/// <summary>
///
/// </summary>
/// <param name="requestString"></param>
/// <returns></returns>
private PfamAlignInfo[] GetPfamFamilyAlignment(string requestString)
{
string jobInfoXml = "pfamjobInfo.xml";
WebClient webClient = new WebClient();
// Thread.Sleep (3000);
webClient.DownloadFile(requestString, jobInfoXml);
PfamJobInfo jobInfo = ParseJobInfoXml(jobInfoXml);
string resultXml = "pfamAlignResult.xml";
long fileSize = 0;
FileInfo resultFileInfo = null;
int numOfTrials = 0;
while (fileSize == 0 && numOfTrials <= 10)
{
numOfTrials++;
Thread.Sleep(jobInfo.estimatedTime * 10000);
webClient.DownloadFile(jobInfo.resultUrl, resultXml);
resultFileInfo = new FileInfo(resultXml);
fileSize = resultFileInfo.Length;
}
resultFileInfo = new FileInfo(resultXml);
fileSize = resultFileInfo.Length;
if (fileSize == 0)
{
throw new Exception("The alginment file is not on PFAM");
}
// string resultXml = "pfamAlignResult0.xml";
PfamAlignInfo[] pfamAlignInfos = ParsePfamResultXmlFile(resultXml);
return(pfamAlignInfos);
}
/// <summary>
///
/// </summary>
/// <param name="jobInfoXml"></param>
/// <returns></returns>
public PfamJobInfo ParseJobInfoXml(string jobInfoXml)
{
PfamJobInfo pfamJobInfo = new PfamJobInfo();
XmlDocument xmlDoc = new XmlDocument();
xmlDoc.Load(jobInfoXml);
// Create an XmlNamespaceManager for resolving namespaces.
XmlNamespaceManager nsManager = new XmlNamespaceManager(xmlDoc.NameTable);
nsManager.AddNamespace("pfam", "http://pfam.sanger.ac.uk/");
XmlNodeList jobNodeList = xmlDoc.DocumentElement.ChildNodes;
string resultUrl = "";
if (jobNodeList != null)
{
XmlNode jobNode = jobNodeList[0];
XmlNodeList jobInfoNodes = jobNode.ChildNodes;
foreach (XmlNode infoNode in jobInfoNodes)
{
if (infoNode.Name.ToLower() == "estimated_time")
{
pfamJobInfo.estimatedTime = Convert.ToInt32(infoNode.InnerText);
}
if (infoNode.Name.ToLower() == "result_url")
{
resultUrl = infoNode.InnerText.TrimEnd();
resultUrl = resultUrl.Trim("\n".ToCharArray());
pfamJobInfo.resultUrl = resultUrl;
}
}
}
return(pfamJobInfo);
}
