import jalview.util.MapList;
import jalview.util.MappingUtils;
+import java.util.AbstractList;
import java.util.ArrayList;
import java.util.List;
/*
* Data bean to hold mappings from one sequence to another
*/
- private class SequenceToSequenceMapping
+ public class SequenceToSequenceMapping
{
private SequenceI fromSeq;
return String.format("From %s %s", fromSeq.getName(),
mapping.toString());
}
+
+ /**
+ * Returns a hashCode derived from the hashcodes of the mappings and fromSeq
+ *
+ * @see SequenceToSequenceMapping#hashCode()
+ */
+ @Override
+ public int hashCode()
+ {
+ return (fromSeq == null ? 0 : fromSeq.hashCode() * 31)
+ + mapping.hashCode();
+ }
+
+ /**
+ * Answers true if the objects hold the same mapping between the same two
+ * sequences
+ *
+ * @see Mapping#equals
+ */
+ @Override
+ public boolean equals(Object obj)
+ {
+ if (!(obj instanceof SequenceToSequenceMapping))
+ {
+ return false;
+ }
+ SequenceToSequenceMapping that = (SequenceToSequenceMapping) obj;
+ if (this.mapping == null)
+ {
+ return that.mapping == null;
+ }
+ // TODO: can simplify by asserting fromSeq is a dataset sequence
+ return (this.fromSeq == that.fromSeq || (this.fromSeq != null
+ && that.fromSeq != null
+ && this.fromSeq.getDatasetSequence() != null && this.fromSeq
+ .getDatasetSequence() == that.fromSeq.getDatasetSequence()))
+ && this.mapping.equals(that.mapping);
+ }
+
+ public SequenceI getFromSeq()
+ {
+ return fromSeq;
+ }
+
+ public Mapping getMapping()
+ {
+ return mapping;
+ }
}
private List<SequenceToSequenceMapping> mappings;
*/
public void addMap(SequenceI dnaseq, SequenceI aaseq, MapList map)
{
+ addMap(dnaseq, aaseq, map, null);
+ }
+
+ /**
+ * Adds a mapping between the dataset sequences for the associated dna and
+ * protein sequence objects
+ *
+ * @param dnaseq
+ * @param aaseq
+ * @param map
+ * @param mapFromId
+ */
+ public void addMap(SequenceI dnaseq, SequenceI aaseq, MapList map,
+ String mapFromId)
+ {
// JBPNote DEBUG! THIS !
// dnaseq.transferAnnotation(aaseq, mp);
// aaseq.transferAnnotation(dnaseq, new Mapping(map.getInverse()));
/*
* if we already hold a mapping between these sequences, just add to it
+ * note that 'adding' a duplicate map does nothing; this protects against
+ * creating duplicate mappings in AlignedCodonFrame
*/
for (SequenceToSequenceMapping ssm : mappings)
{
* otherwise, add a new sequence mapping
*/
Mapping mp = new Mapping(toSeq, map);
+ mp.setMappedFromId(mapFromId);
mappings.add(new SequenceToSequenceMapping(fromSeq, mp));
}
* where highlighted regions go
*/
public void markMappedRegion(SequenceI seq, int index,
- SearchResults results)
+ SearchResultsI results)
{
int[] codon;
SequenceI ds = seq.getDatasetSequence();
/**
* Convenience method to return the first aligned sequence in the given
- * alignment whose dataset has a mapping with the given dataset sequence.
+ * alignment whose dataset has a mapping with the given (aligned or dataset)
+ * sequence.
*
* @param seq
*
*/
for (SequenceToSequenceMapping ssm : mappings)
{
- if (ssm.fromSeq == seq)
+ if (ssm.fromSeq == seq || ssm.fromSeq == seq.getDatasetSequence())
{
for (SequenceI sourceAligned : al.getSequences())
{
*/
for (SequenceToSequenceMapping ssm : mappings)
{
- if (ssm.mapping.to == seq)
+ if (ssm.mapping.to == seq
+ || ssm.mapping.to == seq.getDatasetSequence())
{
for (SequenceI sourceAligned : al.getSequences())
{
for (SequenceToSequenceMapping ssm : mappings)
{
- if (ssm.mapping.to == protein)
+ if (ssm.mapping.to == protein
+ && ssm.mapping.getMap().getFromRatio() == 3)
{
ml = ssm.mapping.map;
dnaSeq = ssm.fromSeq;
}
/**
- * Returns any mappings found which are to (or from) the given sequence, and
- * to distinct sequences.
+ * Returns any mappings found which are from the given sequence, and to
+ * distinct sequences.
*
* @param seq
* @return
*/
- public List<Mapping> getMappingsForSequence(SequenceI seq)
+ public List<Mapping> getMappingsFromSequence(SequenceI seq)
{
List<Mapping> result = new ArrayList<Mapping>();
List<SequenceI> related = new ArrayList<SequenceI>();
for (SequenceToSequenceMapping ssm : mappings)
{
final Mapping mapping = ssm.mapping;
- if (ssm.fromSeq == seqDs || mapping.to == seqDs)
+ if (ssm.fromSeq == seqDs)
{
if (!related.contains(mapping.to))
{
{
return mappings == null ? "null" : mappings.toString();
}
+
+ /**
+ * Returns the first mapping found that is between 'fromSeq' and 'toSeq', or
+ * null if none found
+ *
+ * @param fromSeq
+ * aligned or dataset sequence
+ * @param toSeq
+ * aligned or dataset sequence
+ * @return
+ */
+ public Mapping getMappingBetween(SequenceI fromSeq, SequenceI toSeq)
+ {
+ SequenceI dssFrom = fromSeq.getDatasetSequence() == null ? fromSeq
+ : fromSeq.getDatasetSequence();
+ SequenceI dssTo = toSeq.getDatasetSequence() == null ? toSeq : toSeq
+ .getDatasetSequence();
+
+ for (SequenceToSequenceMapping mapping : mappings)
+ {
+ SequenceI from = mapping.fromSeq;
+ SequenceI to = mapping.mapping.to;
+ if ((from == dssFrom && to == dssTo)
+ || (from == dssTo && to == dssFrom))
+ {
+ return mapping.mapping;
+ }
+ }
+ return null;
+ }
+
+ /**
+ * Returns a hashcode derived from the list of sequence mappings
+ *
+ * @see SequenceToSequenceMapping#hashCode()
+ * @see AbstractList#hashCode()
+ */
+ @Override
+ public int hashCode()
+ {
+ return this.mappings.hashCode();
+ }
+
+ /**
+ * Two AlignedCodonFrame objects are equal if they hold the same ordered list
+ * of mappings
+ *
+ * @see SequenceToSequenceMapping#
+ */
+ @Override
+ public boolean equals(Object obj)
+ {
+ if (!(obj instanceof AlignedCodonFrame))
+ {
+ return false;
+ }
+ return this.mappings.equals(((AlignedCodonFrame) obj).mappings);
+ }
+
+ public List<SequenceToSequenceMapping> getMappings()
+ {
+ return mappings;
+ }
}