/// <summary>
/// Returns list of citation references in this metadata which are referred in the specified feature.
/// </summary>
/// <param name="item">Feature Item.</param>
public List <CitationReference> GetCitationsReferredInFeature(FeatureItem item)
{
List <CitationReference> list = new List <CitationReference>();
if (item == null || !item.Qualifiers.ContainsKey(StandardQualifierNames.Citation))
{
return(list);
}
foreach (string str in item.Qualifiers[StandardQualifierNames.Citation])
{
if (!string.IsNullOrEmpty(str))
{
string strCitationNumber = str.Replace("[", string.Empty).Replace("]", string.Empty);
int citationNumber = -1;
if (int.TryParse(strCitationNumber, out citationNumber))
{
CitationReference citation = References.FirstOrDefault(F => F.Number == citationNumber);
if (citation != null && !list.Contains(citation))
{
list.Add(citation);
}
}
}
}
return(list);
}
/// <summary>
/// Parses the GenBank Reference information from the GenBank file.
/// </summary>
/// <param name="line">parse line</param>
/// <param name="sequence">The sequence.</param>
/// <param name="stream">The stream reader.</param>
/// <returns>The parsed line.</returns>
private string ParseReferences(string line, ref Sequence sequence, StreamReader stream)
{
GenBankMetadata metadata = (GenBankMetadata)sequence.Metadata[Helper.GenBankMetadataKey];
IList <CitationReference> referenceList = metadata.References;
CitationReference reference = null;
while (line != null)
{
string lineHeader = GetLineHeader(line, DataIndent);
if (lineHeader == "REFERENCE")
{
// add previous reference
if (reference != null)
{
referenceList.Add(reference);
}
// check for start/end e.g. (bases 1 to 118), or prose notes
string lineData = GetLineData(line, DataIndent);
Match m = Regex.Match(lineData, @"^(?<number>\d+)(\s+\((?<location>.*)\))?");
if (!m.Success)
{
string message = String.Format(
CultureInfo.CurrentCulture,
Properties.Resource.ParserReferenceError,
lineData);
Trace.Report(message);
throw new InvalidDataException(message);
}
// create new reference
string number = m.Groups["number"].Value;
string location = m.Groups["location"].Value;
reference = new CitationReference();
int outValue;
if (!int.TryParse(number, out outValue))
{
throw new InvalidOperationException(string.Format(CultureInfo.CurrentCulture, Properties.Resource.InvalidRefNumber, number));
}
reference.Number = outValue;
reference.Location = location;
line = GoToNextLine(line, stream);
}
else if (line.StartsWith(" ", StringComparison.Ordinal))
{
switch (lineHeader)
{
// all the following are extracted the same way - possibly multiline
case "AUTHORS":
reference.Authors = ParseMultiLineData(ref line, " ", DataIndent, stream);
break;
case "CONSRTM":
reference.Consortiums = ParseMultiLineData(ref line, " ", DataIndent, stream);
break;
case "TITLE":
reference.Title = ParseMultiLineData(ref line, " ", DataIndent, stream);
break;
case "JOURNAL":
reference.Journal = ParseMultiLineData(ref line, " ", DataIndent, stream);
break;
case "REMARK":
reference.Remarks = ParseMultiLineData(ref line, " ", DataIndent, stream);
break;
case "MEDLINE":
reference.Medline = ParseMultiLineData(ref line, " ", DataIndent, stream);
break;
case "PUBMED":
reference.PubMed = ParseMultiLineData(ref line, " ", DataIndent, stream);
break;
default:
string message = String.Format(
CultureInfo.CurrentCulture,
Properties.Resource.ParserInvalidReferenceField,
lineHeader);
Trace.Report(message);
throw new InvalidDataException(message);
}
}
else
{
// add last reference
if (reference != null)
{
referenceList.Add(reference);
}
// don't go to next line; current line still needs to be processed
break;
}
}
return(line);
}
/// <summary>
/// Parses reference info.
/// </summary>
/// <param name="metadata">Metadata object</param>
/// <param name="cellRange">Range of cells</param>
/// <param name="rowIndex">Current index of row</param>
/// <returns>Index of row</returns>
private static int ParseReference(GenBankMetadata metadata, object[,] cellRange, int rowIndex)
{
string Key;
string subKey;
string value;
string message;
value = cellRange[rowIndex, ValueColumnIndex] != null ? cellRange[rowIndex, ValueColumnIndex].ToString() : string.Empty;
rowIndex++;
CitationReference reference = new CitationReference();
if (!string.IsNullOrWhiteSpace(value))
{
// check for start/end e.g. (bases 1 to 118), or prose notes
Match m = Regex.Match(value,
@"^(?<number>\d+)(\s+\((?<location>.*)\))?");
if (m.Success)
{
// create new reference
string number = m.Groups["number"].Value;
string location = m.Groups["location"].Value;
int outValue;
if (!int.TryParse(number, out outValue))
{
message = String.Format(
CultureInfo.InvariantCulture,
Resources.UnrecognizedGenBankMetadataFormat,
REFERENCE);
throw new FormatException(message);
}
reference.Number = outValue;
reference.Location = location;
}
}
while (rowIndex < cellRange.GetLength(0))
{
if (3 > cellRange.GetLength(1))
{
message = String.Format(
CultureInfo.InvariantCulture,
Resources.UnrecognizedGenBankMetadataFormat,
REFERENCE);
throw new FormatException(message);
}
if (null != cellRange[rowIndex, KeyColumnIndex])
{
Key = cellRange[rowIndex, KeyColumnIndex].ToString();
if (!string.IsNullOrWhiteSpace(Key))
{
break;
}
}
if (null == cellRange[rowIndex, SubKeyColumnIndex] || string.IsNullOrWhiteSpace(cellRange[rowIndex, SubKeyColumnIndex].ToString()))
{
message = String.Format(
CultureInfo.InvariantCulture,
Resources.UnrecognizedGenBankMetadataFormat,
REFERENCE);
throw new FormatException(message);
}
subKey = cellRange[rowIndex, SubKeyColumnIndex].ToString().ToUpperInvariant();
value = cellRange[rowIndex, ValueColumnIndex] != null ? cellRange[rowIndex, ValueColumnIndex].ToString() : string.Empty;
if (string.IsNullOrWhiteSpace(value))
{
continue;
}
switch (subKey)
{
case REFERENCE_AUTHORS:
reference.Authors = value;
break;
case REFERENCE_CONSORTIUMS:
reference.Consortiums = value;
break;
case REFERENCE_JOURNAL:
reference.Journal = value;
break;
case REFERENCE_MEDLINE:
reference.Medline = value;
break;
case REFERENCE_PUBMED:
reference.PubMed = value;
break;
case REFERENCE_REMARK:
reference.Remarks = value;
break;
case REFERENCE_TITLE:
reference.Title = value;
break;
}
rowIndex++;
}
metadata.References.Add(reference);
return rowIndex;
}
/// <summary>
/// Parses the GenBank Reference information from the GenBank file.
/// </summary>
/// <param name="line">parse line</param>
/// <param name="sequence">The sequence.</param>
/// <param name="stream">The stream reader.</param>
/// <returns>The parsed line.</returns>
private string ParseReferences(string line, ref Sequence sequence, StreamReader stream)
{
GenBankMetadata metadata = (GenBankMetadata)sequence.Metadata[Helper.GenBankMetadataKey];
IList<CitationReference> referenceList = metadata.References;
CitationReference reference = null;
while (line != null)
{
string lineHeader = GetLineHeader(line, DataIndent);
if (lineHeader == "REFERENCE")
{
// add previous reference
if (reference != null)
{
referenceList.Add(reference);
}
// check for start/end e.g. (bases 1 to 118), or prose notes
string lineData = GetLineData(line, DataIndent);
Match m = Regex.Match(lineData, @"^(?<number>\d+)(\s+\((?<location>.*)\))?");
if (!m.Success)
{
string message = String.Format(
CultureInfo.CurrentCulture,
Properties.Resource.ParserReferenceError,
lineData);
Trace.Report(message);
throw new InvalidDataException(message);
}
// create new reference
string number = m.Groups["number"].Value;
string location = m.Groups["location"].Value;
reference = new CitationReference();
int outValue;
if (!int.TryParse(number, out outValue))
throw new InvalidOperationException(string.Format(CultureInfo.CurrentCulture, Properties.Resource.InvalidRefNumber, number));
reference.Number = outValue;
reference.Location = location;
line = GoToNextLine(line, stream);
}
else if (line.StartsWith(" ", StringComparison.Ordinal))
{
switch (lineHeader)
{
// all the following are extracted the same way - possibly multiline
case "AUTHORS":
reference.Authors = ParseMultiLineData(ref line, " ", DataIndent, stream);
break;
case "CONSRTM":
reference.Consortiums = ParseMultiLineData(ref line, " ", DataIndent, stream);
break;
case "TITLE":
reference.Title = ParseMultiLineData(ref line, " ", DataIndent, stream);
break;
case "JOURNAL":
reference.Journal = ParseMultiLineData(ref line, " ", DataIndent, stream);
break;
case "REMARK":
reference.Remarks = ParseMultiLineData(ref line, " ", DataIndent, stream);
break;
case "MEDLINE":
reference.Medline = ParseMultiLineData(ref line, " ", DataIndent, stream);
break;
case "PUBMED":
reference.PubMed = ParseMultiLineData(ref line, " ", DataIndent, stream);
break;
default:
string message = String.Format(
CultureInfo.CurrentCulture,
Properties.Resource.ParserInvalidReferenceField,
lineHeader);
Trace.Report(message);
throw new InvalidDataException(message);
}
}
else
{
// add last reference
if (reference != null)
{
referenceList.Add(reference);
}
// don't go to next line; current line still needs to be processed
break;
}
}
return line;
}
