public override IMatrixData ProcessData(IMatrixData[] inputData, Parameters param, ref IMatrixData[] supplTables,
ref IDocumentData[] documents, ProcessInfo processInfo)
{
string proteinGroupsFile = param.GetFileParam(parameter[0]).Value;
Constants.ValidateColumnNames(proteinGroupsFile, processInfo.Status, true);
string peptidesFile = param.GetFileParam(parameter[1]).Value;
Constants.ValidateColumnNames(proteinGroupsFile, processInfo.Status, true);
string msmsFile = param.GetFileParam(parameter[2]).Value;
Constants.ValidateColumnNames(proteinGroupsFile, processInfo.Status, true);
string outputFolder = param.GetFolderParam(parameter[3]).Value;
Stream databaseRefTable = new MatrixStream(GetMatrixData(Matrix.DatabaseRef, inputData), true);
Stream spectraRefTable = new MatrixStream(GetMatrixData(Matrix.SpectraRef, inputData), true);
Stream metadataFile = new MatrixStream(GetMatrixData(Matrix.MetadataSection, inputData), true);
Converter convert = new Converter(databaseRefTable, spectraRefTable, metadataFile, proteinGroupsFile,
peptidesFile, msmsFile, outputFolder){
Status = processInfo.Status,
Progress = processInfo.Progress
};
convert.Start();
return new MatrixData();
}