Matrix Science Mascot Parser toolkit
 
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resfile_info.java

Example program for retrieving general search information.

/*
##############################################################################
# file: resfile_info.java #
# 'msparser' toolkit #
# Test harness / example code #
##############################################################################
# COPYRIGHT NOTICE #
# Copyright 1998-2003 Matrix Science Limited All Rights Reserved. #
# #
##############################################################################
# $Archive:: /MowseBranches/ms_mascotresfile_dat_1.2/test_java/test_searchi $ #
# $Author: robertog@matrixscience.com $ #
# $Date: 2024-09-04 10:23:46 +0100 $ #
# $Revision: 526921a73137894bb1eae0b0fc8ccb4bb52ea662 | MSPARSER_REL_3_0_0-2024-09-24-0-g93ebaeb4f4 $ #
# $NoKeywords:: $ #
##############################################################################
*/
import java.util.Date;
import matrix_science.msparser.*;
public class resfile_info {
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.out.println("Must specify results filename as parameter");
System.exit(0);
}
ms_mascotresfilebase file = ms_mascotresfilebase.createResfile(argv[0], 0, "");
if (file.isValid()) {
searchInformation(file);
} else {
System.out.println("Error number: "+file.getLastError());
System.out.println("Error string: "+file.getLastErrorString());
System.exit(0);
}
}
private static void searchInformation(ms_mascotresfilebase file) {
Date searchDate = null; // Java.util.date object
int seconds = file.getDate(); // get date of search in seconds since midnight GMT Jan 1st 1970
long milliseconds = (long) seconds * 1000; // convert to milliseconds
searchDate=new Date(milliseconds); // create the date object
System.out.println("Search information from ms_mascotresfilebase");
System.out.println("========================================");
System.out.println("Number of queries : "+file.getNumQueries());
System.out.println("Number of sequences : "+file.getNumSeqs());
System.out.println("Sequences after tax : "+file.getNumSeqsAfterTax());
System.out.println("Number of residues : "+(int)file.getNumResidues());
System.out.println("Execution time : "+file.getExecTime());
System.out.println("Date (seconds) : "+file.getDate());
// make java output identical to perl output
System.out.print("Date : ");
String toPerlDate = searchDate.toString();
if(toPerlDate.indexOf("GMT ") > -1) {
String beforeGMT = toPerlDate.substring(0,toPerlDate.indexOf("GMT"));
String afterGMT = toPerlDate.substring(toPerlDate.indexOf("GMT ")+4,toPerlDate.length());
System.out.println(beforeGMT+afterGMT);
} else {
System.out.println(searchDate);
}
System.out.println("Mascot version : "+file.getMascotVer());
System.out.println("Fasta version : "+file.getFastaVer());
// make java output identical to perl output
System.out.println("Is PMF? : "+toBinary(file.isPMF()));
System.out.println("Is MSMS? : "+toBinary(file.isMSMS()));
System.out.println("Is SQ? : "+toBinary(file.isSQ()));
System.out.println("Is Error tolerant : "+toBinary(file.isErrorTolerant()));
System.out.println("Any PMF? : "+toBinary(file.anyPMF()));
System.out.println("Any MSMS? : "+toBinary(file.anyMSMS()));
System.out.println("Any SQ? : "+toBinary(file.anySQ()));
System.out.println("Any peptides section: "+toBinary(file.doesSectionExist(ms_mascotresfilebase.SEC_PEPTIDES)));
System.out.println("Any peptide matches : "+toBinary(file.anyFastaMatches()));
System.out.println();
}
private static int toBinary(boolean bool) {
if(bool) return 1;
return 0;
}
}
/*
will give the output:
C:>java -classpath .;../java/msparser.jar resfile_info F981123.dat
Search information from ms_mascotresfilebase
========================================
Number of queries : 4
Number of hits : 50
Number of sequences : 820227
Sequences after tax : 820227
Number of residues : 255696937
Execution time : 14
Date (seconds) : 1014568786
Date : Sun Feb 24 16:39:46 2002
Mascot version : 1.7.17
Fasta version : MSDB_20020121.fasta
Is PMF? : 0
Is MSMS? : 1
Is SQ? : 0
Is Error tolerant : 0
Any PMF? : 0
Any MSMS? : 1
Any SQ? : 0
Any peptides section: 1
Any peptide matches : 1
*/