private string ExtractDescriptionFromHeader(string headerLine)
{
var description = headerLine;
try
{
if (headerLine.StartsWith(ProteinLineStartChar.ToString()))
{
// Remove the > character from the start of the line
headerLine = headerLine.TrimStart(ProteinLineStartChar).Trim();
}
var charIndex = headerLine.IndexOfAny(ProteinLineAccessionEndChars);
if (charIndex > 0)
{
description = headerLine.Substring(charIndex + 1).Trim();
}
else
{
description = headerLine;
}
}
catch (Exception)
{
// Ignore any errors
}
return(description);
}
/// <summary>
/// Header line (protein name and description)
/// </summary>
/// <param name="includeStartChar">If true then include the start character (<)</param>
public string GetHeaderLine(bool includeStartChar)
{
try
{
if (!includeStartChar && mCurrentEntry.HeaderLine.StartsWith(ProteinLineStartChar.ToString()))
{
// Remove the > character from the start of the line
return(mCurrentEntry.HeaderLine.TrimStart(ProteinLineStartChar).Trim());
}
return(mCurrentEntry.HeaderLine);
}
catch (Exception)
{
return(mCurrentEntry.HeaderLine);
}
}
/// <summary>
/// Extract the accession name from the header line by looking for mProteinLineAccessionEndChar
/// </summary>
/// <param name="headerLine"></param>
/// <returns>Accession (protein) name</returns>
/// <remarks>HeaderLine should not start with the > character; it should have already been removed when the file was read</remarks>
private string ExtractAccessionNameFromHeader(string headerLine)
{
try
{
if (headerLine.StartsWith(ProteinLineStartChar.ToString()))
{
// Remove the > character from the start of the line
headerLine = headerLine.TrimStart(ProteinLineStartChar).Trim();
}
var charIndex = headerLine.IndexOfAny(ProteinLineAccessionEndChars);
if (charIndex > 0)
{
return(headerLine.Substring(0, charIndex).Trim());
}
return(headerLine);
}
catch (Exception)
{
// Ignore any errors; return the full line
return(headerLine);
}
}
/// <summary>
/// Reads the next entry in a Fasta file
/// </summary>
/// <returns>True if an entry is found, otherwise false</returns>
public override bool ReadNextProteinEntry()
{
mCurrentEntry.Clear();
var proteinEntryFound = false;
// This is always 0 for Fasta files
mFileLineSkipCount = 0;
if (mProteinFileInputStream == null)
{
return(false);
}
try
{
var proteinLineStartChar = ProteinLineStartChar.ToString();
while (!proteinEntryFound && !mProteinFileInputStream.EndOfStream)
{
string lineIn;
if (!string.IsNullOrWhiteSpace(mCachedHeaderLine))
{
lineIn = string.Copy(mCachedHeaderLine);
mCachedHeaderLine = string.Empty;
}
else
{
lineIn = mProteinFileInputStream.ReadLine();
mFileLinesRead++;
if (lineIn == null)
{
mFileBytesRead += 2;
}
else
{
mFileBytesRead += lineIn.Length + 2;
}
}
if (string.IsNullOrWhiteSpace(lineIn))
{
continue;
}
var dataLine = lineIn.Trim();
// See if lineIn starts with the protein header start character
if (!dataLine.StartsWith(ProteinLineStartChar.ToString()))
{
continue;
}
mCurrentEntry.HeaderLine = dataLine;
mCurrentEntry.Name = ExtractAccessionNameFromHeader(dataLine);
mCurrentEntry.Description = ExtractDescriptionFromHeader(dataLine);
mCurrentEntry.Sequence = string.Empty;
mProteinResidues.Clear();
proteinEntryFound = true;
// Now continue reading until the next protein header start character is found
while (!mProteinFileInputStream.EndOfStream)
{
var lineIn2 = mProteinFileInputStream.ReadLine();
mFileLinesRead++;
if (lineIn2 == null)
{
mFileBytesRead += 2;
continue;
}
mFileBytesRead += lineIn2.Length + 2;
if (lineIn2.TrimStart().StartsWith(proteinLineStartChar))
{
// Found the next protein entry
// Store in mCachedHeaderLine and jump out of the loop
mCachedHeaderLine = string.Copy(lineIn2);
break;
}
if (DiscardProteinResidues)
{
continue;
}
// lineIn2 has additional residues for the current protein
mProteinResidues.Append(lineIn2.Trim());
}
mCurrentEntry.Sequence = mProteinResidues.ToString();
}
if (!proteinEntryFound)
{
AdjustBytesReadForEOF();
}
}
catch (Exception ex)
{
// Error reading the input file
proteinEntryFound = false;
Console.WriteLine("Exception in FastaFileReader.ReadNextProteinEntry: " + ex.Message);
}
return(proteinEntryFound);
}
