umcg.genetica.ncbi.dbsnp

Class SNPAnnotation

java.lang.Object

umcg.genetica.ncbi.dbsnp.SNPAnnotation

All Implemented Interfaces:

Serializable

public class SNPAnnotation
extends Object
implements Serializable

Author:

harmjan

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
HashMap<String,ArrayList<Integer>>	chrToSNP
HashMap<String,HashSet<Integer>>	chrToUniquePositions
HashMap<Integer,Integer>	rsToChrPos

Constructor Summary

Constructors

Constructor and Description
SNPAnnotation(String contigInfoLoc, String snpInfoLoc)
SNPAnnotation(String contigInfoLoc, String snpInfoLoc, String ref)

Method Summary

Modifier and Type	Method and Description
HashSet<String>	getContigs()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

rsToChrPos

public HashMap<Integer,Integer> rsToChrPos

chrToSNP

public HashMap<String,ArrayList<Integer>> chrToSNP

chrToUniquePositions

public HashMap<String,HashSet<Integer>> chrToUniquePositions

Constructor Detail

SNPAnnotation

public SNPAnnotation(String contigInfoLoc,
                     String snpInfoLoc)
              throws IOException

Throws:

IOException

SNPAnnotation

public SNPAnnotation(String contigInfoLoc,
                     String snpInfoLoc,
                     String ref)
              throws IOException

Throws:

IOException

Method Detail

getContigs

public HashSet<String> getContigs()