/// <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);
}
private static void ParseReferences(MBFTextReader mbfReader, ref Sequence sequence)
{
GenBankMetadata metadata = (GenBankMetadata)sequence.Metadata[Helper.GenBankMetadataKey];
IList <CitationReference> referenceList = metadata.References;
CitationReference reference = null;
//List<MetadataListItem<string>> referenceList = new List<MetadataListItem<string>>();
//MetadataListItem<string> reference = null;
while (mbfReader.HasLines)
{
if (mbfReader.LineHeader == "REFERENCE")
{
// add previous reference
if (reference != null)
{
referenceList.Add(reference);
}
// check for start/end e.g. (bases 1 to 118), or prose notes
Match m = Regex.Match(mbfReader.LineData,
@"^(?<number>\d+)(\s+\((?<location>.*)\))?");
if (!m.Success)
{
string message = String.Format(
CultureInfo.CurrentCulture,
Properties.Resource.ParserReferenceError,
mbfReader.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();
}
reference.Number = outValue;
reference.Location = location;
mbfReader.GoToNextLine();
}
else if (mbfReader.Line.StartsWith(" ", StringComparison.Ordinal))
{
switch (mbfReader.LineHeader)
{
// all the following are extracted the same way - possibly multiline
case "AUTHORS":
reference.Authors = ParseMultiLineData(mbfReader, " ");
break;
case "CONSRTM":
reference.Consortiums = ParseMultiLineData(mbfReader, " ");
break;
case "TITLE":
reference.Title = ParseMultiLineData(mbfReader, " ");
break;
case "JOURNAL":
reference.Journal = ParseMultiLineData(mbfReader, " ");
break;
case "REMARK":
reference.Remarks = ParseMultiLineData(mbfReader, " ");
break;
case "MEDLINE":
reference.Medline = ParseMultiLineData(mbfReader, " ");
break;
case "PUBMED":
reference.PubMed = ParseMultiLineData(mbfReader, " ");
break;
default:
string message = String.Format(
CultureInfo.CurrentCulture,
Properties.Resource.ParserInvalidReferenceField,
mbfReader.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;
}
}
}
