public List <IProtein> Read(string path)
{
List <IProtein> proteins = new List <IProtein>();
using (FileStream fileStream = new FileStream(path, FileMode.Open, FileAccess.Read))
{
using (StreamReader sr = new StreamReader(fileStream))
{
string line;
StringBuilder sequence = new StringBuilder();
IProtein entry = null;
// Read lines from the file until end of file (EOD) is reached.
while ((line = sr.ReadLine()) != null)
{
// ignore comment lines
if (line.StartsWith(";"))
{
continue;
}
//e.g. >gi|186681228|ref|YP_001864424.1| phycoerythrobilin:ferredoxin oxidoreductase
else if (line.StartsWith(">"))
{
if (entry != null)
{
entry.SetSequence(sequence.ToString());
proteins.Add(entry);
}
sequence.Clear();
entry = new BaseProtein();
entry.SetID(line.TrimStart('>'));
}
else
{
sequence.Append(line.Trim());
}
}
if (sequence.Length > 0)
{
entry.SetSequence(sequence.ToString());
proteins.Add(entry);
}
}
}
return(proteins);
}
