/// <summary>
/// Parses the sequences from the open file.
/// </summary>
/// <param name="parser">Sequence Parser</param>
/// <returns>Set of parsed sequences.</returns>
public static IEnumerable <WiggleAnnotation> Parse(this WiggleParser parser)
{
var fs = ParserFormatterExtensions <WiggleParser> .GetOpenStream(parser, false);
if (fs != null)
{
foreach (var item in parser.Parse(fs))
{
yield return(item);
}
}
}
/// <summary>
/// Writes a single sequence to the formatter.
/// </summary>
/// <param name="formatter">Formatter</param>
/// <param name="annotation">Wiggle Annotation</param>
public static void Format(this WiggleFormatter formatter, WiggleAnnotation annotation)
{
var fs = ParserFormatterExtensions <WiggleFormatter> .GetOpenStream(formatter, true);
if (fs != null)
{
formatter.Format(fs, annotation);
}
else
{
throw new Exception("You must open a formatter before calling Write.");
}
}
/// <summary>
/// Write out a set of contigs to the given file.
/// </summary>
/// <param name="formatter">Formatter</param>
/// <param name="contig">Contig to write</param>
public static void Format(this XsvContigFormatter formatter, Contig contig)
{
if (formatter == null)
{
throw new ArgumentNullException("formatter");
}
if (contig == null)
{
throw new ArgumentNullException("contig");
}
var fs = ParserFormatterExtensions <ISequenceFormatter> .GetOpenStream(formatter, true);
if (fs != null)
{
formatter.Write(fs, contig);
}
else
{
throw new Exception("You must open a formatter before calling Write.");
}
}
/// <summary>
/// Closes the formatter.
/// </summary>
/// <param name="formatter">Formatter.</param>
public static void Close(this WiggleFormatter formatter)
{
ParserFormatterExtensions <WiggleFormatter> .Close(formatter);
}
/// <summary>
/// Open a file and parse it with the sequence formatter.
/// </summary>
/// <param name="formatter">Formatter</param>
/// <param name="filename">Filename</param>
/// <returns>IDisposable to close stream.</returns>
public static IDisposable Open(this WiggleFormatter formatter, string filename)
{
return(ParserFormatterExtensions <WiggleFormatter>
.Open(formatter, filename));
}