/// <summary>
/// Returns standard feature class instance, if the key in the specified feature item is found
/// in the map; otherwise returns the specified feature item itself.
/// For example:
/// If the specified feature item has the key "Gene" then this method returns instance of the Gene class
/// with data copied from the specified item.
/// </summary>
/// <param name="item">Feature item instance to which the standard feature item instance is needed.</param>
/// <returns>If found returns appropriate class instance for the specified feature item, otherwise returns
/// the specified item itself.</returns>
public static FeatureItem GetStandardFeatureItem(FeatureItem item)
{
Type type = null;
if (featureMap.ContainsKey(item.Key))
{
type = featureMap[item.Key];
}
if (type != null)
{
FeatureItem newItem = (FeatureItem)Activator.CreateInstance(type, item.Location);
foreach (KeyValuePair <string, List <string> > kvp in item.Qualifiers)
{
newItem.Qualifiers.Add(kvp.Key, kvp.Value);
}
item = newItem;
}
return(item);
}
private void ParseFeatures(MBFTextReader mbfReader, ref Sequence sequence)
{
ILocationBuilder locBuilder = LocationBuilder;
if (locBuilder == null)
{
throw new InvalidOperationException(Resource.NullLocationBuild);
}
// set data indent for features
mbfReader.DataIndent = _featureDataIndent;
// The sub-items of a feature are referred to as qualifiers. These do not have unique
// keys, so they are stored as lists in the SubItems dictionary.
SequenceFeatures features = new SequenceFeatures();
IList <FeatureItem> featureList = features.All;
while (mbfReader.HasLines)
{
if (String.IsNullOrEmpty(mbfReader.Line) || mbfReader.LineHeader == "FEATURES")
{
mbfReader.GoToNextLine();
continue;
}
if (mbfReader.Line[0] != ' ')
{
// start of non-feature text
break;
}
if (!mbfReader.LineHasHeader)
{
string message = Properties.Resource.GenbankEmptyFeature;
Trace.Report(message);
throw new InvalidDataException(message);
}
// check for multi-line location string
string featureKey = mbfReader.LineHeader;
string location = mbfReader.LineData;
mbfReader.GoToNextLine();
while (mbfReader.HasLines && !mbfReader.LineHasHeader &&
mbfReader.LineHasData && !mbfReader.LineData.StartsWith("/", StringComparison.Ordinal))
{
location += mbfReader.LineData;
mbfReader.GoToNextLine();
}
// create features as MetadataListItems
FeatureItem feature = new FeatureItem(featureKey, locBuilder.GetLocation(location));
// process the list of qualifiers, which are each in the form of
// /key="value"
string qualifierKey = string.Empty;
string qualifierValue = string.Empty;
while (mbfReader.HasLines)
{
if (!mbfReader.LineHasHeader && mbfReader.LineHasData)
{
// '/' denotes a continuation of the previous line
if (mbfReader.LineData.StartsWith("/", StringComparison.Ordinal))
{
// new qualifier; save previous if this isn't the first
if (!String.IsNullOrEmpty(qualifierKey))
{
AddQualifierToFeature(feature, qualifierKey, qualifierValue);
}
// set the key and value of this qualifier
int equalsIndex = mbfReader.LineData.IndexOf('=');
if (equalsIndex < 0)
{
// no value, just key (this is allowed, see NC_005213.gbk)
qualifierKey = mbfReader.LineData.Substring(1);
qualifierValue = string.Empty;
}
else if (equalsIndex > 0)
{
qualifierKey = mbfReader.LineData.Substring(1, equalsIndex - 1);
qualifierValue = mbfReader.LineData.Substring(equalsIndex + 1);
}
else
{
string message = String.Format(
CultureInfo.CurrentCulture,
Properties.Resource.GenbankInvalidFeature,
mbfReader.Line);
Trace.Report(message);
throw new InvalidDataException(message);
}
}
else
{
// Continuation of previous line; "note" gets a line break, and
// everything else except "translation" and "transl_except" gets a
// space to separate words.
if (qualifierKey == "note")
{
qualifierValue += Environment.NewLine;
}
else if (qualifierKey != "translation" && qualifierKey != "transl_except")
{
qualifierValue += " ";
}
qualifierValue += mbfReader.LineData;
}
mbfReader.GoToNextLine();
}
else if (mbfReader.Line.StartsWith("\t", StringComparison.Ordinal))
{
// this seems to be data corruption; but BioPerl test set includes
// (old, 2003) NT_021877.gbk which has this problem, so we
// handle it
ApplicationLog.WriteLine("WARN: nonstandard line format at line {0}: '{1}'",
mbfReader.LineNumber, mbfReader.Line);
qualifierValue += " " + mbfReader.Line.Trim();
mbfReader.GoToNextLine();
}
else
{
break;
}
}
// add last qualifier
if (!String.IsNullOrEmpty(qualifierKey))
{
AddQualifierToFeature(feature, qualifierKey, qualifierValue);
}
// still add feature, even if it has no qualifiers
featureList.Add(StandardFeatureMap.GetStandardFeatureItem(feature));
}
if (featureList.Count > 0)
{
((GenBankMetadata)sequence.Metadata[Helper.GenBankMetadataKey]).Features = features;
}
}
