public void Test()
{
GenebankFeature cds = new GenebankFeature();
cds.Location = "141..539";
Assert.IsFalse(cds.IsComplement);
Assert.AreEqual(141, cds.Start);
Assert.AreEqual(539, cds.End);
cds.Location = "complement(141..539)";
Assert.IsTrue(cds.IsComplement);
Assert.AreEqual(141, cds.Start);
Assert.AreEqual(539, cds.End);
cds.Context = new List<string>();
cds.FeatureName = "CDS";
List<string> paragraph = cds.GetParagraph(false);
Assert.AreEqual(" CDS complement(141..539)", paragraph[0]);
paragraph = cds.GetParagraph(true);
Assert.AreEqual("FT CDS complement(141..539)", paragraph[0]);
cds.FeatureName = "Contig";
paragraph = cds.GetParagraph(false);
Assert.AreEqual(" Contig complement(141..539)", paragraph[0]);
paragraph = cds.GetParagraph(true);
Assert.AreEqual("FT Contig complement(141..539)", paragraph[0]);
}
public List <GenebankItem> ReadFromFile(string fileName)
{
List <GenebankItem> result = new List <GenebankItem>();
using (StreamReader sr = new StreamReader(fileName))
{
string line;
while ((line = sr.ReadLine()) != null)
{
if (line.StartsWith("LOCUS"))
{
GenebankItem item = new GenebankItem();
result.Add(item);
item.Accession = line.StringAfter("LOCUS").Trim().StringBefore(" ");
while ((line = sr.ReadLine()) != null)
{
if (line.StartsWith("FEATURES"))
{
GenebankFeature feature = null;
while ((line = sr.ReadLine()) != null)
{
if (line[0] != ' ')
{
break;
}
if (line[5] != ' ')
{
feature = new GenebankFeature();
item.Features.Add(feature);
feature.FeatureName = line.Substring(5).StringBefore(" ");
feature.Location = line;
}
else
{
feature.Context.Add(line.Substring(3).Trim());
}
}
}
if (line.Equals("//"))
{
break;
}
}
}
}
}
return(result);
}