public void Write(string filename, SequenceAlignment alignment)
{
if (filename == null)
{
return; //Error condition, output filename not specified.
}
CreateTempWorkingDirectory();
if (_tempDirectory != null)
{
WriteManifest(alignment);
WriteAlignment(alignment);
if (File.Exists(filename))
{
try
{
File.Delete(filename);
}
catch
{
DeleteTempWorkingDirectory(); //Error condition, failed to remove an existing copy of the target file
return;
}
}
Package outputfile = ZipPackage.Open(filename, FileMode.Create);
PackagePart manifestFilePart = outputfile.CreatePart(new Uri("/" + CRWSequenceAlignmentFormatTags.ManifestFileName, UriKind.Relative), System.Net.Mime.MediaTypeNames.Text.Xml, CompressionOption.Fast);
PackagePart alignmentFilePart = outputfile.CreatePart(new Uri("/" + CRWSequenceAlignmentFormatTags.AlignmentFileName, UriKind.Relative), System.Net.Mime.MediaTypeNames.Text.Plain, CompressionOption.Maximum);
Stream manifestFileStream = manifestFilePart.GetStream();
Stream alignmentFileStream = alignmentFilePart.GetStream();
using (var manifestFile = new BufferedStream(File.Open((_tempDirectory + CRWSequenceAlignmentFormatTags.ManifestFileName), FileMode.Open)))
{
byte[] buf = new byte[1024]; //We read with 1MB buffer
int count = 0;
while ((count = manifestFile.Read(buf, 0, buf.Length)) > 0)
{
manifestFileStream.Write(buf, 0, count); //We write into the zip archive
}
}
using (var alignmentFile = new BufferedStream(File.Open((_tempDirectory + CRWSequenceAlignmentFormatTags.AlignmentFileName), FileMode.Open)))
{
byte[] buf = new byte[1024]; //We read with 1MB buffer
int count = 0;
while ((count = alignmentFile.Read(buf, 0, buf.Length)) > 0)
{
alignmentFileStream.Write(buf, 0, count); //We write into the zip archive
}
}
outputfile.Close();
DeleteTempWorkingDirectory();
return;
}
else
{
DeleteTempWorkingDirectory();
return;
} //Error condition, failed to create a working directory.
}
private XElement WriteAlignmentMetadata(SequenceAlignment alignment)
{
XElement output = new XElement(CRWSequenceAlignmentFormatTags.AlignmentLabel);
output.Add(new XElement(CRWSequenceAlignmentFormatTags.AlignmentFileNameLabel, CRWSequenceAlignmentFormatTags.AlignmentFileName));
output.Add(new XElement(CRWSequenceAlignmentFormatTags.AlignmentLogicalNameLabel, alignment.LogicalName));
output.Add(new XElement(CRWSequenceAlignmentFormatTags.SequenceTypeLabel,
new XElement(CRWSequenceAlignmentFormatTags.MoleculeTypeLabel, alignment.MoleculeType),
new XElement(CRWSequenceAlignmentFormatTags.GeneTypeLabel, alignment.GeneType),
new XElement(CRWSequenceAlignmentFormatTags.GeneNameLabel, alignment.GeneName)));
return(output);
}
private void WriteAlignment(SequenceAlignment alignment)
{
FastaFormatter formatter = new FastaFormatter();
StreamWriter alnoutput = new StreamWriter(_tempDirectory + CRWSequenceAlignmentFormatTags.AlignmentFileName);
alnoutput.AutoFlush = true;
foreach (ISequence sequence in alignment.Sequences)
{
alnoutput.Write(formatter.FormatString(sequence));
}
alnoutput.Close();
}
private bool LoadAlignment()
{
Uri alignmentURI = new Uri("/" + _alignmentFileName, UriKind.Relative);
var alnfileentry = from entry in _crwFile.GetParts()
where entry.Uri.Equals(alignmentURI)
select entry;
PackagePart alnEntry = alnfileentry.First();
if (alnEntry != null)
{
//Extract the alignment file from the zip archive.
using (var reader = new BufferedStream(alnEntry.GetStream(FileMode.Open)))
{
using (var writer = new BufferedStream(File.Create(_tempDirectory + _alignmentFileName)))
{
byte[] buf = new byte[1024];
int readCount = 0;
while ((readCount = reader.Read(buf, 0, buf.Length)) > 0)
{
writer.Write(buf, 0, readCount);
}
}
}
ISequenceParser parser = SequenceParsers.FindParserByFile(_tempDirectory + _alignmentFileName);
_alignment = new SequenceAlignment(parser.Parse(_tempDirectory + _alignmentFileName));
_alignment.MoleculeType = _moleculeType;
_alignment.GeneType = _geneType;
_alignment.GeneName = _geneName;
_alignment.LogicalName = _logicalAlignmentName;
foreach (var seq in _alignment.Sequences)
{
//Workaround for MBF Framework, have to cast Sequence objects as writeable, opened feature request.
Sequence s = seq as Sequence;
if (s != null)
{
s.IsReadOnly = false;
}
}
return(true);
}
else
{
return(false);
} //Error condition, missing alignment file.
}
private void WriteManifest(SequenceAlignment alignment)
{
XElement manifest = new XElement(CRWSequenceAlignmentFormatTags.ManifestLabel);
XElement alnMetadata = WriteAlignmentMetadata(alignment);
manifest.Add(WriteAlignmentMetadata(alignment));
foreach (var sequence in alignment.Sequences)
{
XElement seqmetdata = WriteSequenceMetadata(sequence);
if (seqmetdata != null)
{
manifest.Add(seqmetdata);
}
}
manifest.Save(_tempDirectory + CRWSequenceAlignmentFormatTags.ManifestFileName);
}
