Package org.biojava3.core.sequence.io

Class FastaReaderHelper

java.lang.Object

org.biojava3.core.sequence.io.FastaReaderHelper

public class FastaReaderHelper
extends Object

Author:

Scooter Willis

Constructor Summary

Constructors

Constructor	Description
FastaReaderHelper()

Method Summary

Modifier and Type	Method	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.

Methods inherited from class java.lang.Object

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

Constructor Details

FastaReaderHelper

public FastaReaderHelper()

Method Details

readFastaDNASequence

public static LinkedHashMap<String,DNASequence> readFastaDNASequence(File file,
 boolean lazySequenceLoad)
                                                              throws 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:

Exception

readFastaProteinSequence

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

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

Parameters:

file -

Returns:

Throws:

Exception

readFastaProteinSequence

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

Exception

readFastaDNASequence

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

Read a fasta DNA sequence

Parameters:

inStream -

Returns:

Throws:

Exception

readFastaDNASequence

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

Parameters:

file -

Returns:

Throws:

Exception

main

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

Throws:

Exception