Read in the mascot.dat file.
/* ############################################################################## # 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_mascotdat { 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[]) { // ----- Object creation ----- if(argv.length < 1) { System.err.println("Location of mascot.dat has to be specified as a parameter"); System.err.println("The location should either be the full path to the enzymes file"); System.err.println("or a URL to a Mascot server - e.g. http://mascot-server/mascot/cgi"); System.exit(0); } // A sessionID can optionally be passed as the second parameter // This will only be required if the 'file' is a URL ms_datfile file; if (argv.length > 1) { ms_connection_settings cs = new ms_connection_settings(); cs.setSessionID(argv[1]); file = new ms_datfile(argv[0], 0, cs); } else { file = new ms_datfile(argv[0]); } if (!file.isValid()) { System.err.println("There are errors. Cannot continue. The last error description:"); System.err.println(file.getLastErrorString()); System.exit(0); } // retrieving Databases-section content ms_databases dbs = file.getDatabases(); // check if there is actually a 'Databases' section in the file if (dbs.isSectionAvailable()) { int n = dbs.getNumberOfDatabases(); System.out.println("There are " + n + " databases configured:"); for(int i=0; i < n; i++) { System.out.print(dbs.getDatabase(i).getName() + " : "); if (dbs.getDatabase(i).isActive()) { System.out.println("active"); } else { System.out.println("inactive"); } } } else { System.out.println("Databases-section is missing"); } System.out.println(""); // retrieving Parse-section content ms_parseoptions parseOptions = file.getParseOptions(); // check if there is 'Parse' section in the file actually if (parseOptions.isSectionAvailable()) { int n = parseOptions.getNumberOfParseRules(); System.out.println("Parse rules configured:"); for (int i=0; i < n; i++) { // not all of them can be specified if (parseOptions.getParseRule(i).isAvailable()) { System.out.print("Rule_" + i + " : "); System.out.println(parseOptions.getParseRule(i).getRuleStr()); } } } else { System.out.println("Parse-section is missing"); } System.out.println(); // retrieving WWW-section content ms_wwwoptions wwwOptions = file.getWWWOptions(); // check if there is 'WWW' section in the file actually if (wwwOptions.isSectionAvailable()) { int n = wwwOptions.getNumberOfEntries(); System.out.println("There are " + n + " sequence report sources configured:"); for(int i=0; i < n; i++) { System.out.print(wwwOptions.getEntry(i).getName() + "_"); if (wwwOptions.getEntry(i).getType() == msparser.WWW_SEQ) { System.out.println("SEQ"); } else { System.out.println("REP"); } } } else { System.out.println("WWW-section is missing"); } System.out.println(); // retrieving Taxonomy-sections System.out.println("Available taxonomy sources:"); int maxtax = file.getMaxTaxonomyRules(); for (int taxind = 1; taxind <= maxtax; taxind++) { // check whether a certain taxonomy section exists if (file.getTaxonomyRules(taxind) != null) { System.out.print("TAXONOMY_" + taxind + " "); System.out.println(file.getTaxonomyRules(taxind).getIdentifier()); } } System.out.println(); // retrieving Cluster-section content ms_clusterparams clusterParams = file.getClusterParams(); // check if there is 'Cluster' section in the file actually if (clusterParams.isSectionAvailable()) { System.out.print("Cluster mode : "); if (clusterParams.isEnabled()) { System.out.println("enabled"); } else { System.out.println("disabled"); } } else { System.out.println("Cluster-section is missing"); } System.out.println(); // retrieving Processor-section content ms_processoroptions procOptions = file.getProcessors(); // check if there is actually a 'Processor' section in the file if (procOptions.isSectionAvailable()) { System.out.println(procOptions.getNumberOfProcessors() + " CPU(s) configured"); } else { System.out.println("Processor-section is missing"); } System.out.println(); // retrieving Options-section content ms_mascotoptions mascotOptions = file.getMascotOptions(); // check if there is actually an 'Options' section in the file if (mascotOptions.isSectionAvailable()) { System.out.print("MascotCmdLine : "); System.out.println(mascotOptions.getMascotCmdLine()); } else { System.out.println("Options-section is missing"); } System.out.println(); // retrieving Cron-section content ms_cronoptions cronOptions = file.getCronOptions(); // check if there is actually a 'Cron' section in the file if (cronOptions.isSectionAvailable()) { if (cronOptions.isCronEnabled()) { int n = cronOptions.getNumberOfCronJobs(); System.out.println("There are " + n + " cron-jobs configured:"); for (int i=0; i < n; i++) { System.out.println(cronOptions.getCronJob(i).getCommandStr()); } } else { System.out.println("Cron functionality is disabled"); } } else { System.out.println("Cron-section is missing"); } System.out.println(); } } /* will give the output: C:>java -classpath .;../java/msparser.jar config_mascotdat mascot.dat There are 10 databases configured: MSDB : active NCBInr : active EST_human : inactive EST_mouse : inactive EST_others : active SwissProt : active Trembl : inactive IPI_human : inactive IPI_mouse : inactive yeastorfn : active Parse rules configured: Rule_1 : >owl[^ ]*|\([^ ]*\) Rule_2 : >owl[^ ]*|[^ ]*[ ]\(.*\) Rule_3 : >[A-Z][0-9];\([^ ]*\) Rule_4 : >\([^ ]*\) Rule_5 : >[^ ]* \(.*\) Rule_6 : >\(gi|[0-9]*\) Rule_7 : >[^ ]* \(.*\) Rule_8 : \*\(.*\)> Rule_9 : \*.*\(>[A-Z][0-9];.*\) Rule_10 : \(LOCUS .*\)ORIGIN Rule_11 : \(LOCUS .*\) Rule_12 : >\([^ ]*\) Rule_13 : >[^ ]* \(.*\) Rule_14 : <pre>\(.*\)</pre> Rule_15 : ^AC \([^ ;]*\) Rule_16 : \*.*\(ID [A-Z0-9]*_[A-Z0-9]* .*\) Rule_17 : >\([^ ]*\) Rule_18 : >[^ ]* \(.*\) Rule_19 : >[A-Z][0-9];\([^ ]*\)[ ]* Rule_20 : >\(.*\) Rule_21 : >IPI:\([^| .]*\) Rule_22 : \*.*\(ID IPI[0-9]* .*\) Rule_23 : \(.*\) Rule_24 : \*.*\(ID [-A-Z0-9_].*\) Rule_25 : >[^(]*.\([^)]*\) Rule_26 : ^AC \([^ ;]*\) Rule_27 : \*.*\(AC [A-Z0-9]*;.*\) There are 19 sequence report sources configured: NCBInr_SEQ NCBInr_REP EST_human_SEQ EST_human_REP EST_mouse_SEQ EST_mouse_REP EST_others_SEQ EST_others_REP SwissProt_SEQ SwissProt_REP Trembl_SEQ Trembl_REP MSDB_SEQ MSDB_REP IPI_human_SEQ IPI_human_REP IPI_mouse_SEQ IPI_mouse_REP yeastorfn_SEQ Available taxonomy sources: TAXONOMY_1 NCBI nr FASTA TAXONOMY_2 OWL REF TAXONOMY_3 Swiss-prot FASTA TAXONOMY_4 NCBI dbEST FASTA TAXONOMY_5 Swiss-prot DAT TAXONOMY_6 MSDB REF (pre 20000621) TAXONOMY_7 MSDB REF TAXONOMY_8 NCBI nr FASTA using GI2TAXID TAXONOMY_9 dbEST FASTA using GI2TAXID TAXONOMY_10 EST_human FASTA with TaxID TAXONOMY_11 EST_mouse FASTA with TaxID Cluster mode : disabled Processor-section is missing MascotCmdLine : ../cgi/nph-mascot.exe Cron functionality is disabled */
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