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## org.biojavax.bio.seq
Class RichSequence.IOTools

    java.lang.Object
      org.biojavax.bio.seq.RichSequence.IOTools

Enclosing interface:
  RichSequence

    public static final class RichSequence.IOTools

extends Object

A set of convenience methods for handling common file formats.

Since:
  1.5
Author:
  Mark Schreiber, Richard Holland

Nested Class Summary
`static class` | `RichSequence.IOTools.SingleRichSeqIterator` Used to iterate over a single rich sequence

Method Summary
`static SymbolTokenization` | `getDNAParser()` Creates a DNA symbol tokenizer.
`static SymbolTokenization` | `getNucleotideParser()` Creates a nucleotide symbol tokenizer.
`static SymbolTokenization` | `getProteinParser()` Creates a protein symbol tokenizer.
`static SymbolTokenization` | `getRNAParser()` Creates a RNA symbol tokenizer.
`static RichSequenceIterator` | `readEMBL(BufferedReader br, SymbolTokenization sTok, RichSequenceBuilderFactory seqFactory, Namespace ns)` Read a EMBL file using a custom type of SymbolList.
`static RichSequenceIterator` | `readEMBLDNA(BufferedReader br, Namespace ns)` Iterate over the sequences in an EMBL-format stream of DNA sequences.
`static RichSequenceIterator` | `readEMBLProtein(BufferedReader br, Namespace ns)` Iterate over the sequences in an EMBL-format stream of Protein sequences.
`static RichSequenceIterator` | `readEMBLRNA(BufferedReader br, Namespace ns)` Iterate over the sequences in an EMBL-format stream of RNA sequences.
`static RichSequenceIterator` | `readEMBLxml(BufferedReader br, SymbolTokenization sTok, RichSequenceBuilderFactory seqFactory, Namespace ns)` Read a EMBLxml file using a custom type of SymbolList.
`static RichSequenceIterator` | `readEMBLxmlDNA(BufferedReader br, Namespace ns)` Iterate over the sequences in an EMBLxml-format stream of DNA sequences.
`static RichSequenceIterator` | `readEMBLxmlProtein(BufferedReader br, Namespace ns)` Iterate over the sequences in an EMBLxml-format stream of Protein sequences.
`static RichSequenceIterator` | `readEMBLxmlRNA(BufferedReader br, Namespace ns)` Iterate over the sequences in an EMBLxml-format stream of RNA sequences.
`static RichSequenceIterator` | `readFasta(BufferedReader br, SymbolTokenization sTok, Namespace ns)` Read a fasta file.
`static RichSequenceIterator` | `readFasta(BufferedReader br, SymbolTokenization sTok, RichSequenceBuilderFactory seqFactory, Namespace ns)` Read a fasta file building a custom type of `RichSequence` .
`static RichSequenceIterator` | `readFastaDNA(BufferedReader br, Namespace ns)` Iterate over the sequences in an FASTA-format stream of DNA sequences.
`static RichSequenceIterator` | `readFastaProtein(BufferedReader br, Namespace ns)` Iterate over the sequences in an FASTA-format stream of Protein sequences.
`static RichSequenceIterator` | `readFastaRNA(BufferedReader br, Namespace ns)` Iterate over the sequences in an FASTA-format stream of RNA sequences.
`static RichSequenceIterator` | `readFile(File file, Namespace ns)` Guess which format a file is then attempt to read it.
`static RichSequenceIterator` | `readFile(File file, RichSequenceBuilderFactory seqFactory, Namespace ns)` Guess which format a file is then attempt to read it.
`static RichSequenceIterator` | `readGenbank(BufferedReader br, SymbolTokenization sTok, RichSequenceBuilderFactory seqFactory, Namespace ns)` Read a GenBank file using a custom type of SymbolList.
`static RichSequenceIterator` | `readGenbankDNA(BufferedReader br, Namespace ns)` Iterate over the sequences in an GenBank-format stream of DNA sequences.
`static RichSequenceIterator` | `readGenbankProtein(BufferedReader br, Namespace ns)` Iterate over the sequences in an GenBank-format stream of Protein sequences.
`static RichSequenceIterator` | `readGenbankRNA(BufferedReader br, Namespace ns)` Iterate over the sequences in an GenBank-format stream of RNA sequences.
`static RichSequenceIterator` | `readHashedFastaDNA(BufferedInputStream is, Namespace ns)` Iterate over the sequences in an FASTA-format stream of DNA sequences.
`static RichSequenceIterator` | `readINSDseq(BufferedReader br, SymbolTokenization sTok, RichSequenceBuilderFactory seqFactory, Namespace ns)` Read a INSDseq file using a custom type of SymbolList.
`static RichSequenceIterator` | `readINSDseqDNA(BufferedReader br, Namespace ns)` Iterate over the sequences in an INSDseq-format stream of DNA sequences.
`static RichSequenceIterator` | `readINSDseqProtein(BufferedReader br, Namespace ns)` Iterate over the sequences in an INSDseq-format stream of Protein sequences.
`static RichSequenceIterator` | `readINSDseqRNA(BufferedReader br, Namespace ns)` Iterate over the sequences in an INSDseq-format stream of RNA sequences.
`static RichSequenceIterator` | `readStream(BufferedInputStream stream, Namespace ns)` Guess which format a stream is then attempt to read it.
`static RichSequenceIterator` | `readStream(BufferedInputStream stream, RichSequenceBuilderFactory seqFactory, Namespace ns)` Guess which format a stream is then attempt to read it.
`static RichSequenceIterator` | `readUniProt(BufferedReader br, Namespace ns)` Iterate over the sequences in an UniProt-format stream of RNA sequences.
`static RichSequenceIterator` | `readUniProt(BufferedReader br, SymbolTokenization sTok, RichSequenceBuilderFactory seqFactory, Namespace ns)` Read a UniProt file using a custom type of SymbolList.
`static RichSequenceIterator` | `readUniProtXML(BufferedReader br, Namespace ns)` Iterate over the sequences in an UniProt XML-format stream of RNA sequences.
`static RichSequenceIterator` | `readUniProtXML(BufferedReader br, SymbolTokenization sTok, RichSequenceBuilderFactory seqFactory, Namespace ns)` Read a UniProt XML file using a custom type of SymbolList.
`static void` | `registerFormat(Class formatClass)` Register a new format with IOTools for auto-guessing.
`static void` | `writeEMBL(OutputStream os, SequenceIterator in, Namespace ns)` Writes sequences from a `SequenceIterator` to an `OutputStream` in EMBL Format.
`static void` | `writeEMBL(OutputStream os, Sequence seq, Namespace ns)` Writes a single `Sequence` to an `OutputStream` in EMBL format.
`static void` | `writeEMBLxml(OutputStream os, SequenceIterator in, Namespace ns)` Writes sequences from a `SequenceIterator` to an `OutputStream` in EMBLxml Format.
`static void` | `writeEMBLxml(OutputStream os, Sequence seq, Namespace ns)` Writes a single `Sequence` to an `OutputStream` in EMBLxml format.
`static void` | `writeFasta(OutputStream os, SequenceIterator in, Namespace ns)` Writes `Sequence`s from a `SequenceIterator` to an `OutputStream` in Fasta Format.
`static void` | `writeFasta(OutputStream os, SequenceIterator in, Namespace ns, FastaHeader header)` Writes `Sequence`s from a `SequenceIterator` to an `OutputStream` in Fasta Format.
`static void` | `writeFasta(OutputStream os, Sequence seq, Namespace ns)` Writes a single `Sequence` to an `OutputStream` in Fasta format.
`static void` | `writeFasta(OutputStream os, Sequence seq, Namespace ns, FastaHeader header)` Writes a single `Sequence` to an `OutputStream` in Fasta format.
`static void` | `writeGenbank(OutputStream os, SequenceIterator in, Namespace ns)` Writes sequences from a `SequenceIterator` to an `OutputStream` in GenBank Format.
`static void` | `writeGenbank(OutputStream os, Sequence seq, Namespace ns)` Writes a single `Sequence` to an `OutputStream` in GenBank format.
`static void` | `writeINSDseq(OutputStream os, SequenceIterator in, Namespace ns)` Writes sequences from a `SequenceIterator` to an `OutputStream` in INSDseq Format.
`static void` | `writeINSDseq(OutputStream os, Sequence seq, Namespace ns)` Writes a single `Sequence` to an `OutputStream` in INSDseq format.
`static void` | `writeUniProt(OutputStream os, SequenceIterator in, Namespace ns)` Writes sequences from a `SequenceIterator` to an `OutputStream` in UniProt Format.
`static void` | `writeUniProt(OutputStream os, Sequence seq, Namespace ns)` Writes a single `Sequence` to an `OutputStream` in UniProt format.
`static void` | `writeUniProtXML(OutputStream os, SequenceIterator in, Namespace ns)` Writes sequences from a `SequenceIterator` to an `OutputStream` in UniProt XML Format.
`static void` | `writeUniProtXML(OutputStream os, Sequence seq, Namespace ns)` Writes a single `Sequence` to an `OutputStream` in UniProt XML format.

Methods inherited from class java.lang.Object
`clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait`

Method Detail

### registerFormat

    public static void registerFormat(Class formatClass)

  Register a new format with IOTools for auto-guessing.

  Parameters:
    `formatClass` - the `RichSequenceFormat` object to register.

### readStream

    public static RichSequenceIterator readStream(BufferedInputStream stream,
                                                  RichSequenceBuilderFactory seqFactory,
                                                  Namespace ns)
                                           throws IOException

  Guess which format a stream is then attempt to read it.

  Parameters:
    `stream` - the `BufferedInputStream` to attempt to read.
    `seqFactory` - a factory used to build a `RichSequence`
    `ns` - a `Namespace` to load the sequences into. Null implies that it should use the namespace specified in the file. If no namespace is specified in the file, then `RichObjectFactory.getDefaultNamespace()` is used.
  Returns:
    a `RichSequenceIterator` over each sequence in the file
  Throws:
    `IOException` - in case the stream is unrecognisable or problems occur in reading it.

### readStream

    public static RichSequenceIterator readStream(BufferedInputStream stream,
                                                  Namespace ns)
                                           throws IOException

  Guess which format a stream is then attempt to read it.

  Parameters:
    `stream` - the `BufferedInputStream` to attempt to read.
    `ns` - a `Namespace` to load the sequences into. Null implies that it should use the namespace specified in the file. If no namespace is specified in the file, then `RichObjectFactory.getDefaultNamespace()` is used.
  Returns:
    a `RichSequenceIterator` over each sequence in the file
  Throws:
    `IOException` - If the file cannot be read.

### readFile

    public static RichSequenceIterator readFile(File file,
                                                RichSequenceBuilderFactory seqFactory,
                                                Namespace ns)
                                         throws IOException

  Guess which format a file is then attempt to read it.

  Parameters:
    `file` - the `File` to attempt to read.
    `seqFactory` - a factory used to build a `RichSequence`
    `ns` - a `Namespace` to load the sequences into. Null implies that it should use the namespace specified in the file. If no namespace is specified in the file, then `RichObjectFactory.getDefaultNamespace()` is used.
  Returns:
    a `RichSequenceIterator` over each sequence in the file
  Throws:
    `IOException` - in case the file is unrecognisable or problems occur in reading it.

### readFile

    public static RichSequenceIterator readFile(File file,
                                                Namespace ns)
                                         throws IOException

  Guess which format a file is then attempt to read it.

  Parameters:
    `file` - the `File` to attempt to read.
    `ns` - a `Namespace` to load the sequences into. Null implies that it should use the namespace specified in the file. If no namespace is specified in the file, then `RichObjectFactory.getDefaultNamespace()` is used.
  Returns:
    a `RichSequenceIterator` over each sequence in the file
  Throws:
    `IOException` - If the file cannot be read.

### readFasta

    public static RichSequenceIterator readFasta(BufferedReader br,
                                                 SymbolTokenization sTok,
                                                 Namespace ns)

  Read a fasta file.

  Parameters:
    `br` - the `BufferedReader`to read data from``
    `sTok` - a `SymbolTokenization` that understands the sequences
    `ns` - a `Namespace` to load the sequences into. Null implies that it should use the namespace specified in the file. If no namespace is specified in the file, then `RichObjectFactory.getDefaultNamespace()` is used.
  Returns:
    a `RichSequenceIterator` over each sequence in the fasta file

### readFasta

    public static RichSequenceIterator readFasta(BufferedReader br,
                                                 SymbolTokenization sTok,
                                                 RichSequenceBuilderFactory seqFactory,
                                                 Namespace ns)

  Read a fasta file building a custom type of `RichSequence` . For example, use `RichSequenceBuilderFactory.FACTORY` to emulate `readFasta(BufferedReader, SymbolTokenization)` and `RichSequenceBuilderFactory.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 `RichSequence`
    `ns` - a `Namespace` to load the sequences into. Null implies that it should use the namespace specified in the file. If no namespace is specified in the file, then `RichObjectFactory.getDefaultNamespace()` is used.
  Returns:
    a `RichSequenceIterator` over each sequence in the fasta file

### readFastaDNA

    public static RichSequenceIterator readFastaDNA(BufferedReader br,
                                                    Namespace ns)

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

  Parameters:
    `br` - the `BufferedReader` to read data from
    `ns` - a `Namespace` to load the sequences into. Null implies that it should use the namespace specified in the file. If no namespace is specified in the file, then `RichObjectFactory.getDefaultNamespace()` is used.
  Returns:
    a `RichSequenceIterator` over each sequence in the fasta file
  See Also:
    `for a speeded up version that can access sequences from memory.`

### readHashedFastaDNA

    public static RichSequenceIterator readHashedFastaDNA(BufferedInputStream is,
                                                          Namespace ns)
                                                   throws BioException

  Iterate over the sequences in an FASTA-format stream of DNA sequences. In contrast to readFastaDNA, this provides a speeded up implementation where all sequences are accessed from memory.

  Parameters:
    `is` - the `BufferedInputStream` to read data from
    `ns` - a `Namespace` to load the sequences into. Null implies that it should use the namespace specified in the file. If no namespace is specified in the file, then `RichObjectFactory.getDefaultNamespace()` is used.
  Returns:
    a `RichSequenceIterator` over each sequence in the fasta file
  Throws:
    `BioException` - if somethings goes wrong while reading the file.
  See Also:
    `readFastaDNA(java.io.BufferedReader, org.biojavax.Namespace)`

### readFastaRNA

    public static RichSequenceIterator readFastaRNA(BufferedReader br,
                                                    Namespace ns)

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

  Parameters:
    `br` - the `BufferedReader` to read data from
    `ns` - a `Namespace` to load the sequences into. Null implies that it should use the namespace specified in the file. If no namespace is specified in the file, then `RichObjectFactory.getDefaultNamespace()` is used.
  Returns:
    a `RichSequenceIterator` over each sequence in the fasta file

### readFastaProtein

    public static RichSequenceIterator readFastaProtein(BufferedReader br,
                                                        Namespace ns)

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

  Parameters:
    `br` - the `BufferedReader` to read data from
    `ns` - a `Namespace` to load the sequences into. Null implies that it should use the namespace specified in the file. If no namespace is specified in the file, then `RichObjectFactory.getDefaultNamespace()` is used.
  Returns:
    a `RichSequenceIterator` over each sequence in the fasta file

### readGenbank

    public static RichSequenceIterator readGenbank(BufferedReader br,
                                                   SymbolTokenization sTok,
                                                   RichSequenceBuilderFactory seqFactory,
                                                   Namespace ns)

  Read a GenBank file using a custom type of SymbolList. For example, use RichSequenceBuilderFactory.FACTORY to emulate readFasta(BufferedReader, SymbolTokenization) and RichSequenceBuilderFactory.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`
    `ns` - a `Namespace` to load the sequences into. Null implies that it should use the namespace specified in the file. If no namespace is specified in the file, then `RichObjectFactory.getDefaultNamespace()` is used.
  Returns:
    a `RichSequenceIterator` over each sequence in the fasta file

### readGenbankDNA

    public static RichSequenceIterator readGenbankDNA(BufferedReader br,
                                                      Namespace ns)

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

  Parameters:
    `br` - the `BufferedReader` to read data from
    `ns` - a `Namespace` to load the sequences into. Null implies that it should use the namespace specified in the file. If no namespace is specified in the file, then `RichObjectFactory.getDefaultNamespace()` is used.
  Returns:
    a `RichSequenceIterator` over each sequence in the fasta file

### readGenbankRNA

    public static RichSequenceIterator readGenbankRNA(BufferedReader br,
                                                      Namespace ns)

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

  Parameters:
    `br` - the `BufferedReader` to read data from
    `ns` - a `Namespace` to load the sequences into. Null implies that it should use the namespace specified in the file. If no namespace is specified in the file, then `RichObjectFactory.getDefaultNamespace()` is used.
  Returns:
    a `RichSequenceIterator` over each sequence in the fasta file

### readGenbankProtein

    public static RichSequenceIterator readGenbankProtein(BufferedReader br,
                                                          Namespace ns)

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

  Parameters:
    `br` - the `BufferedReader` to read data from
    `ns` - a `Namespace` to load the sequences into. Null implies that it should use the namespace specified in the file. If no namespace is specified in the file, then `RichObjectFactory.getDefaultNamespace()` is used.
  Returns:
    a `RichSequenceIterator` over each sequence in the fasta file

### readINSDseq

    public static RichSequenceIterator readINSDseq(BufferedReader br,
                                                   SymbolTokenization sTok,
                                                   RichSequenceBuilderFactory seqFactory,
                                                   Namespace ns)

  Read a INSDseq file using a custom type of SymbolList. For example, use RichSequenceBuilderFactory.FACTORY to emulate readFasta(BufferedReader, SymbolTokenization) and RichSequenceBuilderFactory.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`
    `ns` - a `Namespace` to load the sequences into. Null implies that it should use the namespace specified in the file. If no namespace is specified in the file, then `RichObjectFactory.getDefaultNamespace()` is used.
  Returns:
    a `RichSequenceIterator` over each sequence in the fasta file

### readINSDseqDNA

    public static RichSequenceIterator readINSDseqDNA(BufferedReader br,
                                                      Namespace ns)

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

  Parameters:
    `br` - the `BufferedReader` to read data from
    `ns` - a `Namespace` to load the sequences into. Null implies that it should use the namespace specified in the file. If no namespace is specified in the file, then `RichObjectFactory.getDefaultNamespace()` is used.
  Returns:
    a `RichSequenceIterator` over each sequence in the fasta file

### readINSDseqRNA

    public static RichSequenceIterator readINSDseqRNA(BufferedReader br,
                                                      Namespace ns)

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

  Parameters:
    `br` - the `BufferedReader` to read data from
    `ns` - a `Namespace` to load the sequences into. Null implies that it should use the namespace specified in the file. If no namespace is specified in the file, then `RichObjectFactory.getDefaultNamespace()` is used.
  Returns:
    a `RichSequenceIterator` over each sequence in the fasta file

### readINSDseqProtein

    public static RichSequenceIterator readINSDseqProtein(BufferedReader br,
                                                          Namespace ns)

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

  Parameters:
    `br` - the `BufferedReader` to read data from
    `ns` - a `Namespace` to load the sequences into. Null implies that it should use the namespace specified in the file. If no namespace is specified in the file, then `RichObjectFactory.getDefaultNamespace()` is used.
  Returns:
    a `RichSequenceIterator` over each sequence in the fasta file

### readEMBLxml

    public static RichSequenceIterator readEMBLxml(BufferedReader br,
                                                   SymbolTokenization sTok,
                                                   RichSequenceBuilderFactory seqFactory,
                                                   Namespace ns)

  Read a EMBLxml file using a custom type of SymbolList. For example, use RichSequenceBuilderFactory.FACTORY to emulate readFasta(BufferedReader, SymbolTokenization) and RichSequenceBuilderFactory.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`
    `ns` - a `Namespace` to load the sequences into. Null implies that it should use the namespace specified in the file. If no namespace is specified in the file, then `RichObjectFactory.getDefaultNamespace()` is used.
  Returns:
    a `RichSequenceIterator` over each sequence in the fasta file

### readEMBLxmlDNA

    public static RichSequenceIterator readEMBLxmlDNA(BufferedReader br,
                                                      Namespace ns)

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

  Parameters:
    `br` - the `BufferedReader` to read data from
    `ns` - a `Namespace` to load the sequences into. Null implies that it should use the namespace specified in the file. If no namespace is specified in the file, then `RichObjectFactory.getDefaultNamespace()` is used.
  Returns:
    a `RichSequenceIterator` over each sequence in the fasta file

### readEMBLxmlRNA

    public static RichSequenceIterator readEMBLxmlRNA(BufferedReader br,
                                                      Namespace ns)

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

  Parameters:
    `br` - the `BufferedReader` to read data from
    `ns` - a `Namespace` to load the sequences into. Null implies that it should use the namespace specified in the file. If no namespace is specified in the file, then `RichObjectFactory.getDefaultNamespace()` is used.
  Returns:
    a `RichSequenceIterator` over each sequence in the fasta file

### readEMBLxmlProtein

    public static RichSequenceIterator readEMBLxmlProtein(BufferedReader br,
                                                          Namespace ns)

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

  Parameters:
    `br` - the `BufferedReader` to read data from
    `ns` - a `Namespace` to load the sequences into. Null implies that it should use the namespace specified in the file. If no namespace is specified in the file, then `RichObjectFactory.getDefaultNamespace()` is used.
  Returns:
    a `RichSequenceIterator` over each sequence in the fasta file

### readEMBL

    public static RichSequenceIterator readEMBL(BufferedReader br,
                                                SymbolTokenization sTok,
                                                RichSequenceBuilderFactory seqFactory,
                                                Namespace ns)

  Read a EMBL file using a custom type of SymbolList. For example, use RichSequenceBuilderFactory.FACTORY to emulate readFasta(BufferedReader, SymbolTokenization) and RichSequenceBuilderFactory.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`
    `ns` - a `Namespace` to load the sequences into. Null implies that it should use the namespace specified in the file. If no namespace is specified in the file, then `RichObjectFactory.getDefaultNamespace()` is used.
  Returns:
    a `RichSequenceIterator` over each sequence in the fasta file

### readEMBLDNA

    public static RichSequenceIterator readEMBLDNA(BufferedReader br,
                                                   Namespace ns)

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

  Parameters:
    `br` - the `BufferedReader` to read data from
    `ns` - a `Namespace` to load the sequences into. Null implies that it should use the namespace specified in the file. If no namespace is specified in the file, then `RichObjectFactory.getDefaultNamespace()` is used.
  Returns:
    a `RichSequenceIterator` over each sequence in the fasta file

### readEMBLRNA

    public static RichSequenceIterator readEMBLRNA(BufferedReader br,
                                                   Namespace ns)

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

  Parameters:
    `br` - the `BufferedReader` to read data from
    `ns` - a `Namespace` to load the sequences into. Null implies that it should use the namespace specified in the file. If no namespace is specified in the file, then `RichObjectFactory.getDefaultNamespace()` is used.
  Returns:
    a `RichSequenceIterator` over each sequence in the fasta file

### readEMBLProtein

    public static RichSequenceIterator readEMBLProtein(BufferedReader br,
                                                       Namespace ns)

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

  Parameters:
    `br` - the `BufferedReader` to read data from
    `ns` - a `Namespace` to load the sequences into. Null implies that it should use the namespace specified in the file. If no namespace is specified in the file, then `RichObjectFactory.getDefaultNamespace()` is used.
  Returns:
    a `RichSequenceIterator` over each sequence in the fasta file

### readUniProt

    public static RichSequenceIterator readUniProt(BufferedReader br,
                                                   SymbolTokenization sTok,
                                                   RichSequenceBuilderFactory seqFactory,
                                                   Namespace ns)

  Read a UniProt file using a custom type of SymbolList. For example, use RichSequenceBuilderFactory.FACTORY to emulate readFasta(BufferedReader, SymbolTokenization) and RichSequenceBuilderFactory.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`
    `ns` - a `Namespace` to load the sequences into. Null implies that it should use the namespace specified in the file. If no namespace is specified in the file, then `RichObjectFactory.getDefaultNamespace()` is used.
  Returns:
    a `RichSequenceIterator` over each sequence in the fasta file

### readUniProt

    public static RichSequenceIterator readUniProt(BufferedReader br,
                                                   Namespace ns)

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

  Parameters:
    `br` - the `BufferedReader` to read data from
    `ns` - a `Namespace` to load the sequences into. Null implies that it should use the namespace specified in the file. If no namespace is specified in the file, then `RichObjectFactory.getDefaultNamespace()` is used.
  Returns:
    a `RichSequenceIterator` over each sequence in the fasta file

### readUniProtXML

    public static RichSequenceIterator readUniProtXML(BufferedReader br,
                                                      SymbolTokenization sTok,
                                                      RichSequenceBuilderFactory seqFactory,
                                                      Namespace ns)

  Read a UniProt XML file using a custom type of SymbolList. For example, use RichSequenceBuilderFactory.FACTORY to emulate readFasta(BufferedReader, SymbolTokenization) and RichSequenceBuilderFactory.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`
    `ns` - a `Namespace` to load the sequences into. Null implies that it should use the namespace specified in the file. If no namespace is specified in the file, then `RichObjectFactory.getDefaultNamespace()` is used.
  Returns:
    a `RichSequenceIterator` over each sequence in the fasta file

### readUniProtXML

    public static RichSequenceIterator readUniProtXML(BufferedReader br,
                                                      Namespace ns)

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

  Parameters:
    `br` - the `BufferedReader` to read data from
    `ns` - a `Namespace` to load the sequences into. Null implies that it should use the namespace specified in the file. If no namespace is specified in the file, then `RichObjectFactory.getDefaultNamespace()` is used.
  Returns:
    a `RichSequenceIterator` over each sequence in the fasta file

### writeFasta

    public static void writeFasta(OutputStream os,
                                  SequenceIterator in,
                                  Namespace ns,
                                  FastaHeader header)
                           throws IOException

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

  Parameters:
    `os` - The stream to write fasta formatted data to
    `in` - The source of input `RichSequence`s
    `ns` - a `Namespace` to write the `RichSequence`s to. `Null` implies that it should use the namespace specified in the individual sequence.
    `header` - the FastaHeader
  Throws:
    `IOException` - if there is an IO problem

### writeFasta

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

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

  Parameters:
    `os` - The stream to write fasta formatted data to
    `in` - The source of input `RichSequence`s
    `ns` - a `Namespace` to write the `RichSequence`s to. `Null` implies that it should use the namespace specified in the individual sequence.
  Throws:
    `IOException` - if there is an IO problem

### writeFasta

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

  Writes a single `Sequence` to an `OutputStream` in Fasta format.

  Parameters:
    `os` - the `OutputStream`.
    `seq` - the `Sequence`.
    `ns` - a `Namespace` to write the sequences to. Null implies that it should use the namespace specified in the individual sequence.
  Throws:
    `IOException` - if there is an IO problem

### writeFasta

    public static void writeFasta(OutputStream os,
                                  Sequence seq,
                                  Namespace ns,
                                  FastaHeader header)
                           throws IOException

  Writes a single `Sequence` to an `OutputStream` in Fasta format.

  Parameters:
    `os` - the `OutputStream`.
    `seq` - the `Sequence`.
    `ns` - a `Namespace` to write the sequences to. Null implies that it should use the namespace specified in the individual sequence.
    `header` - a `FastaHeader` that controls the fields in the header.
  Throws:
    `IOException` - if there is an IO problem

### writeGenbank

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

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

  Parameters:
    `os` - The stream to write fasta formatted data to
    `in` - The source of input Sequences
    `ns` - a `Namespace` to write the sequences to. Null implies that it should use the namespace specified in the individual sequence.
  Throws:
    `IOException` - if there is an IO problem

### writeGenbank

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

  Writes a single `Sequence` to an `OutputStream` in GenBank format.

  Parameters:
    `os` - the `OutputStream`.
    `seq` - the `Sequence`.
    `ns` - a `Namespace` to write the sequences to. Null implies that it should use the namespace specified in the individual sequence.
  Throws:
    `IOException` - if there is an IO problem

### writeINSDseq

    public static void writeINSDseq(OutputStream os,
                                    SequenceIterator in,
                                    Namespace ns)
                             throws IOException

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

  Parameters:
    `os` - The stream to write fasta formatted data to
    `in` - The source of input Sequences
    `ns` - a `Namespace` to write the sequences to. Null implies that it should use the namespace specified in the individual sequence.
  Throws:
    `IOException` - if there is an IO problem

### writeINSDseq

    public static void writeINSDseq(OutputStream os,
                                    Sequence seq,
                                    Namespace ns)
                             throws IOException

  Writes a single `Sequence` to an `OutputStream` in INSDseq format.

  Parameters:
    `os` - the `OutputStream`.
    `seq` - the `Sequence`.
    `ns` - a `Namespace` to write the sequences to. Null implies that it should use the namespace specified in the individual sequence.
  Throws:
    `IOException` - if there is an IO problem

### writeEMBLxml

    public static void writeEMBLxml(OutputStream os,
                                    SequenceIterator in,
                                    Namespace ns)
                             throws IOException

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

  Parameters:
    `os` - The stream to write fasta formatted data to
    `in` - The source of input Sequences
    `ns` - a `Namespace` to write the sequences to. Null implies that it should use the namespace specified in the individual sequence.
  Throws:
    `IOException` - if there is an IO problem

### writeEMBLxml

    public static void writeEMBLxml(OutputStream os,
                                    Sequence seq,
                                    Namespace ns)
                             throws IOException

  Writes a single `Sequence` to an `OutputStream` in EMBLxml format.

  Parameters:
    `os` - the `OutputStream`.
    `seq` - the `Sequence`.
    `ns` - a `Namespace` to write the sequences to. Null implies that it should use the namespace specified in the individual sequence.
  Throws:
    `IOException` - if there is an IO problem

### writeEMBL

    public static void writeEMBL(OutputStream os,
                                 SequenceIterator in,
                                 Namespace ns)
                          throws IOException

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

  Parameters:
    `os` - The stream to write fasta formatted data to
    `in` - The source of input Sequences
    `ns` - a `Namespace` to write the sequences to. Null implies that it should use the namespace specified in the individual sequence.
  Throws:
    `IOException` - if there is an IO problem

### writeEMBL

    public static void writeEMBL(OutputStream os,
                                 Sequence seq,
                                 Namespace ns)
                          throws IOException

  Writes a single `Sequence` to an `OutputStream` in EMBL format.

  Parameters:
    `os` - the `OutputStream`.
    `seq` - the `Sequence`.
    `ns` - a `Namespace` to write the sequences to. Null implies that it should use the namespace specified in the individual sequence.
  Throws:
    `IOException` - if there is an IO problem

### writeUniProt

    public static void writeUniProt(OutputStream os,
                                    SequenceIterator in,
                                    Namespace ns)
                             throws IOException

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

  Parameters:
    `os` - The stream to write fasta formatted data to
    `in` - The source of input Sequences
    `ns` - a `Namespace` to write the sequences to. Null implies that it should use the namespace specified in the individual sequence.
  Throws:
    `IOException` - if there is an IO problem

### writeUniProt

    public static void writeUniProt(OutputStream os,
                                    Sequence seq,
                                    Namespace ns)
                             throws IOException

  Writes a single `Sequence` to an `OutputStream` in UniProt format.

  Parameters:
    `os` - the `OutputStream`.
    `seq` - the `Sequence`.
    `ns` - a `Namespace` to write the sequences to. Null implies that it should use the namespace specified in the individual sequence.
  Throws:
    `IOException` - if there is an IO problem

### writeUniProtXML

    public static void writeUniProtXML(OutputStream os,
                                       SequenceIterator in,
                                       Namespace ns)
                                throws IOException

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

  Parameters:
    `os` - The stream to write fasta formatted data to
    `in` - The source of input Sequences
    `ns` - a `Namespace` to write the sequences to. Null implies that it should use the namespace specified in the individual sequence.
  Throws:
    `IOException` - if there is an IO problem

### writeUniProtXML

    public static void writeUniProtXML(OutputStream os,
                                       Sequence seq,
                                       Namespace ns)
                                throws IOException

  Writes a single `Sequence` to an `OutputStream` in UniProt XML format.

  Parameters:
    `os` - the `OutputStream`.
    `seq` - the `Sequence`.
    `ns` - a `Namespace` to write the sequences to. Null implies that it should use the namespace specified in the individual sequence.
  Throws:
    `IOException` - if there is an IO problem

### getDNAParser

    public static SymbolTokenization getDNAParser()

  Creates a DNA symbol tokenizer.

  Returns:
    a `SymbolTokenization` for parsing DNA.

### getRNAParser

    public static SymbolTokenization getRNAParser()

  Creates a RNA symbol tokenizer.

  Returns:
    a `SymbolTokenization` for parsing RNA.

### getNucleotideParser

    public static SymbolTokenization getNucleotideParser()

  Creates a nucleotide symbol tokenizer.

  Returns:
    a `SymbolTokenization` for parsing nucleotides.

### getProteinParser

    public static SymbolTokenization getProteinParser()

  Creates a protein symbol tokenizer.

  Returns:
    a `SymbolTokenization` for parsing protein.

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