequence-specific annotations.
+ *
+ * @param alignmentAnnotations
+ * @param order
+ */
+ public void sort(AlignmentAnnotation[] alignmentAnnotations,
+ SequenceAnnotationOrder order)
+ {
+ // cache 'alignment sequence position' for the annotations
+ saveSequenceIndices(alignmentAnnotations);
+
+ Comparator<? super AlignmentAnnotation> comparator = getComparator(order);
+
+ if (alignmentAnnotations != null)
+ {
+ synchronized (alignmentAnnotations)
+ {
+ 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);
+ }
+ }
+ }
+
+ /**
+ * Get the comparator for the specified sort order.
+ *
+ * @param order
+ * @return
+ */
+ private Comparator<? super AlignmentAnnotation> getComparator(
+ SequenceAnnotationOrder order)
+ {
+ if (order == null)
+ {
+ return noSort;
+ }
+ switch (order)
+ {
+ 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());
+ }
+ }
+
+ /**
+ * Non-case-sensitive comparison of annotation labels. Returns zero if either
+ * argument is null.
+ *
+ * @param o1
+ * @param o2
+ * @return
+ */
+ private int compareLabels(AlignmentAnnotation o1, AlignmentAnnotation o2)
+ {
+ if (o1 == null || o2 == null)
+ {
+ return 0;
+ }
+ String label1 = o1.label;
+ String label2 = o2.label;
+ if (label1 == null && label2 == null)
+ {
+ return 0;
+ }
+ if (label1 == null)
+ {
+ return -1;
+ }
+ if (label2 == null)
+ {
+ return 1;
+ }
+ return label1.toUpperCase().compareTo(label2.toUpperCase());
+ }
+
+ /**
+ * Comparison based on position of associated sequence (if any) in the
+ * alignment. Returns zero if either argument is null.
+ *
+ * @param o1
+ * @param o2
+ * @return
+ */
+ private int compareSequences(AlignmentAnnotation o1,
+ AlignmentAnnotation o2)
+ {
+ SequenceI seq1 = o1.sequenceRef;
+ SequenceI seq2 = o2.sequenceRef;
+ if (seq1 == null && seq2 == null)
+ {
+ return 0;
+ }
+ /*
+ * Sort non-sequence-related before or after sequence-related.
+ */
+ if (seq1 == null)
+ {
+ return showAutocalcAbove ? -1 : 1;
+ }
+ if (seq2 == null)
+ {
+ 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)
+ {
+ return -1;
+ }
+ if (index2 == -1)
+ {
+ return 1;
+ }
+ return Integer.compare(index1, index2);
+ }
+}
git://source.jalview.org / jalview.git / blobdiff