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## 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
`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 `Sequence`s 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.

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