Exemplo n.º 1
0
        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.
        }
Exemplo n.º 2
0
        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);
        }
Exemplo n.º 3
0
        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();
        }
Exemplo n.º 4
0
        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.
        }
Exemplo n.º 5
0
        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);
        }