/// <summary>
///
/// </summary>
/// <param name="nonAlignedPairsFile"></param>
public string GetFatcatAlignmentsOnLinux(string nonAlignedPairsFile)
{
if (ProtCidSettings.dirSettings == null)
{
ProtCidSettings.LoadDirSettings();
}
if (ProtCidSettings.alignmentDbConnection == null)
{
ProtCidSettings.alignmentDbConnection = new DbLib.DbConnect();
ProtCidSettings.alignmentDbConnection.ConnectString = "DRIVER=Firebird/InterBase(r) driver;UID=SYSDBA;" +
"PWD=fbmonkeyox;DATABASE=" + ProtCidSettings.dirSettings.alignmentDbPath;
}
string repChainPairsFileName = "NonAlignRepEntryPairs.txt";
WriteRepChainPairsToFile(nonAlignedPairsFile, repChainPairsFileName);
CmdOperations linuxOperator = new CmdOperations();
linuxOperator.CopyWindowsDataToLinux(repChainPairsFileName, exeFatcatDir + repChainPairsFileName);
string cmdLineFile = WriteFatcatCommandFile(repChainPairsFileName);
linuxOperator.RunPlink(cmdLineFile);
string alignFileInLinux = fatcatDir + repChainPairsFileName.Replace(".txt", ".aln");
string alignFileInWindows = Path.Combine(ProtCidSettings.dirSettings.fatcatPath, repChainPairsFileName.Replace(".txt", ".aln"));
linuxOperator.CopyLinuxDataToWindows(alignFileInLinux, alignFileInWindows);
return(alignFileInWindows);
}
