public static bool TryGetLikelyFormatterForFile(string filename, out SequenceFormatter formatter)
{
string firstLine = Bio.Util.FileUtils.ReadLine(filename);
Helper.CheckCondition(!string.IsNullOrEmpty(firstLine), "First line of file cannot be empty.");
return(TryGetLikelyFormatterForFirstLineOfFile(firstLine, out formatter));
}
public static bool TryGetMatrixFromSequenceFileAndPossiblyConvertDna2Aa <TRow, TCol, TVal>(string filename, TVal missing, bool keepOneValueVariables, ParallelOptions parallelOptions, out Matrix <TRow, TCol, TVal> matrix)
{
SequenceFormatter formatter;
matrix = null;
if (SequenceFormatter.TryGetLikelyFormatterForFile(filename, out formatter))
{
// only support true sequence formats.
if (formatter is SequenceMatrix)
{
return(false);
}
var seqs = formatter.Parse(filename);
if (seqs.Count == 0)
{
return(false);
}
if (seqs[0].IsDna())
{
seqs = Translate(seqs, true);
}
matrix = NamedSequencesToMatrix <TRow, TCol, TVal>(seqs, missing, keepOneValueVariables, parallelOptions);
return(true);
}
return(false);
}
public static bool TryGetMatrixFromSequenceFile <TRow, TCol, TVal>(string filename, TVal missing, bool keepOneValueVariables, ParallelOptions parallelOptions, out Matrix <TRow, TCol, TVal> matrix)
{
SequenceFormatter formatter;
matrix = null;
if (SequenceFormatter.TryGetLikelyFormatterForFile(filename, out formatter))
{
// only support true sequence formats.
if (formatter is SequenceMatrix)// || formatter is SequenceFormatterSparse)
{
return(false);
}
var seqs = formatter.Parse(filename);
if (seqs.Count == 0)
{
Console.Error.WriteLine("No sequences in sequence file of format {0}", formatter.FileFormat);
return(false);
}
matrix = NamedSequencesToMatrix <TRow, TCol, TVal>(seqs, missing, keepOneValueVariables, parallelOptions);
return(true);
//if (IsDna(seqs[0].Sequence))
//{
// seqs = NucSeqToAaSeq(seqs, true);
//}
}
Console.Error.WriteLine("No SequenceFormatter matches this file type.");
return(false);
}
public static SequenceFormatter GetInstance(SequenceFileFormat format)
{
SequenceFormatter formatter = null;
switch (format)
{
case SequenceFileFormat.Phylip:
formatter = new Phylip();
break;
case SequenceFileFormat.Fasta:
formatter = new Fasta();
break;
case SequenceFileFormat.Tab:
formatter = new Tab();
break;
//case SequenceFileFormat.Sparse:
// formatter = new SequenceFormatterSparse();
// break;
case SequenceFileFormat.Matrix:
formatter = new SequenceMatrix();
break;
default:
throw new Exception("Should never get here.");
}
formatter._formatType = format;
return(formatter);
}
public static List <NamedSequence> ParseWithMostLikelyFormatter(TextReader reader)
{
string firstLine = reader.ReadLine();
string allButFirstLine = reader.ReadToEnd();
SequenceFormatter formatter = null;
TryGetLikelyFormatterForFirstLineOfFile(firstLine, out formatter).Enforce("Could not find a suitable sequence formatter for first line " + firstLine);
TextReader newReader = new StringReader(firstLine + "\n" + allButFirstLine);
List <NamedSequence> result = formatter.Parse(newReader);
return(result);
}
public static bool TryGetLikelyFormatterForFirstLineOfFile(string firstLine, out SequenceFormatter formatter)
{
foreach (string format in Enum.GetNames(typeof(SequenceFileFormat)))
{
formatter = GetInstance(format);
if (formatter.ConformsToFileFormat(firstLine))
{
return(true);
}
}
formatter = null;
return(false);
}
public void FinalizeParse()
{
this.AddRange(SequenceFormatter.ParseWithMostLikelyFormatter(File));
}
public override bool Equals(object obj)
{
SequenceFormatter other = obj as SequenceFormatter;
return(other != null && _formatType == other._formatType);
}
