private void LoadSequenceMetadata()
{
//Associate available metadata with Sequence objects.
var seqmetadata = from e in _manifestRoot.Descendants(SequenceMetadata.SequenceMetadataLabel)
join s in _alignment.Sequences
on e.Element(SequenceMetadata.AlignmentRowNameLabel).Value equals s.ID
select new { e, s };
//Load the metadata
foreach (var sm in seqmetadata)
{
sm.s.Metadata.Add(SequenceMetadata.SequenceMetadataLabel, new SequenceMetadata());
SequenceMetadata metadata = (SequenceMetadata)sm.s.Metadata[SequenceMetadata.SequenceMetadataLabel];
if (sm.e.Element(SequenceMetadata.ScientificNameLabel) != null)
{
metadata.ScientificName = sm.e.Element(SequenceMetadata.ScientificNameLabel).Value;
}
if (sm.e.Element(SequenceMetadata.TaxIDLabel) != null)
{
int taxID = 0;
Int32.TryParse(sm.e.Element(SequenceMetadata.TaxIDLabel).Value, out taxID);
metadata.TaxID = taxID;
}
if (sm.e.Element(SequenceMetadata.LineageLabel) != null)
{
metadata.Lineage = sm.e.Element(SequenceMetadata.LineageLabel).Value;
}
if (sm.e.Element(SequenceMetadata.SequenceLengthLabel) != null)
{
int seqLength = 0;
Int32.TryParse(sm.e.Element(SequenceMetadata.SequenceLengthLabel).Value, out seqLength);
metadata.SequenceLength = seqLength;
}
if (sm.e.Element(SequenceMetadata.LocationDescriptionLabel) != null)
{
metadata.LocationDescription = sm.e.Element(SequenceMetadata.LocationDescriptionLabel).Value;
}
if (sm.e.Element(SequenceMetadata.AlignmentRowNameLabel) != null)
{
metadata.AlignmentRowName = sm.e.Element(SequenceMetadata.AlignmentRowNameLabel).Value;
}
if (sm.e.Element(SequenceMetadata.AccessionsLabel) != null)
{
var accessions = from accession in sm.e.Element(SequenceMetadata.AccessionsLabel).Descendants(SequenceMetadata.GenbankAccessionLabel)
select new GenBankVersion
{
Accession = accession.Element(SequenceMetadata.GenbankAccessionIDLabel).Value,
Version = accession.Element(SequenceMetadata.GenbankAccessionVersionLabel).Value
};
foreach (var accession in accessions)
{
metadata.Accessions.Add(accession);
}
}
if (sm.e.Element(SequenceMetadata.StructureModelLabel) != null)
{
StructureModel strmodel = new StructureModel(metadata.SequenceLength);
var pairs = from pair in sm.e.Element(SequenceMetadata.StructureModelLabel).Descendants(SequenceMetadata.StructureModelPairLabel)
select pair;
foreach (var pair in pairs)
{
int fivePrimeIndex, threePrimeIndex;
if (Int32.TryParse(pair.Element(SequenceMetadata.StructureModelPairFivePrimeIndexLabel).Value, out fivePrimeIndex) &&
Int32.TryParse(pair.Element(SequenceMetadata.StructureModelPairThreePrimeIndexLabel).Value, out threePrimeIndex))
{
strmodel.Pairs.Add(fivePrimeIndex, threePrimeIndex);
}
}
strmodel.DecomposeStructure();
metadata.StructureModel = strmodel;
}
}
}
