Class TwoBitFacade
- java.lang.Object
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- org.biojava.nbio.genome.parsers.twobit.TwoBitFacade
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public class TwoBitFacade extends java.lang.Object
A facade that makes it easier to work with a 2bit file. Created by yana on 3/27/17.
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Constructor Summary
Constructors Constructor Description TwoBitFacade(java.io.File file)
Reads a genome from a locally stored .2bit file.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
close()
Closes .2bit file twoBitParser.java.lang.String
getSequence(java.lang.String chromosomeName, int start, int end)
Extract a sequence from a chromosome, using chromosomal coordinatesvoid
setChromosome(java.lang.String chr)
Sets a chromosome for TwoBitParser.
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Method Detail
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close
public void close() throws java.lang.Exception
Closes .2bit file twoBitParser.- Throws:
java.lang.Exception
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setChromosome
public void setChromosome(java.lang.String chr) throws java.lang.Exception
Sets a chromosome for TwoBitParser.- Parameters:
chr
- The chromosome name (e.g. chr21)- Throws:
java.lang.Exception
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getSequence
public java.lang.String getSequence(java.lang.String chromosomeName, int start, int end) throws java.lang.Exception
Extract a sequence from a chromosome, using chromosomal coordinates- Parameters:
chromosomeName
-start
-end
-- Returns:
- the DNASequence from the requested coordinates.
- Throws:
java.lang.Exception
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