uni.bielefeld.cmg.reflexiv.io

Class ReadFasta

java.lang.Object

uni.bielefeld.cmg.reflexiv.io.ReadFasta

All Implemented Interfaces:

FileManager, InputFileManager

public class ReadFasta
extends java.lang.Object
implements InputFileManager

Returns an object for buffering input fasta files. This class is used for loading reference genomes located in local file system.

See Also:

Field Summary

Fields

Modifier and Type	Field and Description
java.io.BufferedReader	fasta

Constructor Summary

Constructors

Constructor and Description
ReadFasta() A constructor that construct an object of ReadFasta class.

Method Summary

Methods

Modifier and Type	Method and Description
void	bufferInputFile(java.lang.String inputFile) This method sets up an input fasta file stream based on an input file path.
void	bufferOutputFile(java.lang.String outputFile) This method sets the full path of an output file.
void	checkFile(java.lang.String cFile) This method checks the path of an input fasta file.
void	createInputFastaStream(java.lang.String inputFastaString) This method sets up an input file stream for an input fasta file.
java.io.BufferedReader	getFastaBufferedReader() This method sets the BufferedReader.

Methods inherited from class java.lang.Object

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

Field Detail

fasta

public java.io.BufferedReader fasta

Constructor Detail

ReadFasta

public ReadFasta()

A constructor that construct an object of ReadFasta class. No constructor option needed.

Method Detail

createInputFastaStream

public void createInputFastaStream(java.lang.String inputFastaString)

This method sets up an input file stream for an input fasta file.

Parameters:

inputFastaString - full path of an input fasta file.

checkFile

public void checkFile(java.lang.String cFile)

This method checks the path of an input fasta file. It classifies the location (via URL) of an input file.

Parameters:

cFile - the full path of an input fasta file.

getFastaBufferedReader

public java.io.BufferedReader getFastaBufferedReader()

This method sets the BufferedReader.

Returns:

Java BufferedReader.

bufferInputFile

public void bufferInputFile(java.lang.String inputFile)

This method sets up an input fasta file stream based on an input file path.

Specified by:

bufferInputFile in interface FileManager

Specified by:

bufferInputFile in interface InputFileManager

Parameters:

inputFile - the full path of an input file.

bufferOutputFile

public void bufferOutputFile(java.lang.String outputFile)

This method sets the full path of an output file.

Specified by:

bufferOutputFile in interface FileManager

Specified by:

bufferOutputFile in interface InputFileManager

Parameters:

outputFile - the full path of an output file.