org.biojava.nbio.core.sequence.io

Class FastaReaderHelper

java.lang.Object

org.biojava.nbio.core.sequence.io.FastaReaderHelper

public class FastaReaderHelper
extends Object

Author:

Scooter Willis

Constructor Summary

Constructors

Constructor and Description
FastaReaderHelper()

Method Summary

Modifier and Type	Method and Description
static void	main(String[] args)
static LinkedHashMap<String,DNASequence>	readFastaDNASequence(File file)
static LinkedHashMap<String,DNASequence>	readFastaDNASequence(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 LinkedHashMap<String,DNASequence>	readFastaDNASequence(InputStream inStream) Read a fasta DNA sequence
static LinkedHashMap<String,ProteinSequence>	readFastaProteinSequence(File file) Read a fasta file containing amino acids with setup that would handle most cases.
static LinkedHashMap<String,ProteinSequence>	readFastaProteinSequence(InputStream inStream) Read a fasta file containing amino acids with setup that would handle most cases.
static LinkedHashMap<String,RNASequence>	readFastaRNASequence(File file)
static LinkedHashMap<String,RNASequence>	readFastaRNASequence(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 LinkedHashMap<String,RNASequence>	readFastaRNASequence(InputStream inStream) Read a fasta RNA sequence

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 LinkedHashMap<String,DNASequence> readFastaDNASequence(File file,
                                                                     boolean lazySequenceLoad)
                                                              throws IOException

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:

IOException

readFastaRNASequence

public static LinkedHashMap<String,RNASequence> readFastaRNASequence(File file,
                                                                     boolean lazySequenceLoad)
                                                              throws IOException

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:

IOException

readFastaProteinSequence

public static LinkedHashMap<String,ProteinSequence> readFastaProteinSequence(File file)
                                                                      throws IOException

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

Parameters:

file -

Returns:

Throws:

IOException

readFastaProteinSequence

public static LinkedHashMap<String,ProteinSequence> readFastaProteinSequence(InputStream inStream)
                                                                      throws IOException

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:

IOException

readFastaDNASequence

public static LinkedHashMap<String,DNASequence> readFastaDNASequence(InputStream inStream)
                                                              throws IOException

Read a fasta DNA sequence

Parameters:

inStream -

Returns:

Throws:

IOException

readFastaDNASequence

public static LinkedHashMap<String,DNASequence> readFastaDNASequence(File file)
                                                              throws IOException

Parameters:

file -

Returns:

Throws:

IOException

readFastaRNASequence

public static LinkedHashMap<String,RNASequence> readFastaRNASequence(InputStream inStream)
                                                              throws IOException

Read a fasta RNA sequence

Parameters:

inStream -

Returns:

Throws:

IOException

readFastaRNASequence

public static LinkedHashMap<String,RNASequence> readFastaRNASequence(File file)
                                                              throws IOException

Parameters:

file -

Returns:

Throws:

IOException

main

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

Throws:

Exception