+/*
+ * 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.datamodel.AlignmentAnnotation;
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
+ {
+ // 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;
}
/**
* <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)
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";
+ }
};
/**
* <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)
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";
+ }
};
/**
- * Sort by annotation type (label), within sequence order.
- * Non-sequence-related annotations sort to the end.
+ * Sort by the specified ordering of sequence-specific annotations.
*
* @param alignmentAnnotations
+ * @param order
*/
- public void sortBySequenceAndType(
- AlignmentAnnotation[] alignmentAnnotations)
+ public void sort(AlignmentAnnotation[] alignmentAnnotations,
+ SequenceAnnotationOrder order)
{
+ if (alignmentAnnotations == null)
+ {
+ return;
+ }
+ // cache 'alignment sequence position' for the annotations
+ saveSequenceIndices(alignmentAnnotations);
+
+ Comparator<? super AlignmentAnnotation> comparator = getComparator(order);
+
if (alignmentAnnotations != null)
{
synchronized (alignmentAnnotations)
{
- Arrays.sort(alignmentAnnotations, bySequenceAndType);
+ Arrays.sort(alignmentAnnotations, comparator);
}
}
}
/**
- * Sort by sequence order within annotation type (label). Non-sequence-related
- * annotations sort to the end.
+ * 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
*/
- public void sortByTypeAndSequence(
+ private void saveSequenceIndices(
AlignmentAnnotation[] alignmentAnnotations)
{
- if (alignmentAnnotations != null)
+ sequenceIndices.clear();
+ for (AlignmentAnnotation ann : alignmentAnnotations)
{
- synchronized (alignmentAnnotations)
+ SequenceI seq = ann.sequenceRef;
+ if (seq != null)
{
- Arrays.sort(alignmentAnnotations, byTypeAndSequence);
+ 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.
*
{
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;
git://source.jalview.org / jalview.git / blobdiff