internal static ReturnCodes LoadSequencesFromFiles(ref Alignment alignmentObject, bool append, string[] fileNames, out List <Tuple <string, int, ReturnCodes> > fileErrors)
// This method provides the main interface for loading sequences. It takes an array of file names and calls LoadSequencesFromFile.
// It then checks the return codes and the number of sequences loaded, then clears the alignment if not appending, then adds the
// new sequences to the alignment. In addition to the main return code, it returns as an output parameter a list containing the error codes.
{
ReturnCodes returnCode = ReturnCodes.OK;
fileErrors = new List <Tuple <string, int, ReturnCodes> >();
//List<Tuple<Macromolecule, int[]>> loadedAlignedMacromolecules = new List<Tuple<Macromolecule, int[]>>();
List <AlignedMacromolecule> loadedAlignedMacromolecules = new List <AlignedMacromolecule>();
foreach (string fileName in fileNames)
{
//List<Tuple<Macromolecule, int[]>> fileAlignedMacromolecules;
List <AlignedMacromolecule> fileAlignedMacromolecules;
ReturnCodes fileReturnCode = ReturnCodes.OK;
fileReturnCode = LoadSequencesFromFile(fileName, out fileAlignedMacromolecules);
if (fileReturnCode != ReturnCodes.OK)
{
// Add any errors to the array
fileErrors.Add(Tuple.Create(fileName, fileAlignedMacromolecules.Count, fileReturnCode));
returnCode = ReturnCodes.FileErrors;
}
if (fileReturnCode == ReturnCodes.OK || fileReturnCode == ReturnCodes.EmptySequencesRemoved)
{
// These codes mean it is okay to add their macromolecules to the main list.
//foreach (Tuple<Macromolecule, int[]> alignedMacromolecule in fileAlignedMacromolecules)
foreach (AlignedMacromolecule alignedMacromolecule in fileAlignedMacromolecules)
{
loadedAlignedMacromolecules.Add(alignedMacromolecule);
}
}
}
// Ensure that some sequences were loaded.
if (loadedAlignedMacromolecules.Count > 0)
{
// Check that all are the same type, force the minority to conform to the majority, and append to the error list.
int numChanged;
ReturnCodes typeReturnCode = EnsureAllSameType(loadedAlignedMacromolecules, out numChanged);
if (typeReturnCode != ReturnCodes.OK) //
{
fileErrors.Add(Tuple.Create("DNA to Protein", numChanged, typeReturnCode));
returnCode = ReturnCodes.FileErrors;
}
if (!append)
{
alignmentObject.Clear();
}
// It's now okay to add macromolecules to the alignment object
alignmentObject.AddAlignedMacromolecules(loadedAlignedMacromolecules);
}
return(returnCode);
}