+/*
+ * 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;
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
{
-
- public enum SortOrder
+ /**
+ * 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_TYPE, TYPE_AND_SEQUENCE
+ // Text descriptions surface in the Preferences Sort by... options
+ 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;
+
+ 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)
+ /*
+ * 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<>();
+
+ /*
+ * if true, sort only repositions auto-calculated annotation (to top or bottom)
+ */
+ private boolean autocalcOnly;
+
+ /**
+ * Constructor
+ *
+ * @param av
+ */
+ public AnnotationSorter(AlignViewportI av)
{
- this.alignment = alignmentI;
+ this.alignment = av.getAlignment();
+ this.showAutocalcAbove = av.isShowAutocalculatedAbove();
}
/**
* <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>
*/
- 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;
+ }
+ 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";
+ }
};
/**
* <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>
*/
- 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;
+ }
+ 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 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";
+ }
};
- private final Comparator<? super AlignmentAnnotation> DEFAULT_COMPARATOR = bySequenceAndType;
-
/**
- * Sort by the specified order.
+ * 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,
- SortOrder order)
+ public void sort(SequenceAnnotationOrder sortBy, boolean autoCalcOnly)
{
- Comparator<? super AlignmentAnnotation> comparator = getComparator(order);
+ if (sortBy == null || sortBy == SequenceAnnotationOrder.CUSTOM)
+ {
+ return;
+ }
+
+ this.autocalcOnly = autoCalcOnly;
+
+ /*
+ * cache 'alignment sequence positions' if required for sorting
+ */
+ if (sortBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL
+ || sortBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE)
+ {
+ saveSequenceIndices();
+ }
+
+ Comparator<? super AlignmentAnnotation> comparator = getComparator(
+ sortBy);
- if (alignmentAnnotations != null)
+ AlignmentAnnotation[] annotations = alignment.getAlignmentAnnotation();
+ synchronized (annotations)
{
- synchronized (alignmentAnnotations)
+ Arrays.sort(annotations, comparator);
+ }
+ }
+
+ /**
+ * 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()
+ {
+ sequenceIndices.clear();
+
+ Map<SequenceI, Integer> seqPositions = alignment.getSequencePositions();
+
+ AlignmentAnnotation[] alignmentAnnotations = alignment
+ .getAlignmentAnnotation();
+ for (AlignmentAnnotation ann : alignmentAnnotations)
+ {
+ SequenceI seq = ann.sequenceRef;
+ if (seq != null)
{
- Arrays.sort(alignmentAnnotations, comparator);
+ Integer index = seqPositions.get(seq);
+ if (index != null)
+ {
+ sequenceIndices.put(seq, index);
+ }
}
}
}
* @return
*/
private Comparator<? super AlignmentAnnotation> getComparator(
- SortOrder order)
+ SequenceAnnotationOrder order)
{
if (order == null)
{
- return DEFAULT_COMPARATOR;
+ return noSort;
}
switch (order)
{
- case SEQUENCE_AND_TYPE:
- return this.bySequenceAndType;
- case TYPE_AND_SEQUENCE:
- return this.byTypeAndSequence;
+ 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());
}
/**
* Comparison based on position of associated sequence (if any) in the
- * alignment. Returns zero if either argument is null.
+ * alignment
*
* @param o1
* @param o2
{
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);
- 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());
}
}
git://source.jalview.org / jalview.git / blobdiff