import jalview.datamodel.AlignedCodon;
import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
*
* @param dna
* aligned dna sequences
- * @param mappings
- * from dna to protein
- * @param al
+ * @param dataset
+ * - throws error if not given a dataset
* @return an alignment whose sequences are the cds-only parts of the dna
* sequences (or null if no mappings are found)
*/
public static AlignmentI makeCdsAlignment(SequenceI[] dna,
- List<AlignedCodonFrame> mappings, AlignmentI al)
+ AlignmentI dataset)
{
+ if (dataset.getDataset() != null)
+ {
+ throw new Error(
+ "IMPLEMENTATION ERROR: dataset.getDataset() must be null!");
+ }
List<SequenceI> cdsSeqs = new ArrayList<SequenceI>();
+ List<AlignedCodonFrame> mappings = dataset.getCodonFrames();
+
+ /*
+ * construct CDS sequences from the (cds-to-protein) mappings made earlier;
+ * this makes it possible to model multiple products from dna (e.g. EMBL);
+ * however it does mean we don't have the EMBL protein_id (a property on
+ * the CDS features) in order to make the CDS sequence name :-(
+ */
for (SequenceI seq : dna)
{
- AlignedCodonFrame cdsMappings = new AlignedCodonFrame();
+ SequenceI seqDss = seq.getDatasetSequence() == null ? seq : seq
+ .getDatasetSequence();
List<AlignedCodonFrame> seqMappings = MappingUtils
.findMappingsForSequence(seq, mappings);
- List<AlignedCodonFrame> alignmentMappings = al.getCodonFrames();
for (AlignedCodonFrame mapping : seqMappings)
{
- for (Mapping aMapping : mapping.getMappingsFromSequence(seq))
+ List<Mapping> mappingsFromSequence = mapping.getMappingsFromSequence(seq);
+
+ for (Mapping aMapping : mappingsFromSequence)
{
- SequenceI cdsSeq = makeCdsSequence(seq.getDatasetSequence(),
- aMapping);
+ if (aMapping.getMap().getFromRatio() == 1)
+ {
+ /*
+ * not a dna-to-protein mapping (likely dna-to-cds)
+ */
+ continue;
+ }
+
+ /*
+ * check for an existing CDS sequence i.e. a 3:1 mapping to
+ * the dna mapping's product
+ */
+ SequenceI cdsSeq = null;
+ // TODO better mappings collection data model so we can do
+ // a table lookup instead of double loops to find mappings
+ SequenceI proteinProduct = aMapping.getTo();
+ for (AlignedCodonFrame acf : MappingUtils
+ .findMappingsForSequence(proteinProduct, mappings))
+ {
+ for (SequenceToSequenceMapping map : acf.getMappings())
+ {
+ if (map.getMapping().getMap().getFromRatio() == 3
+ && proteinProduct == map.getMapping().getTo()
+ && seqDss != map.getFromSeq())
+ {
+ /*
+ * found a 3:1 mapping to the protein product which is not
+ * from the dna sequence...assume it is from the CDS sequence
+ * TODO mappings data model that brings together related
+ * dna-cds-protein mappings in one object
+ */
+ cdsSeq = map.getFromSeq();
+ }
+ }
+ }
+ if (cdsSeq != null)
+ {
+ /*
+ * mappings are always to dataset sequences so create an aligned
+ * sequence to own it; add the dataset sequence to the dataset
+ */
+ SequenceI derivedSequence = cdsSeq.deriveSequence();
+ cdsSeqs.add(derivedSequence);
+ if (!dataset.getSequences().contains(cdsSeq))
+ {
+ dataset.addSequence(cdsSeq);
+ }
+ continue;
+ }
+
+ /*
+ * didn't find mapped CDS sequence - construct it and add
+ * its dataset sequence to the dataset
+ */
+ cdsSeq = makeCdsSequence(seq.getDatasetSequence(), aMapping);
+ SequenceI cdsSeqDss = cdsSeq.createDatasetSequence();
cdsSeqs.add(cdsSeq);
-
+ if (!dataset.getSequences().contains(cdsSeqDss))
+ {
+ dataset.addSequence(cdsSeqDss);
+ }
+
/*
* add a mapping from CDS to the (unchanged) mapped to range
*/
MapList map = new MapList(cdsRange, aMapping.getMap()
.getToRanges(), aMapping.getMap().getFromRatio(),
aMapping.getMap().getToRatio());
- cdsMappings.addMap(cdsSeq, aMapping.getTo(), map);
+ AlignedCodonFrame cdsToProteinMapping = new AlignedCodonFrame();
+ cdsToProteinMapping.addMap(cdsSeq, proteinProduct, map);
+
+ /*
+ * guard against duplicating the mapping if repeating this action
+ */
+ if (!mappings.contains(cdsToProteinMapping))
+ {
+ mappings.add(cdsToProteinMapping);
+ }
/*
* add another mapping from original 'from' range to CDS
*/
+ AlignedCodonFrame dnaToProteinMapping = new AlignedCodonFrame();
map = new MapList(aMapping.getMap().getFromRanges(), cdsRange, 1,
1);
- cdsMappings.addMap(seq.getDatasetSequence(), cdsSeq, map);
+ dnaToProteinMapping.addMap(seq.getDatasetSequence(), cdsSeq, map);
+ if (!mappings.contains(dnaToProteinMapping))
+ {
+ mappings.add(dnaToProteinMapping);
+ }
- alignmentMappings.add(cdsMappings);
/*
* transfer any features on dna that overlap the CDS
}
}
- /*
- * add CDS seqs to shared dataset
- */
- Alignment dataset = al.getDataset();
- for (SequenceI seq : cdsSeqs)
- {
- if (!dataset.getSequences().contains(seq.getDatasetSequence()))
- {
- dataset.addSequence(seq.getDatasetSequence());
- }
- }
AlignmentI cds = new Alignment(cdsSeqs.toArray(new SequenceI[cdsSeqs
.size()]));
- cds.setDataset(dataset);
+ cds.setDataset((Alignment) dataset);
return cds;
}
*
* @param seq
* @param mapping
- * @return
+ * @return CDS sequence (as a dataset sequence)
*/
static SequenceI makeCdsSequence(SequenceI seq, Mapping mapping)
{
SequenceI newSeq = new Sequence(seq.getName() + "|"
+ mapping.getTo().getName(), newSeqChars, 1, newPos);
- newSeq.createDatasetSequence();
return newSeq;
}
* sort to get sequence features in start position order
* - would be better to store in Sequence as a TreeSet or NCList?
*/
- Arrays.sort(peptide.getSequenceFeatures(),
- new Comparator<SequenceFeature>()
- {
- @Override
- public int compare(SequenceFeature o1, SequenceFeature o2)
+ if (peptide.getSequenceFeatures() != null)
+ {
+ Arrays.sort(peptide.getSequenceFeatures(),
+ new Comparator<SequenceFeature>()
{
- int c = Integer.compare(o1.getBegin(), o2.getBegin());
- return c == 0 ? Integer.compare(o1.getEnd(), o2.getEnd())
- : c;
- }
- });
+ @Override
+ public int compare(SequenceFeature o1, SequenceFeature o2)
+ {
+ int c = Integer.compare(o1.getBegin(), o2.getBegin());
+ return c == 0 ? Integer.compare(o1.getEnd(), o2.getEnd())
+ : c;
+ }
+ });
+ }
return count;
}
git://source.jalview.org / jalview.git / blobdiff