Read in the modifications file - modfile.
/* ############################################################################## # file: config_quantitation.java # # 'msparser' toolkit # # Test harness / example code # ############################################################################## # COPYRIGHT NOTICE # # Copyright 1998-2003 Matrix Science Limited All Rights Reserved. # # # ############################################################################## # Archive:: /MowseBranches/ms_mascotresfile_1.2/test_java/test_searchi # # Author: yuryr # # Date: 2006/02/06 17:53:44 # # Revision: 1.1 # # NoKeywords:: # ############################################################################## */ import java.util.Date; import matrix_science.msparser.*; public class config_modfile { static { try { System.loadLibrary("msparserj"); } catch (UnsatisfiedLinkError e) { System.err.println("Native code library failed to load. " + "Is msparserj.dll on the path?\n" + e); System.exit(0); } } public static void main(String argv[]) { if (argv.length < 1) { System.out.println("The location of mod_file has to be specified as a parameter"); System.out.println("The location should either be the full path to the mod_file"); System.out.println("or a URL to a Mascot server - e.g. http://mascot-server/mascot/cgi"); System.exit(0); } // we need ms_masses class instance // in practice, it has to be also read from a disc file // but, for simplicity, we will use default masses ms_masses massesFile = new ms_masses(); // A sessionID can optionally be passed as the second parameter // This will only be required if the 'file' is a URL ms_modfile file; if (argv.length > 1) { ms_connection_settings cs = new ms_connection_settings(); cs.setSessionID(argv[1]); file = new ms_modfile(argv[0], massesFile, false, cs); } else { file = new ms_modfile(argv[0], massesFile, false); } if (!file.isValid()) { System.out.println("There are errors. Cannot continue. The last error description:"); System.out.println(file.getLastErrorString()); System.exit(0); } int n = file.getNumberOfModifications(); System.out.println("There are " + n + " modifications configured:"); // now get'em all! for (int i=0; i < n; i++) { System.out.println(file.getModificationByNumber(i).getTitle()); } // Now change Acetyl (K) ms_modification mod = file.getModificationByName("Acetyl (K)"); mod.setHidden(true); file.updateModificationByName("Acetyl (K)", mod); // And delete Methyl (R) file.deleteModificationByName("Methyl (R)"); // Finally, save the file under a new name file.setFileName(argv[0] + ".new"); file.save_file(); System.out.println("There are now " + file.getNumberOfModifications() + " modifications configured:"); } } /* will give the output: C:>java -classpath .;../java/msparser.jar config_modfile mod_file There are 12 modifications configured: Acetyl (N-term) Acetyl (K) Acetyl/Methyl (K) Propionyl/Methyl (K) Methyl (R) Dimethyl (R) Succininyl (K) Succininyl+Methyl (K) Biotinylated (N-term) Biotinylated (K) Carbamidomethyl (C) Carbamyl (N-term) ... */
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