public SrmDocument AddFasta(SrmDocument document, ref IdentityPath selectedPath, out int emptyPeptideGroups)
{
emptyPeptideGroups = 0;
var text = TbxFasta.Text;
if (text.Length == 0)
{
return document;
}
if (!text.StartsWith(">")) // Not L10N
{
ShowFastaError(new PasteError
{
Message = Resources.ImportFastaHelper_AddFasta_This_must_start_with____,
Column = 0,
Length = 1,
Line = 0,
});
return null;
}
string[] lines = text.Split('\n');
int lastNameLine = -1;
int aa = 0;
for (int i = 0; i < lines.Length; i++)
{
string line = lines[i];
if (line.StartsWith(">")) // Not L10N
{
if (line.Trim().Length == 1)
{
ShowFastaError(new PasteError
{
Message = Resources.ImportFastaHelper_AddFasta_There_is_no_name_for_this_protein,
Column = 0,
Line = i,
Length = 1
});
return null;
}
if (!CheckSequence(aa, lastNameLine, lines))
return null;
lastNameLine = i;
aa = 0;
continue;
}
for (int column = 0; column < line.Length; column++)
{
char c = line[column];
if (AminoAcid.IsExAA(c))
aa++;
else if (!Char.IsWhiteSpace(c) && c != '*')
{
ShowFastaError(new PasteError
{
Message =
String.Format(Resources.ImportFastaHelper_AddFasta___0___is_not_a_capital_letter_that_corresponds_to_an_amino_acid_, c),
Column = column,
Line = i,
Length = 1,
});
return null;
}
}
}
if (!CheckSequence(aa, lastNameLine, lines))
return null;
var importer = new FastaImporter(document, false);
try
{
var reader = new StringReader(TbxFasta.Text);
IdentityPath to = selectedPath;
IdentityPath firstAdded, nextAdd;
// TODO: support long-wait broker
document = document.AddPeptideGroups(importer.Import(reader, null, -1), false,
to, out firstAdded, out nextAdd);
emptyPeptideGroups = importer.EmptyPeptideGroupCount;
selectedPath = firstAdded;
}
catch (Exception exception)
{
ShowFastaError(new PasteError
{
Message = Resources.ImportFastaHelper_AddFasta_An_unexpected_error_occurred__ + exception.Message + " (" + exception.GetType() + ")" // Not L10N
});
return null;
}
return document;
}
public static SrmDocument ImportFasta(SrmDocument document, string fastaPath, IProgressMonitor monitor,
IdentityPath to, out IdentityPath firstAdded, out IdentityPath nextAdd, out int emptyProteinCount)
{
var importer = new FastaImporter(document, false);
using (TextReader reader = File.OpenText(fastaPath))
{
document = document.AddPeptideGroups(importer.Import(reader, monitor, Helpers.CountLinesInFile(fastaPath)),
false, null, out firstAdded, out nextAdd);
}
emptyProteinCount = importer.EmptyPeptideGroupCount;
return document;
}
