package jalview.analysis;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import java.util.Arrays;
import java.util.Comparator;
/**
* 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;
}
}
private final AlignmentI alignment;
private boolean showAutocalcAbove;
/**
* 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:
*
* - annotations with a reference to a sequence in the alignment are sorted
* on sequence ordering
* - other annotations go 'at the end', with their mutual order unchanged
* - within the same sequence ref, sort by label (non-case-sensitive)
*
*/
private final Comparator super AlignmentAnnotation> bySequenceAndLabel = new Comparator()
{
@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
*
* - annotations with a reference to a sequence in the alignment are sorted
* on label (non-case-sensitive)
* - other annotations go 'at the end', with their mutual order unchanged
* - within the same label, sort by order of the related sequences
*
*/
private final Comparator super AlignmentAnnotation> byLabelAndSequence = new Comparator()
{
@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()
{
@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)
{
Comparator super AlignmentAnnotation> comparator = getComparator(order);
if (alignmentAnnotations != null)
{
synchronized (alignmentAnnotations)
{
Arrays.sort(alignmentAnnotations, comparator);
}
}
}
/**
* 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 = AlignmentUtils.getSequenceIndex(alignment, seq1);
int index2 = AlignmentUtils.getSequenceIndex(alignment, seq2);
if (index1 == index2)
{
return 0;
}
if (index1 == -1)
{
return -1;
}
if (index2 == -1)
{
return 1;
}
return Integer.compare(index1, index2);
}
}