org.biojava3.core.sequence.io

Class FastaReaderHelper

java.lang.Object

org.biojava3.core.sequence.io.FastaReaderHelper

public class FastaReaderHelper
extends java.lang.Object

Author:

Scooter Willis

Constructor Summary

Constructors

Constructor and Description
FastaReaderHelper()

Method Summary

Methods

Modifier and Type	Method and Description
static void	main(java.lang.String[] args)
static java.util.LinkedHashMap<java.lang.String,DNASequence>	readFastaDNASequence(java.io.File file)
static java.util.LinkedHashMap<java.lang.String,DNASequence>	readFastaDNASequence(java.io.File file, boolean lazySequenceLoad) Selecting lazySequenceLoad=true will parse the FASTA file and figure out the accessionid and offsets and return sequence objects that can in the future read the sequence from the disk.
static java.util.LinkedHashMap<java.lang.String,DNASequence>	readFastaDNASequence(java.io.InputStream inStream) Read a fasta DNA sequence
static java.util.LinkedHashMap<java.lang.String,ProteinSequence>	readFastaProteinSequence(java.io.File file) Read a fasta file containing amino acids with setup that would handle most cases.
static java.util.LinkedHashMap<java.lang.String,ProteinSequence>	readFastaProteinSequence(java.io.InputStream inStream) Read a fasta file containing amino acids with setup that would handle most cases.

Methods inherited from class java.lang.Object

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

Constructor Detail

FastaReaderHelper

public FastaReaderHelper()

Method Detail

readFastaDNASequence

public static java.util.LinkedHashMap<java.lang.String,DNASequence> readFastaDNASequence(java.io.File file,
                                                                         boolean lazySequenceLoad)
                                                                                  throws java.lang.Exception

Selecting lazySequenceLoad=true will parse the FASTA file and figure out the accessionid and offsets and return sequence objects that can in the future read the sequence from the disk. This allows the loading of large fasta files where you are only interested in one sequence based on accession id.

Parameters:

file -

lazySequenceLoad -

Returns:

Throws:

java.lang.Exception

readFastaProteinSequence

public static java.util.LinkedHashMap<java.lang.String,ProteinSequence> readFastaProteinSequence(java.io.File file)
                                                                                          throws java.lang.Exception

Read a fasta file containing amino acids with setup that would handle most cases.

Parameters:

file -

Returns:

Throws:

java.lang.Exception

readFastaProteinSequence

public static java.util.LinkedHashMap<java.lang.String,ProteinSequence> readFastaProteinSequence(java.io.InputStream inStream)
                                                                                          throws java.lang.Exception

Read a fasta file containing amino acids with setup that would handle most cases. User is responsible for closing InputStream because you opened it

Parameters:

inStream -

Returns:

Throws:

java.lang.Exception

readFastaDNASequence

public static java.util.LinkedHashMap<java.lang.String,DNASequence> readFastaDNASequence(java.io.InputStream inStream)
                                                                                  throws java.lang.Exception

Read a fasta DNA sequence

Parameters:

inStream -

Returns:

Throws:

java.lang.Exception

readFastaDNASequence

public static java.util.LinkedHashMap<java.lang.String,DNASequence> readFastaDNASequence(java.io.File file)
                                                                                  throws java.lang.Exception

Parameters:

file -

Returns:

Throws:

java.lang.Exception

main

public static void main(java.lang.String[] args)
                 throws java.lang.Exception

Throws:

java.lang.Exception