RichSequence.IOTools (biojava-legacy 1.9.1 API)

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

Nested Classes
Modifier and Type Class and Description

static class RichSequence.IOTools.SingleRichSeqIterator
Used to iterate over a single rich sequence

Nested Classes
Modifier and Type	Class and Description
`static class`	`RichSequence.IOTools.SingleRichSeqIterator` Used to iterate over a single rich sequence

Method Summary

Methods
Modifier and Type	Method and Description
`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 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.

Class RichSequence.IOTools

Nested Class Summary

Method Summary

Methods inherited from class java.lang.Object

Method Detail

registerFormat

readStream

readStream

readFile

readFile

readFasta

readFasta

readFastaDNA

readHashedFastaDNA

readFastaRNA

readFastaProtein

readGenbank

readGenbankDNA

readGenbankRNA

readGenbankProtein

readINSDseq

readINSDseqDNA

readINSDseqRNA

readINSDseqProtein

readEMBLxml

readEMBLxmlDNA

readEMBLxmlRNA

readEMBLxmlProtein

readEMBL

readEMBLDNA

readEMBLRNA

readEMBLProtein

readUniProt

readUniProt

readUniProtXML

readUniProtXML

writeFasta

writeFasta

writeFasta

writeFasta

writeGenbank

writeGenbank

writeINSDseq

writeINSDseq

writeEMBLxml

writeEMBLxml

writeEMBL

writeEMBL

writeUniProt

writeUniProt

writeUniProtXML

writeUniProtXML

getDNAParser

getRNAParser

getNucleotideParser

getProteinParser