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 Sequences from a SequenceIterator to an OutputStream in Fasta Format.
static void	writeFasta(OutputStream os, SequenceIterator in, Namespace ns, FastaHeader header) Writes Sequences 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 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 RichStreamWriter after formatting.

Parameters:

os - The stream to write fasta formatted data to

in - The source of input RichSequences

ns - a Namespace to write the RichSequences 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 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 RichStreamWriter after formatting.

Parameters:

os - The stream to write fasta formatted data to

in - The source of input RichSequences

ns - a Namespace to write the RichSequences 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.