From 55c1b688bd30ef3ee95b9291bcb9a862eeae76a1 Mon Sep 17 00:00:00 2001 From: hanna Date: Fri, 8 May 2009 22:31:16 +0000 Subject: [PATCH] Fix mediocre javadoc. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@646 348d0f76-0448-11de-a6fe-93d51630548a --- .../dataSources/providers/ReferenceProvider.java | 16 +++++++++++++++- 1 file changed, 15 insertions(+), 1 deletion(-) diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/providers/ReferenceProvider.java b/java/src/org/broadinstitute/sting/gatk/dataSources/providers/ReferenceProvider.java index f61595b01..350bc9d2c 100755 --- a/java/src/org/broadinstitute/sting/gatk/dataSources/providers/ReferenceProvider.java +++ b/java/src/org/broadinstitute/sting/gatk/dataSources/providers/ReferenceProvider.java @@ -18,15 +18,29 @@ public class ReferenceProvider { private IndexedFastaSequenceFile sequenceFile; private Shard shard; - // Lazy + /** + * Track the reference sequence and the last point accessed. Used to + * track state when traversing over the reference. + */ private ReferenceSequence referenceSequence; private GenomeLoc referenceInterval; + /** + * Create a new reference provider supplying data from the given reference. + * @param sequenceFile Reference file to use. + * @param shard Shard over which to retrieve data. + */ public ReferenceProvider( IndexedFastaSequenceFile sequenceFile, Shard shard ) { this.sequenceFile = sequenceFile; this.shard = shard; } + /** + * Gets the reference base at a single point. + * @param genomeLoc The location at which to fetch the reference base. + * @return The character representing the reference base. + * @throws InvalidPositionException in case the position is invalid. + */ public char getReferenceBase( GenomeLoc genomeLoc ) throws InvalidPositionException { if( referenceSequence == null ) lazyInitializeLocusAccess();