From ff98e28abffd43bc5fb7e29248ced4b3c081dc64 Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 25 Mar 2009 02:17:48 +0000
Subject: [PATCH] High-performance interval list implement -- uses
 StringBuilder to avoid n^2 calculation.  Can handle millions of locations
 quickly now

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@182 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../org/broadinstitute/sting/gatk/TraversalEngine.java | 10 +++++-----
 java/src/org/broadinstitute/sting/utils/GenomeLoc.java |  4 ++--
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/TraversalEngine.java b/java/src/org/broadinstitute/sting/gatk/TraversalEngine.java
index 0621d6ccb..76875393e 100755
--- a/java/src/org/broadinstitute/sting/gatk/TraversalEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/TraversalEngine.java
@@ -187,7 +187,7 @@ public class TraversalEngine {
      * @param file_name
      */
     public void setLocationFromFile(final String file_name) {
-        String locStr = "";
+        StringBuilder locStr = new StringBuilder();
 
         Scanner scanner = null;
         try {
@@ -195,9 +195,9 @@ public class TraversalEngine {
             while (scanner.hasNextLine()) {
                 String line = scanner.nextLine();
                 line.replaceAll("\n", "");
-                locStr += line;
+                locStr.append(line);
                 if (scanner.hasNextLine()) {
-                    locStr += ";";
+                    locStr.append(";");
                 }
             }
         }
@@ -210,9 +210,9 @@ public class TraversalEngine {
             scanner.close();
         }
 
-        logger.debug("DEBUG: locStr: " + locStr);
+        logger.debug("DEBUG: locStr: " + locStr.toString());
 
-        this.locs = parseGenomeLocs(locStr);
+        this.locs = parseGenomeLocs(locStr.toString());
     }
 
     /**
diff --git a/java/src/org/broadinstitute/sting/utils/GenomeLoc.java b/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
index b570a08b3..37ea726f5 100644
--- a/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
+++ b/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
@@ -59,7 +59,7 @@ public class GenomeLoc implements Comparable<GenomeLoc> {
 
     public static GenomeLoc parseGenomeLoc( final String str ) {
         // Ôchr2Õ, Ôchr2:1000000Õ or Ôchr2:1,000,000-2,000,000Õ
-        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
@@ -102,7 +102,7 @@ public class GenomeLoc implements Comparable<GenomeLoc> {
         }
 
         GenomeLoc loc = new GenomeLoc(contig, start, stop);
-        System.out.printf("  => Parsed location '%s' into %s%n", str, loc);
+        //System.out.printf("  => Parsed location '%s' into %s%n", str, loc);
 
         return loc;
     }