Example #1
0
        /// <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);
        }
Example #2
0
        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);
            }
        }
Example #3
0
 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);
     }
 }
Example #4
0
        /// <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;
        }
Example #5
0
        /// <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);
        }