uni.bielefeld.cmg.reflexiv.io

Class ContigReader

java.lang.Object

uni.bielefeld.cmg.reflexiv.io.ContigReader

All Implemented Interfaces:

java.io.Serializable

public class ContigReader
extends java.lang.Object
implements java.io.Serializable

Returns an object for reading contigs in the Fasta format. Providing Fasta unit buffer for multi-thread Fastq input stream. This class is used in local mode only. For cluster mode, Spark "textFile" function is used to access input Fastq file.

See Also:

, Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
java.lang.String[]	contigIDArray
java.util.HashMap<java.lang.Integer,java.lang.String>	contigIDTable
java.util.HashMap<java.lang.String,java.lang.String>	contigPrimerTable
DefaultParam	param
java.lang.String[]	primerArray
java.util.ArrayList<scala.Tuple2<java.lang.Long,scala.Tuple4<java.lang.Integer,java.lang.Long[],java.lang.Integer,java.lang.Integer>>>	reflexivContigList
int	totalNum

Constructor Summary

Constructors

Constructor and Description
ContigReader()

Method Summary

Methods

Modifier and Type	Method and Description
java.lang.String[]	getContigIDArray() not ready yet
java.util.HashMap<java.lang.Integer,java.lang.String>	getContigIDTable() under construction
java.lang.String[]	getPrimerArray() This method returns an Array of String for searching re-assembled contigs
java.util.ArrayList<scala.Tuple2<java.lang.Long,scala.Tuple4<java.lang.Integer,java.lang.Long[],java.lang.Integer,java.lang.Integer>>>	getReflexivContigList() This method returns a List of Reflexible K-mers that represents contigs
void	loadRef(java.lang.String inputFaPath) This method load the genome sequences from the input reference file.
void	setParameter(DefaultParam param) This method sets all correspond parameters for reference data structure construction.

Methods inherited from class java.lang.Object

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

Field Detail

param

public DefaultParam param

contigIDTable

public java.util.HashMap<java.lang.Integer,java.lang.String> contigIDTable

contigPrimerTable

public java.util.HashMap<java.lang.String,java.lang.String> contigPrimerTable

contigIDArray

public java.lang.String[] contigIDArray

primerArray

public java.lang.String[] primerArray

reflexivContigList

public java.util.ArrayList<scala.Tuple2<java.lang.Long,scala.Tuple4<java.lang.Integer,java.lang.Long[],java.lang.Integer,java.lang.Integer>>> reflexivContigList

totalNum

public int totalNum

Constructor Detail

ContigReader

public ContigReader()

Method Detail

setParameter

public void setParameter(DefaultParam param)

This method sets all correspond parameters for reference data structure construction.

Parameters:

param - DefaultParam.

loadRef

public void loadRef(java.lang.String inputFaPath)

This method load the genome sequences from the input reference file.

Parameters:

inputFaPath - the full path of the input file for reference genomes.

getReflexivContigList

public java.util.ArrayList<scala.Tuple2<java.lang.Long,scala.Tuple4<java.lang.Integer,java.lang.Long[],java.lang.Integer,java.lang.Integer>>> getReflexivContigList()

This method returns a List of Reflexible K-mers that represents contigs

Returns:

an ArrayList of Reflexible K-mers

getContigIDTable

public java.util.HashMap<java.lang.Integer,java.lang.String> getContigIDTable()

under construction

Returns:

getContigIDArray

public java.lang.String[] getContigIDArray()

not ready yet

Returns:

getPrimerArray

public java.lang.String[] getPrimerArray()

This method returns an Array of String for searching re-assembled contigs

Returns: