+/*
+ * 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;
*/
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
public enum SequenceAnnotationOrder
{
// Text descriptions surface in the Preferences Sort by... options
- SEQUENCE_AND_LABEL("Sequence"), LABEL_AND_SEQUENCE("Label"), NONE(
- "No sort");
+ 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 boolean showAutocalcAbove;
// working map of sequence index in alignment
- private final Map<SequenceI, Integer> sequenceIndices = new HashMap<SequenceI, Integer>();
+ private final Map<SequenceI, Integer> sequenceIndices = new HashMap<>();
+
+ // if true, sort only repositions auto-calculated annotation (to top or
+ // bottom)
+ private final boolean autocalcOnly;
/**
* Constructor given an alignment and the location (top or bottom) of
*
* @param alignmentI
* @param showAutocalculatedAbove
+ * @param autoCalcOnly
*/
public AnnotationSorter(AlignmentI alignmentI,
- boolean showAutocalculatedAbove)
+ boolean showAutocalculatedAbove, boolean autoCalcOnly)
{
this.alignment = alignmentI;
this.showAutocalcAbove = showAutocalculatedAbove;
+ this.autocalcOnly = autoCalcOnly;
}
/**
* <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>
*/
{
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;
}
* <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>
*/
{
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;
}
public void sort(AlignmentAnnotation[] alignmentAnnotations,
SequenceAnnotationOrder order)
{
- if (alignmentAnnotations == null)
+ if (alignmentAnnotations == null
+ || order == SequenceAnnotationOrder.CUSTOM)
{
return;
}
- // cache 'alignment sequence position' for the annotations
- saveSequenceIndices(alignmentAnnotations);
- Comparator<? super AlignmentAnnotation> comparator = getComparator(order);
+ /*
+ * cache 'alignment sequence positions' if required for sorting
+ */
+ if (order == SequenceAnnotationOrder.SEQUENCE_AND_LABEL
+ || order == SequenceAnnotationOrder.LABEL_AND_SEQUENCE)
+ {
+ saveSequenceIndices(alignmentAnnotations);
+ }
+
+ Comparator<? super AlignmentAnnotation> comparator = getComparator(
+ order);
if (alignmentAnnotations != null)
{
AlignmentAnnotation[] alignmentAnnotations)
{
sequenceIndices.clear();
+
+ Map<SequenceI, Integer> seqPositions = alignment.getSequencePositions();
+
for (AlignmentAnnotation ann : alignmentAnnotations)
{
SequenceI seq = ann.sequenceRef;
if (seq != null)
{
- int index = AlignmentUtils.getSequenceIndex(alignment, seq);
- sequenceIndices.put(seq, index);
+ Integer index = seqPositions.get(seq);
+ if (index != null)
+ {
+ sequenceIndices.put(seq, index);
+ }
}
}
}
/**
* 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.
+ * Sort non-sequence-related before or after sequence-related
*/
if (seq1 == 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)
+
+ /*
+ * 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