/// <summary>
/// Get the alignment results
/// </summary>
/// <param name="serviceParameters">job id, control id</param>
/// <returns>alignment</returns>
public ClustalWResult FetchResultsAsync(ServiceParameters serviceParameters)
{
string output = _baseClient.GetOutputAsString(serviceParameters.JobId, serviceParameters.Parameters[CONTROLID].ToString());
IList <ISequenceAlignment> alignments = _ClustalWParser.Parse(new StringReader(output));
return(new ClustalWResult(alignments[0]));
}
/// <summary>
/// Get the alignment results
/// </summary>
/// <param name="serviceParameters">job id, control id</param>
/// <returns>alignment</returns>
public ClustalWResult FetchResultsAsync(ServiceParameters serviceParameters)
{
IList <ISequenceAlignment> alignments = null;
if (null == serviceParameters)
{
throw new ArgumentNullException("Parameters");
}
string output = _baseClient.GetOutputAsString(serviceParameters.JobId, serviceParameters.Parameters[CONTROLID].ToString());
using (StringReader reader = new StringReader(output))
{
alignments = _ClustalWParser.Parse(reader);
}
return(new ClustalWResult(alignments[0]));
}
/// <summary>
/// Parses the sequences from the given filename.
/// </summary>
/// <param name="parser">Sequence Parser</param>
/// <param name="fileName">Filename to open/close</param>
/// <returns>Set of parsed sequences.</returns>
public static IEnumerable <ISequenceAlignment> Parse(this ISequenceAlignmentParser parser, string fileName)
{
using (FileStream fs = File.OpenRead(fileName))
{
foreach (var item in parser.Parse(fs))
{
yield return(item);
}
}
}
/// <summary>
/// Parses the sequences from the open file.
/// </summary>
/// <param name="parser">Sequence Parser</param>
/// <returns>Set of parsed sequences.</returns>
public static IEnumerable <ISequenceAlignment> Parse(this ISequenceAlignmentParser parser)
{
var fs = ParserFormatterExtensions <ISequenceAlignmentParser> .GetOpenStream(parser, false);
if (fs == null)
{
throw new Exception("You must open a parser before calling Parse.");
}
return(parser.Parse(fs));
}
public void ValidateSamParserWithDVIscFile()
{
// Gets the expected sequence from the Xml
string filePath = _utilityObj._xmlUtil.GetTextValue(
Constants.SAMFileWithRefNode, Constants.FilePathNode);
ISequenceAlignmentParser iSeqParser =
SequenceAlignmentParsers.FindParserByFile(filePath);
if (null != iSeqParser)
{
IVirtualSequenceAlignmentParser vParserObj =
iSeqParser as IVirtualSequenceAlignmentParser;
if (null != vParserObj)
{
vParserObj.EnforceDataVirtualization = true;
}
else
{
Assert.Fail("SAM P1 Cases : Could not find the SAM Parser Object.");
}
string iscFilePath =
string.Concat(filePath, ".isc");
iSeqParser.Parse(filePath);
if (File.Exists(iscFilePath))
{
Console.WriteLine(
"SAM P1 Cases : DV enabled as expected and isc file created successfully.");
ApplicationLog.WriteLine(
"SAM P1 Cases : DV enabled as expected and isc file created successfully.");
}
else
{
Assert.Fail("SAM P1 Cases : DV not enabled as expected.");
}
}
else
{
Assert.Fail("SAM P1 Cases : Could not find the SAM file");
}
}
