org.biojava.bio.seq.io

Class SeqIOTools

java.lang.Object

org.biojava.bio.seq.io.SeqIOTools

Deprecated.

use org.biojavax.bio.seq.RichSequence.IOTools

public final class SeqIOTools
extends Object

A set of convenience methods for handling common file formats.

Since:

1.1

Author:

Thomas Down, Mark Schreiber, Nimesh Singh, Matthew Pocock, Keith James

Method Summary

Methods

Modifier and Type	Method and Description
static void	biojavaToFile(int fileType, OutputStream os, Object biojava) Deprecated. Converts a Biojava object to the given filetype.
static void	biojavaToFile(String formatName, String alphabetName, OutputStream os, Object biojava) Deprecated. Writes a Biojava SequenceIterator, SequenceDB, Sequence or Aligment to an OutputStream
static Object	fileToBiojava(int fileType, BufferedReader br) Deprecated. Reads a file and returns the corresponding Biojava object.
static Object	fileToBiojava(String formatName, String alphabetName, BufferedReader br) Deprecated. Reads a file with the specified format and alphabet
static SequenceBuilderFactory	formatToFactory(SequenceFormat format, Alphabet alpha) Deprecated. as this essentially duplicates the operation available in the method identifyBuilderFactory.
static FiniteAlphabet	getAlphabet(int identifier) Deprecated. getAlphabet accepts a value which represents a sequence format and returns the relevant FiniteAlphabet object.
static SequenceBuilderFactory	getBuilderFactory(int identifier) Deprecated. getBuilderFactory accepts a value which represents a sequence format and returns the relevant SequenceBuilderFactory object.
static SequenceBuilderFactory	getEmblBuilderFactory() Deprecated. Get a default SequenceBuilderFactory for handling EMBL files.
static SequenceBuilderFactory	getFastaBuilderFactory() Deprecated. Get a default SequenceBuilderFactory for handling FASTA files.
static SequenceBuilderFactory	getGenbankBuilderFactory() Deprecated. Get a default SequenceBuilderFactory for handling GenBank files.
static SequenceBuilderFactory	getGenpeptBuilderFactory() Deprecated. Get a default SequenceBuilderFactory for handling Genpept files.
static SequenceFormat	getSequenceFormat(int identifier) Deprecated. getSequenceFormat accepts a value which represents a sequence format and returns the relevant SequenceFormat object.
static SequenceBuilderFactory	getSwissprotBuilderFactory() Deprecated. Get a default SequenceBuilderFactory for handling Swissprot files.
static int	guessFileType(File seqFile) Deprecated. because there is no standard file naming convention and guessing by file name is inherantly error prone and bad.
static int	identifyFormat(String formatName, String alphabetName) Deprecated. identifyFormat performs a case-insensitive mapping of a pair of common sequence format name (such as 'embl', 'genbank' or 'fasta') and alphabet name (such as 'dna', 'rna', 'protein', 'aa') to an integer.
static SequenceIterator	readEmbl(BufferedReader br) Deprecated. Iterate over the sequences in an EMBL-format stream.
static SequenceIterator	readEmblNucleotide(BufferedReader br) Deprecated. Iterate over the sequences in an EMBL-format stream.
static SequenceIterator	readEmblRNA(BufferedReader br) Deprecated. Iterate over the sequences in an EMBL-format stream, but for RNA.
static SequenceIterator	readFasta(BufferedReader br, SymbolTokenization sTok) Deprecated. Read a fasta file.
static SequenceIterator	readFasta(BufferedReader br, SymbolTokenization sTok, SequenceBuilderFactory seqFactory) Deprecated. Read a fasta file using a custom type of SymbolList.
static SequenceDB	readFasta(InputStream seqFile, Alphabet alpha) Deprecated. Create a sequence database from a fasta file provided as an input stream.
static SequenceIterator	readFastaDNA(BufferedReader br) Deprecated. Iterate over the sequences in an FASTA-format stream of DNA sequences.
static SequenceIterator	readFastaProtein(BufferedReader br) Deprecated. Iterate over the sequences in an FASTA-format stream of Protein sequences.
static SequenceIterator	readFastaRNA(BufferedReader br) Deprecated. Iterate over the sequences in an FASTA-format stream of RNA sequences.
static SequenceIterator	readGenbank(BufferedReader br) Deprecated. Iterate over the sequences in an Genbank-format stream.
static SequenceIterator	readGenbankXml(BufferedReader br) Deprecated. Iterate over the sequences in an GenbankXML-format stream.
static SequenceIterator	readGenpept(BufferedReader br) Deprecated. Iterate over the sequences in an Genpept-format stream.
static SequenceIterator	readSwissprot(BufferedReader br) Deprecated. Iterate over the sequences in an Swissprot-format stream.
static void	writeEmbl(OutputStream os, Sequence seq) Deprecated. Writes a single Sequence to an OutputStream in EMBL format.
static void	writeEmbl(OutputStream os, SequenceIterator in) Deprecated. Writes a stream of Sequences to an OutputStream in EMBL format.
static void	writeFasta(OutputStream os, Sequence seq) Deprecated. Writes a single Sequence to an OutputStream in Fasta format.
static void	writeFasta(OutputStream os, SequenceDB db) Deprecated. Write a sequenceDB to an output stream in fasta format.
static void	writeFasta(OutputStream os, SequenceIterator in) Deprecated. Writes sequences from a SequenceIterator to an OutputStream in Fasta Format.
static void	writeGenbank(OutputStream os, Sequence seq) Deprecated. Writes a single Sequence to an OutputStream in Genbank format.
static void	writeGenbank(OutputStream os, SequenceIterator in) Deprecated. Writes a stream of Sequences to an OutputStream in Genbank format.
static void	writeGenpept(OutputStream os, Sequence seq) Deprecated. Writes a single Sequence to an OutputStream in Genpept format.
static void	writeGenpept(OutputStream os, SequenceIterator in) Deprecated. Writes a stream of Sequences to an OutputStream in Genpept format.
static void	writeSwissprot(OutputStream os, Sequence seq) Deprecated. Writes a single Sequence to an OutputStream in SwissProt format.
static void	writeSwissprot(OutputStream os, SequenceIterator in) Deprecated. Writes a stream of Sequences to an OutputStream in SwissProt format.

Methods inherited from class java.lang.Object

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

Method Detail

getEmblBuilderFactory

public static SequenceBuilderFactory getEmblBuilderFactory()

Deprecated.

Get a default SequenceBuilderFactory for handling EMBL files.

Returns:

a SmartSequenceBuilder.FACTORY

readEmbl

public static SequenceIterator readEmbl(BufferedReader br)

Deprecated.

Iterate over the sequences in an EMBL-format stream.

Parameters:

br - A reader for the EMBL source or file

Returns:

a SequenceIterator that iterates over each Sequence in the file

readEmblRNA

public static SequenceIterator readEmblRNA(BufferedReader br)

Deprecated.

Iterate over the sequences in an EMBL-format stream, but for RNA.

Parameters:

br - A reader for the EMBL source or file

Returns:

a SequenceIterator that iterates over each Sequence in the file

readEmblNucleotide

public static SequenceIterator readEmblNucleotide(BufferedReader br)

Deprecated.

Iterate over the sequences in an EMBL-format stream.

Parameters:

br - A reader for the EMBL source or file

Returns:

a SequenceIterator that iterates over each Sequence in the file

getGenbankBuilderFactory

public static SequenceBuilderFactory getGenbankBuilderFactory()

Deprecated.

Get a default SequenceBuilderFactory for handling GenBank files.

Returns:

a SmartSequenceBuilder.FACTORY

readGenbank

public static SequenceIterator readGenbank(BufferedReader br)

Deprecated.

Iterate over the sequences in an Genbank-format stream.

Parameters:

br - A reader for the Genbank source or file

Returns:

a SequenceIterator that iterates over each Sequence in the file

readGenbankXml

public static SequenceIterator readGenbankXml(BufferedReader br)

Deprecated.

Iterate over the sequences in an GenbankXML-format stream.

Parameters:

br - A reader for the GenbanXML source or file

Returns:

a SequenceIterator that iterates over each Sequence in the file

getGenpeptBuilderFactory

public static SequenceBuilderFactory getGenpeptBuilderFactory()

Deprecated.

Get a default SequenceBuilderFactory for handling Genpept files.

Returns:

a SmartSequenceBuilder.FACTORY

readGenpept

public static SequenceIterator readGenpept(BufferedReader br)

Deprecated.

Iterate over the sequences in an Genpept-format stream.

Parameters:

br - A reader for the Genpept source or file

Returns:

a SequenceIterator that iterates over each Sequence in the file

getSwissprotBuilderFactory

public static SequenceBuilderFactory getSwissprotBuilderFactory()

Deprecated.

Get a default SequenceBuilderFactory for handling Swissprot files.

Returns:

a SmartSequenceBuilder.FACTORY

readSwissprot

public static SequenceIterator readSwissprot(BufferedReader br)

Deprecated.

Iterate over the sequences in an Swissprot-format stream.

Parameters:

br - A reader for the Swissprot source or file

Returns:

a SequenceIterator that iterates over each Sequence in the file

getFastaBuilderFactory

public static SequenceBuilderFactory getFastaBuilderFactory()

Deprecated.

Get a default SequenceBuilderFactory for handling FASTA files.

Returns:

a SmartSequenceBuilder.FACTORY

readFasta

public static SequenceIterator readFasta(BufferedReader br,
                         SymbolTokenization sTok)

Deprecated.

Read a fasta file.

Parameters:

br - the BufferedReader to read data from

sTok - a SymbolTokenization that understands the sequences

Returns:

a SequenceIterator over each sequence in the fasta file

readFasta

public static SequenceIterator readFasta(BufferedReader br,
                         SymbolTokenization sTok,
                         SequenceBuilderFactory seqFactory)

Deprecated.

Read a fasta file using a custom type of SymbolList. For example, use SmartSequenceBuilder.FACTORY to emulate readFasta(BufferedReader, SymbolTokenization) and SmartSequenceBuilder.BIT_PACKED to force all symbols to be encoded using bit-packing.

Parameters:

br - the BufferedReader to read data from

sTok - a SymbolTokenization that understands the sequences

seqFactory - a factory used to build a SymbolList

Returns:

a SequenceIterator that iterates over each Sequence in the file

readFastaDNA

public static SequenceIterator readFastaDNA(BufferedReader br)

Deprecated.

Iterate over the sequences in an FASTA-format stream of DNA sequences.

Parameters:

br - the BufferedReader to read data from

Returns:

a SequenceIterator that iterates over each Sequence in the file

readFastaRNA

public static SequenceIterator readFastaRNA(BufferedReader br)

Deprecated.

Iterate over the sequences in an FASTA-format stream of RNA sequences.

Parameters:

br - the BufferedReader to read data from

Returns:

a SequenceIterator that iterates over each Sequence in the file

readFastaProtein

public static SequenceIterator readFastaProtein(BufferedReader br)

Deprecated.

Iterate over the sequences in an FASTA-format stream of Protein sequences.

Parameters:

br - the BufferedReader to read data from

Returns:

a SequenceIterator that iterates over each Sequence in the file

readFasta

public static SequenceDB readFasta(InputStream seqFile,
                   Alphabet alpha)
                            throws BioException

Deprecated.

Create a sequence database from a fasta file provided as an input stream. Note this somewhat duplicates functionality in the readFastaDNA and readFastaProtein methods but uses a stream rather than a reader and returns a SequenceDB rather than a SequenceIterator. If the returned DB is likely to be large then the above mentioned methods should be used.

Parameters:

seqFile - The file containg the fasta formatted sequences

alpha - The Alphabet of the sequence, ie DNA, RNA etc

Returns:

a SequenceDB containing all the Sequences in the file.

Throws:

BioException - if problems occur during reading of the stream.

Since:

1.2

writeFasta

public static void writeFasta(OutputStream os,
              SequenceDB db)
                       throws IOException

Deprecated.

Write a sequenceDB to an output stream in fasta format.

Parameters:

os - the stream to write the fasta formatted data to.

db - the database of Sequences to write

Throws:

IOException - if there was an error while writing.

Since:

1.2

writeFasta

public static void writeFasta(OutputStream os,
              SequenceIterator in)
                       throws IOException

Deprecated.

Writes sequences from a SequenceIterator to an OutputStream in Fasta Format. This makes for a useful format filter where a StreamReader can be sent to the StreamWriter after formatting.

Parameters:

os - The stream to write fasta formatted data to

in - The source of input Sequences

Throws:

IOException - if there was an error while writing.

Since:

1.2

writeFasta

public static void writeFasta(OutputStream os,
              Sequence seq)
                       throws IOException

Deprecated.

Writes a single Sequence to an OutputStream in Fasta format.

Parameters:

os - the OutputStream.

seq - the Sequence.

Throws:

IOException - if there was an error while writing.

writeEmbl

public static void writeEmbl(OutputStream os,
             SequenceIterator in)
                      throws IOException

Deprecated.

Writes a stream of Sequences to an OutputStream in EMBL format.

Parameters:

os - the OutputStream.

in - a SequenceIterator.

Throws:

IOException - if there was an error while writing.

writeEmbl

public static void writeEmbl(OutputStream os,
             Sequence seq)
                      throws IOException

Deprecated.

Writes a single Sequence to an OutputStream in EMBL format.

Parameters:

os - the OutputStream.

seq - the Sequence.

Throws:

IOException - if there was an error while writing.

writeSwissprot

public static void writeSwissprot(OutputStream os,
                  SequenceIterator in)
                           throws IOException,
                                  BioException

Deprecated.

Writes a stream of Sequences to an OutputStream in SwissProt format.

Parameters:

os - the OutputStream.

in - a SequenceIterator.

Throws:

BioException - if the Sequence cannot be converted to SwissProt format

IOException - if there was an error while writing.

writeSwissprot

public static void writeSwissprot(OutputStream os,
                  Sequence seq)
                           throws IOException,
                                  BioException

Deprecated.

Writes a single Sequence to an OutputStream in SwissProt format.

Parameters:

os - the OutputStream.

seq - the Sequence.

Throws:

BioException - if the Sequence cannot be written to SwissProt format

IOException - if there was an error while writing.

writeGenpept

public static void writeGenpept(OutputStream os,
                SequenceIterator in)
                         throws IOException,
                                BioException

Deprecated.

Writes a stream of Sequences to an OutputStream in Genpept format.

Parameters:

os - the OutputStream.

in - a SequenceIterator.

Throws:

BioException - if the Sequence cannot be written to Genpept format

IOException - if there was an error while writing.

writeGenpept

public static void writeGenpept(OutputStream os,
                Sequence seq)
                         throws IOException,
                                BioException

Deprecated.

Writes a single Sequence to an OutputStream in Genpept format.

Parameters:

os - the OutputStream.

seq - the Sequence.

Throws:

BioException - if the Sequence cannot be written to Genpept format

IOException - if there was an error while writing.

writeGenbank

public static void writeGenbank(OutputStream os,
                SequenceIterator in)
                         throws IOException

Deprecated.

Writes a stream of Sequences to an OutputStream in Genbank format.

Parameters:

os - the OutputStream.

in - a SequenceIterator.

Throws:

IOException - if there was an error while writing.

writeGenbank

public static void writeGenbank(OutputStream os,
                Sequence seq)
                         throws IOException

Deprecated.

Writes a single Sequence to an OutputStream in Genbank format.

Parameters:

os - the OutputStream.

seq - the Sequence.

Throws:

IOException - if there was an error while writing.

identifyFormat

public static int identifyFormat(String formatName,
                 String alphabetName)

Deprecated.

identifyFormat performs a case-insensitive mapping of a pair of common sequence format name (such as 'embl', 'genbank' or 'fasta') and alphabet name (such as 'dna', 'rna', 'protein', 'aa') to an integer. The value returned will be one of the public static final fields in SeqIOConstants, or a bitwise-or combination of them. The method will reject known illegal combinations of format and alphabet (such as swissprot + dna) by throwing an IllegalArgumentException. It will return the SeqIOConstants.UNKNOWN value when either format or alphabet are unknown.

Parameters:

formatName - a String.

alphabetName - a String.

Returns:

an int.

getSequenceFormat

public static SequenceFormat getSequenceFormat(int identifier)
                                        throws BioException

Deprecated.

getSequenceFormat accepts a value which represents a sequence format and returns the relevant SequenceFormat object.

Parameters:

identifier - an int which represents a binary value with bits set according to the scheme described in SeqIOConstants.

Returns:

a SequenceFormat.

Throws:

BioException - if an error occurs.

getBuilderFactory

public static SequenceBuilderFactory getBuilderFactory(int identifier)
                                                throws BioException

Deprecated.

getBuilderFactory accepts a value which represents a sequence format and returns the relevant SequenceBuilderFactory object.

Parameters:

identifier - an int which represents a binary value with bits set according to the scheme described in SeqIOConstants.

Returns:

a SequenceBuilderFactory.

Throws:

BioException - if an error occurs.

getAlphabet

public static FiniteAlphabet getAlphabet(int identifier)
                                  throws BioException

Deprecated.

getAlphabet accepts a value which represents a sequence format and returns the relevant FiniteAlphabet object.

Parameters:

identifier - an int which represents a binary value with bits set according to the scheme described in SeqIOConstants.

Returns:

a FiniteAlphabet.

Throws:

BioException - if an error occurs.

guessFileType

public static int guessFileType(File seqFile)
                         throws IOException,
                                FileNotFoundException

Deprecated. because there is no standard file naming convention and guessing by file name is inherantly error prone and bad.

Attempts to guess the filetype of a file given the name. For use with the functions below that take an int fileType as a parameter. EMBL and Genbank files are assumed to contain DNA sequence.

Parameters:

seqFile - the File to read from.

Returns:

a value that describes the file type.

Throws:

IOException - if seqFile cannot be read

FileNotFoundException - if seqFile cannot be found

formatToFactory

public static SequenceBuilderFactory formatToFactory(SequenceFormat format,
                                     Alphabet alpha)
                                              throws BioException

Deprecated. as this essentially duplicates the operation available in the method identifyBuilderFactory.

Attempts to retrieve the most appropriate SequenceBuilder object for some combination of Alphabet and SequenceFormat

Parameters:

format - currently supports FastaFormat, GenbankFormat, EmblLikeFormat

alpha - currently only supports the DNA and Protein alphabets

Returns:

the SequenceBuilderFactory

Throws:

BioException - if the combination of alpha and format is unrecognized.

fileToBiojava

public static Object fileToBiojava(String formatName,
                   String alphabetName,
                   BufferedReader br)
                            throws BioException

Deprecated.

Reads a file with the specified format and alphabet

Parameters:

formatName - the name of the format eg genbank or swissprot (case insensitive)

alphabetName - the name of the alphabet eg dna or rna or protein (case insensitive)

br - a BufferedReader for the input

Returns:

either an Alignment object or a SequenceIterator (depending on the format read)

Throws:

BioException - if an error occurs while reading or a unrecognized format, alphabet combination is used (eg swissprot and DNA).

Since:

1.3

fileToBiojava

public static Object fileToBiojava(int fileType,
                   BufferedReader br)
                            throws BioException

Deprecated.

Reads a file and returns the corresponding Biojava object. You need to cast it as an Alignment or a SequenceIterator as appropriate.

Parameters:

fileType - a value that describes the file type

br - the reader for the input

Returns:

either a SequenceIterator if the file type is a sequence file, or a Alignment if the file is a sequence alignment.

Throws:

BioException - if the file cannot be parsed

biojavaToFile

public static void biojavaToFile(String formatName,
                 String alphabetName,
                 OutputStream os,
                 Object biojava)
                          throws BioException,
                                 IOException,
                                 IllegalSymbolException

Deprecated.

Writes a Biojava SequenceIterator, SequenceDB, Sequence or Aligment to an OutputStream

Parameters:

formatName - eg fasta, GenBank (case insensitive)

alphabetName - eg DNA, RNA (case insensititve)

os - where to write to

biojava - the object to write

Throws:

BioException - problems getting data from the biojava object.

IOException - if there are IO problems

IllegalSymbolException - a Symbol cannot be parsed

biojavaToFile

public static void biojavaToFile(int fileType,
                 OutputStream os,
                 Object biojava)
                          throws BioException,
                                 IOException,
                                 IllegalSymbolException

Deprecated.

Converts a Biojava object to the given filetype.

Parameters:

fileType - a value that describes the type of sequence file

os - the stream to write the formatted results to

biojava - a SequenceIterator, SequenceDB, Sequence, or Alignment

Throws:

BioException - if biojava cannot be converted to that format.

IOException - if the output cannot be written to os

IllegalSymbolException - if biojava contains a Symbol that cannot be understood by the parser.