/**
* 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())
{
}
/**
- * 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))
{