public string GetNextTitle()
{
string result = string.Empty;
long position = StreamUtils.GetCharpos(this.reader);
try
{
string line;
while ((line = this.reader.ReadLine()) != null)
{
if (line.StartsWith(MascotGenericFormatConstants.TITLE_TAG))
{
result = line.Substring(line.IndexOf('=') + 1);
break;
}
}
}
finally
{
this.reader.SetCharpos(position);
}
return(result);
}
public void TestGetCharpos()
{
using (StreamReader sr = new StreamReader(@TestContext.CurrentContext.TestDirectory + "/../../../data//20030428_4_29L_15.outs"))
{
Assert.AreEqual(0, StreamUtils.GetCharpos(sr));
char[] buffer = new char[100];
sr.Read(buffer, 0, 90);
Assert.AreEqual(90, StreamUtils.GetCharpos(sr));
}
}
public override void Open(string fileName)
{
Close();
sr = new StreamReader(fileName);
this.FileName = fileName;
iter = new MascotGenericFormatIterator <Peak>(sr);
string line;
int scan = 1;
long position = 0;
while ((line = sr.ReadLine()) != null)
{
if (line.StartsWith(MascotGenericFormatConstants.MSMS_SCAN_TAG))
{
Match m = scanRegex.Match(line);
scan = Convert.ToInt32(m.Groups[1].Value);
positions[scan] = new PositionClass()
{
Position = position
};
}
else if (line.StartsWith(MascotGenericFormatConstants.RETENTION_TIME_TAG))
{
positions[scan].RetentionTimeInSecond = MyConvert.ToDouble(line.Substring(MascotGenericFormatConstants.RETENTION_TIME_TAG.Length + 1));
}
else if (line.StartsWith(MascotGenericFormatConstants.END_PEAK_LIST_TAG))
{
position = StreamUtils.GetCharpos(sr);
}
}
List <int> scans = new List <int>(positions.Keys);
if (scans.Count > 0)
{
firstScan = scans[0];
lastScan = scans[scans.Count - 1];
}
else
{
firstScan = 0;
lastScan = -1;
}
}
private void ReadFile(List <Sequence> sw, string filename, StringBuilder sb, List <int> seqLengths)
{
using (StreamReader sr = new StreamReader(filename))
{
Progress.SetRange(0, sr.BaseStream.Length);
Sequence seq;
while ((seq = ff.ReadSequence(sr)) != null)
{
Progress.SetPosition(StreamUtils.GetCharpos(sr));
if (combined)
{
sw.Add(seq);
}
sb.Append(seq.SeqString);
seqLengths.Add(seq.SeqString.Length);
}
}
}
private void ProcessFile(ref int index, StreamWriter sw, string fastaFile, bool isContaminant)
{
FastaFormat ff = new FastaFormat();
using (StreamReader sr = new StreamReader(fastaFile))
{
Progress.SetRange(0, sr.BaseStream.Length);
Sequence seq;
while ((seq = ff.ReadSequence(sr)) != null)
{
Progress.SetPosition(StreamUtils.GetCharpos(sr));
if (isContaminant)
{
if (!seq.Reference.StartsWith("CON_"))
{
seq.Reference = "CON_" + seq.Reference;
}
}
if (combined)
{
ff.WriteSequence(sw, seq);
}
if (pseudoAminoacid)
{
builder.Build(seq);
}
index++;
Sequence reversedSeq = SequenceUtils.GetReversedSequence(seq.SeqString, index);
ff.WriteSequence(sw, reversedSeq);
}
}
}
public override IEnumerable <string> Process(string fileName)
{
FastaFormat ff = new FastaFormat();
var result = Path.ChangeExtension(fileName, ".dM.fasta");
using (StreamReader sr = new StreamReader(fileName))
using (StreamWriter sw = new StreamWriter(result))
{
Sequence seq;
Progress.SetRange(1, sr.BaseStream.Length);
while ((seq = ff.ReadSequence(sr)) != null)
{
Progress.SetPosition(StreamUtils.GetCharpos(sr));
if (seq.SeqString.StartsWith("M"))
{
seq.SeqString = seq.SeqString.Substring(1);
seq.Reference = seq.Name + " N-terminal-M-Removed " + seq.Description;
}
ff.WriteSequence(sw, seq);
}
}
return(new string[] { result });
}
public List <PeakList <Peak> > ReadFromFile(string fileName)
{
List <PeakList <Peak> > result = new List <PeakList <Peak> >();
using (StreamReader sr = new StreamReader(fileName))
{
Progress.SetRange(0, sr.BaseStream.Length);
string line;
Dictionary <string, string> headers = new Dictionary <string, string>();
List <string> peaks = new List <string>();
while ((line = sr.ReadLine()) != null)
{
if (line.Trim().Equals("peaklist start"))
{
Progress.SetPosition(StreamUtils.GetCharpos(sr));
headers.Clear();
peaks.Clear();
bool inHeader = true;
while ((line = sr.ReadLine()) != null)
{
var tline = line.Trim();
if (tline.Equals("peaklist end"))
{
break;
}
if (tline.Length == 0)
{
continue;
}
if (!inHeader)
{
peaks.Add(tline);
}
else if (Char.IsLetter(tline[0]))
{
var pos = tline.IndexOf('=');
var key = tline.Substring(0, pos);
var value = tline.Substring(pos + 1);
headers[key] = value;
}
else
{
inHeader = false;
peaks.Add(tline);
}
}
if (headers.Count > 0 && peaks.Count > 0)
{
PeakList <Peak> pkl = new PeakList <Peak>();
pkl.PrecursorMZ = MyConvert.ToDouble(headers["mz"]);
pkl.PrecursorCharge = Convert.ToInt32(headers["charge"]);
pkl.MsLevel = 2;
pkl.ScanMode = headers["fragmentation"];
SequestFilename sf = parser.GetValue(headers["header"]);
pkl.ScanTimes.Add(new ScanTime(sf.FirstScan, 0.0));
pkl.Experimental = sf.Experimental;
result.Add(pkl);
foreach (var l in peaks)
{
var p = l.Split('\t');
if (p.Length > 1)
{
pkl.Add(new Peak(MyConvert.ToDouble(p[0]), MyConvert.ToDouble(p[1])));
}
}
}
}
}
}
return(result);
}
