/// <summary>
/// copy files to linux machine, added on July 16, 2010
/// </summary>
/// <param name="pdbCodes"></param>
private void CopyPdbFilesToLinux(string[] pdbCodes)
{
ProtCidSettings.progressInfo.ResetCurrentProgressInfo();
ProtCidSettings.progressInfo.currentOperationLabel = "Copy files";
string pdbFileInLinux = "";
string pdbFileInWindows = "";
ProtCidSettings.progressInfo.totalOperationNum = pdbCodes.Length;
ProtCidSettings.progressInfo.totalStepNum = pdbCodes.Length;
foreach (string pdbCode in pdbCodes)
{
ProtCidSettings.progressInfo.currentOperationNum++;
ProtCidSettings.progressInfo.currentStepNum++;
ProtCidSettings.progressInfo.currentFileName = pdbCode;
pdbFileInWindows = Path.Combine(pdbTextPath, pdbCode.Substring(1, 2) + "\\" + pdbCode + ".ent.gz");
if (File.Exists(pdbFileInWindows))
{
pdbFileInLinux = pdbFilePathInLinux + pdbCode.Substring(1, 2) + "/" + pdbCode + ".ent.gz";
fileCopy.CopyWindowsDataToLinux(pdbFileInWindows, pdbFileInLinux);
}
}
}
/// <summary>
/// copy files to linux machine, added on July 16, 2010
/// </summary>
/// <param name="pdbCodes"></param>
private void CopyEntryBuFilesToLinux(string[] entryBuFilesInWindows)
{
string buFileInLinux = "";
foreach (string buFileInWindows in entryBuFilesInWindows)
{
if (File.Exists(buFileInWindows))
{
FileInfo fileInfo = new FileInfo(buFileInWindows);
buFileInLinux = buFilePathInLinux + fileInfo.Name;
fileCopy.CopyWindowsDataToLinux(buFileInWindows, buFileInLinux);
}
}
}
/// <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);
}