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
{
public enum SortOrder
{
SEQUENCE_AND_TYPE, TYPE_AND_SEQUENCE
}
private final AlignmentI alignment;
public AnnotationSorter(AlignmentI alignmentI)
{
this.alignment = alignmentI;
}
/**
* 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> bySequenceAndType = 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> byTypeAndSequence = 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 after sequence-related.
*/
if (o1.sequenceRef == null)
{
return 1;
}
if (o2.sequenceRef == null)
{
return -1;
}
int labelOrder = compareLabels(o1, o2);
return labelOrder == 0 ? compareSequences(o1, o2) : labelOrder;
}
};
private final Comparator super AlignmentAnnotation> DEFAULT_COMPARATOR = bySequenceAndType;
/**
* Sort by the specified order.
*
* @param alignmentAnnotations
* @param order
*/
public void sort(AlignmentAnnotation[] alignmentAnnotations,
SortOrder 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(
SortOrder order)
{
if (order == null)
{
return DEFAULT_COMPARATOR;
}
switch (order)
{
case SEQUENCE_AND_TYPE:
return this.bySequenceAndType;
case TYPE_AND_SEQUENCE:
return this.byTypeAndSequence;
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;
}
if (seq1 == null)
{
return 1;
}
if (seq2 == null)
{
return -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);
}
}