/// <summary>
/// Writes a set of sequences to the formatter.
/// </summary>
/// <param name="formatter">Formatter</param>
/// <param name="sequences">Sequences to write.</param>
/// <param name="fileName">Filename to write to</param>
public static void Format(this ISequenceAlignmentFormatter formatter, IEnumerable <ISequenceAlignment> sequences, string fileName)
{
using (FileStream fs = File.OpenWrite(fileName))
{
formatter.Format(fs, sequences);
}
}
/// <summary>
/// Writes a single sequence to the formatter.
/// </summary>
/// <param name="formatter">Formatter</param>
/// <param name="sequence">Sequence</param>
public static void Format(this ISequenceAlignmentFormatter formatter, ISequenceAlignment sequence)
{
var fs = ParserFormatterExtensions <ISequenceAlignmentFormatter> .GetOpenStream(formatter, true);
if (fs != null)
{
formatter.Format(fs, sequence);
}
else
{
throw new Exception("You must open a formatter before calling Write.");
}
}
/// <summary>
/// Writes a sequence to the formatter.
/// </summary>
/// <param name="formatter">Formatter</param>
/// <param name="sequence">Sequence to write.</param>
/// <param name="fileName">Filename to write to</param>
public static void Format(this ISequenceAlignmentFormatter formatter, ISequenceAlignment sequence, string fileName)
{
// In case this extensions method is in scope, we will forward
// to the BAMFormatter extension to properly handle the index
// file.
if (formatter is BAMFormatter &&
sequence is SequenceAlignmentMap)
{
BAMFormatterExtensions.Format((BAMFormatter)formatter,
(SequenceAlignmentMap)sequence, fileName);
}
else
{
using (FileStream fs = File.Create(fileName))
{
formatter.Format(fs, sequence);
}
}
}