+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 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
return description;
}
- public static SequenceAnnotationOrder forDescription(String d) {
+ public static SequenceAnnotationOrder forDescription(String d)
+ {
for (SequenceAnnotationOrder order : values())
{
if (order.toString().equals(d))
}
}
+ // 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 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";
+ }
};
/**
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 before or after sequence-related.
+ * Sort autocalculated before or after sequence-related.
*/
- if (o1.sequenceRef == null)
+ if (o1auto)
{
return showAutocalcAbove ? -1 : 1;
}
- if (o2.sequenceRef == null)
+ if (o2auto)
{
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
- * 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).
+ * 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 (o1.sequenceRef == null && o2.sequenceRef != null)
+ if (o1auto && !o2auto)
{
return showAutocalcAbove ? -1 : 1;
}
- if (o1.sequenceRef != null && o2.sequenceRef == null)
+ if (!o1auto && o2auto)
{
return showAutocalcAbove ? 1 : -1;
}
}
return 0;
}
+
+ @Override
+ public String toString()
+ {
+ return "No sort";
+ }
};
/**
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)
}
/**
+ * 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 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