public ActionResult AddTreePicture(FormCollection col, TreeModel model)
{
if (Request.Files.Count > 0)
{
var file = Request.Files[0];
if (file != null && file.ContentLength > 0)
{
string fileName = Path.GetFileName(file.FileName);
var path = Path.Combine(Server.MapPath("~/ServiceResults/Trees/"), fileName);
file.SaveAs(path);
ObjectId projId = ObjectId.Parse(model.ProjectId);
SequenceProject project = db.GetItem <SequenceProject>(x => x._id == projId);
if (project != null && model.AlignmentId != String.Empty)
{
AlignmentSequence alignment = project.Alligments.First(x => x.IdString == model.AlignmentId);
if (alignment != null)
{
alignment.TreePicture = path;
db.UpdateItem(project);
}
}
}
}
return(RedirectToAction("ViewTree", new { projectId = model.ProjectId, alignmentId = model.AlignmentId }));
}
public ActionResult ViewTree(string projectId, string alignmentId)
{
ObjectId projId = ObjectId.Parse(projectId);
SequenceProject project = db.GetItem <SequenceProject>(x => x._id == projId);
if (project != null && alignmentId != String.Empty)
{
AlignmentSequence alignment = project.Alligments.First(x => x.IdString == alignmentId);
if (alignment != null && !String.IsNullOrEmpty(alignment.PhylogeneticTree))
{
string fileContent = String.Empty;
if (System.IO.File.Exists(alignment.TreePicture))
{
using (StreamReader sr = new StreamReader(alignment.TreePicture))
{
fileContent = sr.ReadToEnd();
}
}
return(View("ViewTree", new TreeModel()
{
TreeString = alignment.PhylogeneticTree, AlignmentName = alignment.Description, ProjectId = projectId, AlignmentId = alignmentId, TreeFile = fileContent
}));
}
}
return(View());
}
public ActionResult ViewAlignment(string projectId, string alignmentId)
{
ObjectId projId = ObjectId.Parse(projectId);
SequenceProject project = db.GetItem <SequenceProject>(x => x._id == projId);
if (project != null && alignmentId != String.Empty)
{
AlignmentSequence alignment = project.Alligments.First(x => x.IdString == alignmentId);
if (alignment != null && alignment.AllignedSequences != null && alignment.AllignedSequences.Any())
{
return(View("ViewAlignmentRaw", new AlignmentModel()
{
AlignmentSequences = alignment.AllignedSequences, AlignmentName = alignment.Description, AlignmentId = alignmentId, ProjectId = projectId
}));
}
}
return(View(new HtmlString("")));
}
public bool GetSimplePhyloResult(SequenceProject project, string alignmentId)
{
IList <string> records = new List <string>();
if (project != null && project.Alligments != null)
{
AlignmentSequence alignment = project.Alligments.First(x => x._id == ObjectId.Parse(alignmentId));
string result = alignment.PhylogeneticFilename + ".tree.ph";
if (alignment != null)
{
if (!File.Exists(result))
{
result = phylologyService.GetResults(alignment.PhylogeneticGuid, alignment.PhylogeneticFilename);
if (String.IsNullOrEmpty(result))
{
return(false);
}
result = result + ".tree.ph";
}
if (!String.IsNullOrEmpty(result))
{
using (StreamReader sr = new StreamReader(result))
{
StringBuilder sb = new StringBuilder();
while (!sr.EndOfStream)
{
string hlpString = sr.ReadLine();
sb.AppendLine(hlpString);
records.Add(hlpString);
}
foreach (string s in records)
{
alignment.PhylogeneticTree += s;
}
db.UpdateItem(project);
return(true);
}
}
}
}
return(false);
}
public bool GetClustalResult(SequenceProject project, string alignmentId)
{
IList <string> records = new List <string>();
if (project != null && project.Alligments != null)
{
AlignmentSequence alignment = project.Alligments.First(x => x._id == ObjectId.Parse(alignmentId));
string result = alignment.AlignmentFilename + ".vienna.aln-vienna.vienna";
if (alignment != null)
{
if (!File.Exists(result))
{
result = clustalService.GetResults(alignment.AlignmentGuid, alignment.AlignmentFilename);
if (String.IsNullOrEmpty(result))
{
return(false);
}
result = result + ".aln-vienna.vienna";
}
if (!String.IsNullOrEmpty(result))
{
using (StreamReader sr = new StreamReader(result))
{
StringBuilder sb = new StringBuilder();
while (!sr.EndOfStream)
{
string hlpString = sr.ReadLine();
sb.AppendLine(hlpString);
records.Add(hlpString);
}
alignment.AllignedSequences = GetRecordsFromResult(project._id, records);
alignment.IsFinished = true;
db.UpdateItem(project);
return(true);
}
}
}
}
return(false);
}
/// <summary>
/// Založení sekvenčního zarovnání v programu ClustalOmega
/// </summary>
/// <param name="projectId"></param>
public void GenerateClustalAligment(ObjectId projectId, string title, string path)
{
IList <Sequence> sequences = db.GetCollection <Sequence>(x => x.ProjectId == projectId && x.Selected == true && String.IsNullOrEmpty(x.BlastAlignedSequence));
string seq = String.Empty;
foreach (Sequence s in sequences)
{
seq += s.FastaProtein;
}
clustalService.SetParams(new ServiceConnector.ClustalConnector.InputParameters()
{
sequence = seq, outfmt = "vienna"
});
var project = db.GetItem <SequenceProject>(x => x._id == projectId);
if (project != null)
{
if (project.Alligments == null)
{
project.Alligments = new List <AlignmentSequence>();
}
AlignmentSequence allign = new AlignmentSequence()
{
Created = DateTime.Now,
CreatorId = project.CreatorId,
Description = title,
IsFinished = false,
_id = ObjectId.GenerateNewId(),
Source = "Cazy"
};
allign.AlignmentGuid = clustalService.Run(title);
allign.Taxons = project.ActualTaxons;
allign.AlignmentFilename = path + allign.AlignmentGuid;
project.Alligments.Add(allign);
db.UpdateItem(project);
SelUnSelAllSequence(project.IdString, false, false);
}
}
public void GenerateTree(ObjectId projectId, string alignmentId, string path)
{
SequenceProject project = db.GetItem <SequenceProject>(x => x._id == projectId);
if (project != null)
{
AlignmentSequence aligment = project.Alligments.FirstOrDefault(x => x.IdString == alignmentId);
if (aligment != null)
{
string seq = String.Empty;
foreach (AlignRecord rec in aligment.AllignedSequences)
{
seq += ">" + rec.Organism.Replace(" ", "_") + "\n" + rec.AlignedSequence + "\n";
}
phylologyService.SetParams(new ServiceConnector.PhylogenyConnector.InputParameters()
{
sequence = seq, tree = "phylip"
});
aligment.PhylogeneticGuid = phylologyService.Run(aligment.Description);
aligment.PhylogeneticFilename = path + aligment.PhylogeneticGuid;
db.UpdateItem(project);
}
}
}
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);
}
