/// <summary> /// ProgramArgs constructor. /// </summary> /// <param name="dnvopt">Type of de novo result.</param> /// <param name="dnvPath">The path to the directory where the de novo files are placed.</param> /// <param name="dbOpt">The file format of the sequence database.</param> /// <param name="dbpPath">The path to the database directory </param> /// <param name="matrixPath">The substitution matrix. Default is pam30ms.</param> /// <param name="Thits">The desirable alignment top hits that will be analysed.</param> /// <param name="minAA">The minimmun size of the peptides to be used in the analysis.</param> /// <param name="decoy">The tag name inserted in the decoy sequences header.</param> /// <param name="oCost">The alignment penalty for open gaps.</param> /// <param name="eCost">The alignment penalty for extending gaps.</param> public ProgramArgs(DeNovoOption dnvopt, string dnvPath, string mPexPath, DataBaseOption dbOpt, string dbpPath, MatrixOption matrix, int Thits, int minAA, string decoy, double minDenovoScore, double minIdent ) { DeNovoOption = dnvopt; DeNovoResultDirectory = dnvPath; MPexResultPath = mPexPath; DataBaseFormat = dbOpt; DataBaseFile = dbpPath; SubstitutionMatrix = matrix; TopHits = Thits; PeptideMinNumAA = minAA; DecoyLabel = decoy; MinDeNovoScore = minDenovoScore; MinIdentity = minIdent; }
private ProgramArgs GetParamsFromScreen() { //Verify if arguments are valid. if (!File.Exists(textBoxDataBaseFile.Text)) { throw new Exception("Database file " + textBoxDataBaseFile.Text + " not found"); } if (!Directory.Exists(textBoxDeNovoOutput.Text) && richTextBoxPeptideList.Text.Length == 0 && textBoxmpexFile.Text.Length == 0) { throw new Exception("Please enter a valid directory containing de novo output files or enter a list of peptides to be considered."); } else if (richTextBoxPeptideList.Text.Length == 0 && buttonBrowseMPEXSearch.Text.Length == 0) { if (Directory.GetFiles(textBoxDeNovoOutput.Text).Count() == 0) { throw new Exception("No files were found in the De novo output directory"); } } if (comboBoxDeNovoSoftware.SelectedText.Equals("Select de novo software")) { throw new Exception("Please select the de novo sequencing tool / format"); } string dbPath = textBoxDataBaseFile.Text; string dnvPath = textBoxDeNovoOutput.Text; string decoy = textBoxDecoyTag.Text; int hits = 1; int pepSize = Convert.ToInt16(numericUpDownPeptideSize.Value); MatrixOption matrix = MatrixOption.PAM30ms; double minDeNovoScore = (double)numericUpDownMinDenovoScore.Value; matrix = MatrixOption.PAM30ms; DataBaseOption dbOpt = DataBaseOption.Generic; if (radioButtonGeneric.Checked == true) { dbOpt = DataBaseOption.Generic; } else if (radioButtonNcbi.Checked == true) { dbOpt = DataBaseOption.NCBI; } else if (radioButtonNextProt.Checked == true) { dbOpt = DataBaseOption.NextProt; } else if (radioButtonSwissProt.Checked == true) { dbOpt = DataBaseOption.SwissProt; } DeNovoOption dnvOpt = DeNovoOption.Peaks75; if (comboBoxDeNovoSoftware.SelectedItem != null) { if (comboBoxDeNovoSoftware.SelectedItem.Equals("PEAKS 7.0")) { dnvOpt = DeNovoOption.Peaks70; } else if (comboBoxDeNovoSoftware.SelectedItem.Equals("PEAKS 7.5")) { dnvOpt = DeNovoOption.Peaks75; } else if (comboBoxDeNovoSoftware.SelectedItem.Equals("PEAKS 8.0")) { dnvOpt = DeNovoOption.Peaks80; } else if (comboBoxDeNovoSoftware.SelectedItem.Equals("PepNovo+ (output_dnv)")) { dnvOpt = DeNovoOption.PepNovo; } else if (comboBoxDeNovoSoftware.SelectedItem.Equals("PNovo+")) { dnvOpt = DeNovoOption.PNovo; } else if (comboBoxDeNovoSoftware.SelectedItem.Equals("PepNovo+ (output_full)")) { dnvOpt = DeNovoOption.PepNovoFull; } else if (comboBoxDeNovoSoftware.SelectedItem.Equals("MSGFDB")) { dnvOpt = DeNovoOption.MSGFDB; } else if (comboBoxDeNovoSoftware.SelectedItem.Equals("NOVOR v1.05.0573")) { dnvOpt = DeNovoOption.NOVOR; } } else { dnvOpt = DeNovoOption.ListOfPeptides; } double minIdentity = (double)numericUpDownMinIdentity.Value; ProgramArgs myArgs = new ProgramArgs( dnvOpt, dnvPath, textBoxmpexFile.Text, dbOpt, dbPath, matrix, hits, pepSize, decoy, minDeNovoScore, minIdentity ); return(myArgs); }
/// <summary> /// Default constructor. /// </summary> public DeNovoParser(DeNovoOption dnvOpt, string path) { DeNovoType = dnvOpt; DirectoryPath = path; DeNovoRegistryList = new List <DeNovoRegistry>(); }