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performance improvement to GenomeLocParser -- moved regex pattern compile out of local field 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1272 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kcibul 2009-07-17 02:56:25 +00:00
parent df1c61e049
commit 129ad97ce5
1 changed files with 5 additions and 4 deletions
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9
java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
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@ -51,6 +51,11 @@ import java.util.regex.Pattern;
public class GenomeLocParser { public class GenomeLocParser {
private static Logger logger = Logger.getLogger(GenomeLocParser.class); private static Logger logger = Logger.getLogger(GenomeLocParser.class);
private static final Pattern regex1 = Pattern.compile("([\\w&&[^:]]+)$"); // matches case 1
private static final Pattern regex2 = Pattern.compile("([\\w&&[^:]]+):([\\d,]+)$"); // matches case 2
private static final Pattern regex3 = Pattern.compile("([\\w&&[^:]]+):([\\d,]+)-([\\d,]+)$"); // matches case 3
private static final Pattern regex4 = Pattern.compile("([\\w&&[^:]]+):([\\d,]+)\\+"); // matches case 4
// -------------------------------------------------------------------------------------------------------------- // --------------------------------------------------------------------------------------------------------------
// //
@ -138,10 +143,6 @@ public class GenomeLocParser {
// 'chr2', 'chr2:1000000' or 'chr2:1,000,000-2,000,000' // 'chr2', 'chr2:1000000' or 'chr2:1,000,000-2,000,000'
//System.out.printf("Parsing location '%s'%n", str); //System.out.printf("Parsing location '%s'%n", str);
final Pattern regex1 = Pattern.compile("([\\w&&[^:]]+)$"); // matches case 1
final Pattern regex2 = Pattern.compile("([\\w&&[^:]]+):([\\d,]+)$"); // matches case 2
final Pattern regex3 = Pattern.compile("([\\w&&[^:]]+):([\\d,]+)-([\\d,]+)$"); // matches case 3
final Pattern regex4 = Pattern.compile("([\\w&&[^:]]+):([\\d,]+)\\+"); // matches case 4
String contig = null; String contig = null;
long start = 1; long start = 1;