/// <summary>
/// This method expects a single XML document and returns one BlastResult.
/// </summary>
/// <param name="doc">A Stringbuilder containing the XML document.</param>
/// <returns>The BlastResult.</returns>
private static BlastResult ParseXML(StringBuilder doc)
{
BlastResult result = new BlastResult();
try
{
XmlReaderSettings settings = new XmlReaderSettings();
settings.DtdProcessing = DtdProcessing.Ignore; // don't error when encountering a DTD spec
// Setting the XmlResolver to null causes the DTDs specified in the XML
// header to be ignored.
settings.XmlResolver = null;
StringReader sr = null;
try
{
sr = new StringReader(doc.ToString());
using (XmlReader r = XmlReader.Create(sr, settings))
{
string curElement = string.Empty;
BlastSearchRecord curRecord = new BlastSearchRecord();
Hit curHit = null;
Hsp curHsp = null;
BlastStatistics curStatistics = null;
BlastXmlMetadata curMetadata = null;
while (r.Read())
{
switch (r.NodeType)
{
case XmlNodeType.Element:
curElement = r.Name;
// ApplicationLog.WriteLine("element: " + curElement);
if (curElement == "Hit")
{
curHit = new Hit();
}
else if (curElement == "Hsp")
{
curHsp = new Hsp();
}
else if (curElement == "Statistics")
{
curStatistics = new BlastStatistics();
}
else if (curElement == "BlastOutput")
{
curMetadata = new BlastXmlMetadata();
}
break;
case XmlNodeType.Text:
// ApplicationLog.WriteLine("text: " + r.Value);
if (curElement.StartsWith("BlastOutput_", StringComparison.OrdinalIgnoreCase))
{
DoBlastOutput(curElement, r.Value, curMetadata);
}
else if (curElement.StartsWith("Parameters_", StringComparison.OrdinalIgnoreCase))
{
DoParameters(curElement, r.Value, curMetadata);
}
else if (curElement.StartsWith("Iteration_", StringComparison.OrdinalIgnoreCase))
{
DoIteration(curElement, r.Value, curRecord);
}
else if (curElement.StartsWith("Statistics_", StringComparison.OrdinalIgnoreCase))
{
DoStatistics(curElement, r.Value, curStatistics);
}
else if (curElement.StartsWith("Hit_", StringComparison.OrdinalIgnoreCase))
{
DoHit(curElement, r.Value, curHit);
}
else if (curElement.StartsWith("Hsp_", StringComparison.OrdinalIgnoreCase))
{
DoHsp(curElement, r.Value, curHsp);
}
else
{
ApplicationLog.WriteLine("BlastXMLParser Unhandled: curElement '{0}'", curElement);
}
break;
case XmlNodeType.XmlDeclaration:
// ApplicationLog.WriteLine("declaration: {0}, {1}", r.Name, r.Value);
break;
case XmlNodeType.ProcessingInstruction:
// ApplicationLog.WriteLine("instruction: {0}, {1}", r.Name, r.Value);
break;
case XmlNodeType.Comment:
// ApplicationLog.WriteLine("comment: " + r.Value);
break;
case XmlNodeType.EndElement:
// ApplicationLog.WriteLine("endelement: " + r.Name);
if (r.Name == "Iteration")
{
result.Records.Add(curRecord);
curRecord = new BlastSearchRecord();
}
else if (r.Name == "Statistics")
{
curRecord.Statistics = curStatistics;
}
else if (r.Name == "Hit")
{
curRecord.Hits.Add(curHit);
}
else if (r.Name == "Hsp")
{
curHit.Hsps.Add(curHsp);
}
else if (r.Name == "BlastOutput")
{
result.Metadata = curMetadata;
}
break;
}
}
}
}
finally
{
if (sr != null)
{
sr.Dispose();
}
}
}
catch (Exception e)
{
ApplicationLog.Exception(e);
throw;
}
return(result);
}
private static void DoHsp(string element, string value, Hsp hsp)
{
switch (element)
{
case "Hsp_num":
// ignore
break;
case "Hsp_bit-score":
hsp.BitScore = double.Parse(value, CultureInfo.InvariantCulture);
break;
case "Hsp_score":
hsp.Score = double.Parse(value, CultureInfo.InvariantCulture);
break;
case "Hsp_evalue":
hsp.EValue = double.Parse(value, CultureInfo.InvariantCulture);
break;
case "Hsp_query-from":
hsp.QueryStart = long.Parse(value, CultureInfo.InvariantCulture);
break;
case "Hsp_query-to":
hsp.QueryEnd = long.Parse(value, CultureInfo.InvariantCulture);
break;
case "Hsp_hit-from":
hsp.HitStart = long.Parse(value, CultureInfo.InvariantCulture);
break;
case "Hsp_hit-to":
hsp.HitEnd = long.Parse(value, CultureInfo.InvariantCulture);
break;
case "Hsp_query-frame":
hsp.QueryFrame = long.Parse(value, CultureInfo.InvariantCulture);
break;
case "Hsp_hit-frame":
hsp.HitFrame = long.Parse(value, CultureInfo.InvariantCulture);
break;
case "Hsp_identity":
hsp.IdentitiesCount = long.Parse(value, CultureInfo.InvariantCulture);
break;
case "Hsp_positive":
hsp.PositivesCount = long.Parse(value, CultureInfo.InvariantCulture);
break;
case "Hsp_align-len":
hsp.AlignmentLength = long.Parse(value, CultureInfo.InvariantCulture);
break;
case "Hsp_density":
hsp.Density = int.Parse(value, CultureInfo.InvariantCulture);
break;
case "Hsp_qseq":
hsp.QuerySequence = value;
break;
case "Hsp_hseq":
hsp.HitSequence = value;
break;
case "Hsp_midline":
hsp.Midline = value;
break;
case "Hsp_pattern-from":
hsp.PatternFrom = int.Parse(value, CultureInfo.InvariantCulture);
break;
case "Hsp_pattern-to":
hsp.PatternTo = int.Parse(value, CultureInfo.InvariantCulture);
break;
case "Hsp_gaps":
hsp.Gaps = int.Parse(value, CultureInfo.InvariantCulture);
break;
default:
string message = String.Format(
CultureInfo.CurrentCulture,
Properties.Resource.UnknownElement,
"DoHsp",
element);
Trace.Report(message);
throw new FormatException(message);
}
}
private static void DoHsp(string element, string value, Hsp hsp)
{
switch (element)
{
case "Hsp_num":
// ignore
break;
case "Hsp_bit-score":
hsp.BitScore = double.Parse(value, CultureInfo.InvariantCulture);
break;
case "Hsp_score":
hsp.Score = double.Parse(value, CultureInfo.InvariantCulture);
break;
case "Hsp_evalue":
hsp.EValue = double.Parse(value, CultureInfo.InvariantCulture);
break;
case "Hsp_query-from":
hsp.QueryStart = long.Parse(value, CultureInfo.InvariantCulture);
break;
case "Hsp_query-to":
hsp.QueryEnd = long.Parse(value, CultureInfo.InvariantCulture);
break;
case "Hsp_hit-from":
hsp.HitStart = long.Parse(value, CultureInfo.InvariantCulture);
break;
case "Hsp_hit-to":
hsp.HitEnd = long.Parse(value, CultureInfo.InvariantCulture);
break;
case "Hsp_query-frame":
hsp.QueryFrame = long.Parse(value, CultureInfo.InvariantCulture);
break;
case "Hsp_hit-frame":
hsp.HitFrame = long.Parse(value, CultureInfo.InvariantCulture);
break;
case "Hsp_identity":
hsp.IdentitiesCount = long.Parse(value, CultureInfo.InvariantCulture);
break;
case "Hsp_positive":
hsp.PositivesCount = long.Parse(value, CultureInfo.InvariantCulture);
break;
case "Hsp_align-len":
hsp.AlignmentLength = long.Parse(value, CultureInfo.InvariantCulture);
break;
case "Hsp_density":
hsp.Density = int.Parse(value, CultureInfo.InvariantCulture);
break;
case "Hsp_qseq":
hsp.QuerySequence = value;
break;
case "Hsp_hseq":
hsp.HitSequence = value;
break;
case "Hsp_midline":
hsp.Midline = value;
break;
case "Hsp_pattern-from":
hsp.PatternFrom = int.Parse(value, CultureInfo.InvariantCulture);
break;
case "Hsp_pattern-to":
hsp.PatternTo = int.Parse(value, CultureInfo.InvariantCulture);
break;
case "Hsp_gaps":
hsp.Gaps = int.Parse(value, CultureInfo.InvariantCulture);
break;
default:
string message = String.Format(
CultureInfo.CurrentCulture,
Properties.Resources.UnknownElement,
"DoHsp",
element);
throw new FormatException(message);
}
}
/// <summary>
/// This method expects a single XML document and returns one BlastResult.
/// </summary>
/// <param name="doc">A Stringbuilder containing the XML document.</param>
/// <returns>The BlastResult.</returns>
private static BlastResult ParseXML(StringBuilder doc)
{
BlastResult result = new BlastResult();
try
{
var settings = new XmlReaderSettings { DtdProcessing = DtdProcessing.Ignore };
StringReader sr = null;
try
{
sr = new StringReader(doc.ToString());
using (XmlReader r = XmlReader.Create(sr, settings))
{
string curElement = string.Empty;
BlastSearchRecord curRecord = new BlastSearchRecord();
Hit curHit = null;
Hsp curHsp = null;
BlastStatistics curStatistics = null;
BlastXmlMetadata curMetadata = null;
while (r.Read())
{
switch (r.NodeType)
{
case XmlNodeType.Element:
curElement = r.Name;
switch (curElement)
{
case "Hit":
curHit = new Hit();
break;
case "Hsp":
curHsp = new Hsp();
break;
case "Statistics":
curStatistics = new BlastStatistics();
break;
case "BlastOutput":
curMetadata = new BlastXmlMetadata();
break;
}
break;
case XmlNodeType.Text:
if (curElement.StartsWith("BlastOutput_", StringComparison.OrdinalIgnoreCase))
{
DoBlastOutput(curElement, r.Value, curMetadata);
}
else if (curElement.StartsWith("Parameters_", StringComparison.OrdinalIgnoreCase))
{
DoParameters(curElement, r.Value, curMetadata);
}
else if (curElement.StartsWith("Iteration_", StringComparison.OrdinalIgnoreCase))
{
DoIteration(curElement, r.Value, curRecord);
}
else if (curElement.StartsWith("Statistics_", StringComparison.OrdinalIgnoreCase))
{
DoStatistics(curElement, r.Value, curStatistics);
}
else if (curElement.StartsWith("Hit_", StringComparison.OrdinalIgnoreCase))
{
DoHit(curElement, r.Value, curHit);
}
else if (curElement.StartsWith("Hsp_", StringComparison.OrdinalIgnoreCase))
{
DoHsp(curElement, r.Value, curHsp);
}
break;
case XmlNodeType.XmlDeclaration:
case XmlNodeType.ProcessingInstruction:
case XmlNodeType.Comment:
break;
case XmlNodeType.EndElement:
if (r.Name == "Iteration") {
result.Records.Add(curRecord);
curRecord = new BlastSearchRecord();
}
else if (r.Name == "Statistics")
curRecord.Statistics = curStatistics;
else if (r.Name == "Hit")
curRecord.Hits.Add(curHit);
else if (r.Name == "Hsp")
curHit.Hsps.Add(curHsp);
else if (r.Name == "BlastOutput")
result.Metadata = curMetadata;
break;
}
}
}
}
finally
{
if (sr != null)
sr.Dispose();
}
}
catch (Exception e)
{
ApplicationLog.Exception(e);
throw;
}
return result;
}
/// <summary>
/// This method expects a single XML document and returns one BlastResult.
/// </summary>
/// <param name="doc">A Stringbuilder containing the XML document.</param>
/// <returns>The BlastResult.</returns>
private static BlastResult ParseXML(StringBuilder doc)
{
BlastResult result = new BlastResult();
try
{
var settings = new XmlReaderSettings {
DtdProcessing = DtdProcessing.Ignore
};
StringReader sr = null;
try
{
sr = new StringReader(doc.ToString());
using (XmlReader r = XmlReader.Create(sr, settings))
{
string curElement = string.Empty;
BlastSearchRecord curRecord = new BlastSearchRecord();
Hit curHit = null;
Hsp curHsp = null;
BlastStatistics curStatistics = null;
BlastXmlMetadata curMetadata = null;
while (r.Read())
{
switch (r.NodeType)
{
case XmlNodeType.Element:
curElement = r.Name;
switch (curElement)
{
case "Hit":
curHit = new Hit();
break;
case "Hsp":
curHsp = new Hsp();
break;
case "Statistics":
curStatistics = new BlastStatistics();
break;
case "BlastOutput":
curMetadata = new BlastXmlMetadata();
break;
}
break;
case XmlNodeType.Text:
if (curElement.StartsWith("BlastOutput_", StringComparison.OrdinalIgnoreCase))
{
DoBlastOutput(curElement, r.Value, curMetadata);
}
else if (curElement.StartsWith("Parameters_", StringComparison.OrdinalIgnoreCase))
{
DoParameters(curElement, r.Value, curMetadata);
}
else if (curElement.StartsWith("Iteration_", StringComparison.OrdinalIgnoreCase))
{
DoIteration(curElement, r.Value, curRecord);
}
else if (curElement.StartsWith("Statistics_", StringComparison.OrdinalIgnoreCase))
{
DoStatistics(curElement, r.Value, curStatistics);
}
else if (curElement.StartsWith("Hit_", StringComparison.OrdinalIgnoreCase))
{
DoHit(curElement, r.Value, curHit);
}
else if (curElement.StartsWith("Hsp_", StringComparison.OrdinalIgnoreCase))
{
DoHsp(curElement, r.Value, curHsp);
}
break;
case XmlNodeType.XmlDeclaration:
case XmlNodeType.ProcessingInstruction:
case XmlNodeType.Comment:
break;
case XmlNodeType.EndElement:
if (r.Name == "Iteration")
{
result.Records.Add(curRecord);
curRecord = new BlastSearchRecord();
}
else if (r.Name == "Statistics")
{
curRecord.Statistics = curStatistics;
}
else if (r.Name == "Hit")
{
curRecord.Hits.Add(curHit);
}
else if (r.Name == "Hsp")
{
curHit.Hsps.Add(curHsp);
}
else if (r.Name == "BlastOutput")
{
result.Metadata = curMetadata;
}
break;
}
}
}
}
finally
{
if (sr != null)
{
sr.Dispose();
}
}
}
catch (Exception e)
{
ApplicationLog.Exception(e);
throw;
}
return(result);
}