private EBIApplicationResult GenerateSequencesFromXml(XmlReader reader)
{
XmlSerializer serializer = new XmlSerializer(typeof(EBIApplicationResult));
EBIApplicationResult result = (EBIApplicationResult)serializer.Deserialize(reader);
return(result);
}
public bool GetBlastSearchResult(SequenceProject project, string path, UserProject userProject)
{
if (project != null)
{
//XmlResult
string result = path + project.BlastSearchGuid + ".xml.xml";
if (!File.Exists(result))
{
result = blastService.GetResults(project.BlastSearchGuid, result);
if (String.IsNullOrEmpty(result))
{
return(false);
}
}
if (!String.IsNullOrEmpty(result))
{
using (StreamReader sr = new StreamReader(result))
{
StringBuilder sb = new StringBuilder();
XmlReader reader = XmlReader.Create(sr);
EBIApplicationResult ebiResult = GenerateSequencesFromXml(reader);
if (ebiResult != null && ebiResult.SequenceSimilaritySearchResult != null)
{
IList <Sequence> sequencies = CreateBlastSequencies(ebiResult.SequenceSimilaritySearchResult.hits, project, userProject);
if (project.Alligments == null)
{
project.Alligments = new List <AlignmentSequence>();
}
if (sequencies != null && sequencies.Any())
{
AlignmentSequence allign = new AlignmentSequence()
{
Created = DateTime.Now,
CreatorId = project.CreatorId,
Description = "BlastAlignment",
IsFinished = false,
_id = ObjectId.GenerateNewId(),
Source = "Blast",
AllignedSequences = new List <AlignRecord>()
};
foreach (Sequence seq in sequencies)
{
allign.AllignedSequences.Add(new AlignRecord()
{
AlignedSequence = seq.BlastAlignedSequence,
Organism = seq.Organism,
SequenceId = seq._id,
SequenceName = seq.Name,
SequenceHeader = seq.Description
});
}
project.Alligments.Add(allign);
db.UpdateItem(project);
return(true);
}
}
}
}
}
return(false);
}