org.biojava.nbio.alignment.io

Class StockholmFileParser

java.lang.Object

org.biojava.nbio.alignment.io.StockholmFileParser

public class StockholmFileParser
extends Object

Stockholm file parser.
for more information about the format refer to

• ftp://ftp.sanger.ac.uk/pub/databases /Pfam/current_release/userman.txt.
• ftp://ftp.sanger.ac.uk/pub/databases/Rfam/CURRENT /USERMAN.
• http://sonnhammer.sbc.su.se/Stockholm.html.

 Pfam DESCRIPTION OF FIELDS

    Compulsory fields:
    ------------------

    AC   Accession number:           Accession number in form PFxxxxx.version or PBxxxxxx.
    ID   Identification:             One word name for family.
    DE   Definition:                 Short description of family.
    AU   Author:                     Authors of the entry.
    SE   Source of seed:             The source suggesting the seed members belong to one family.
    GA   Gathering method:           Search threshold to build the full alignment.
    TC   Trusted Cutoff:             Lowest sequence score and domain score of match in the full alignment.
    NC   Noise Cutoff:               Highest sequence score and domain score of match not in full alignment.
    TP   Type:                       Type of family -- presently Family, Domain, Motif or Repeat.
    SQ   Sequence:                   Number of sequences in alignment.
    //                               End of alignment.

    Optional fields:
    ----------------

    DC   Database Comment:           Comment about database reference.
    DR   Database Reference:         Reference to external database.
    RC   Reference Comment:          Comment about literature reference.
    RN   Reference Number:           Reference Number.
    RM   Reference Medline:          Eight digit medline UI number.
    RT   Reference Title:            Reference Title.
    RA   Reference Author:           Reference Author
    RL   Reference Location:         Journal location.
    PI   Previous identifier:        Record of all previous ID lines.
    KW   Keywords:                   Keywords.
    CC   Comment:                    Comments.
    NE   Pfam accession:             Indicates a nested domain.
    NL   Location:                   Location of nested domains - sequence ID, start and end of insert.
    WK   Wikipedia Reference:        Reference to wikipedia.

    Obsolete fields:
    -----------
    AL   Alignment method of seed:   The method used to align the seed members.
    AM   Alignment Method:          The order ls and fs hits are aligned to the model to build the full align.

 

Since:

3.0.5

Author:

Amr AL-Hossary, Marko Vaz

Field Summary

Fields

Modifier and Type	Field and Description
static int	INFINITY indicates reading as much as possible, without limits

Constructor Summary

Constructors

Constructor and Description
StockholmFileParser()

Method Summary

Modifier and Type	Method and Description
StockholmStructure	parse(InputStream inStream) parses InputStream and returns a the first contained alignment in a StockholmStructure object.
List<StockholmStructure>	parse(InputStream inStream, int max) parses an InputStream and returns at maximum max objects contained in that file. This method leaves the stream open for further calls of parse(InputStream, int) (same function) or parseNext(int).
StockholmStructure	parse(String filename) Parses a Stockholm file and returns a StockholmStructure object with its content. This function is meant to be used for single access to specific file and it closes the file after doing its assigned job.
List<StockholmStructure>	parse(String filename, int max) Parses a Stockholm file and returns a StockholmStructure object with its content. This function doesn't close the file after doing its assigned job; to allow for further calls of parseNext(int).
List<StockholmStructure>	parseNext(int max) Tries to parse and return as maximum as max structures in the last used file or input stream. Please consider calling either parse(InputStream), parse(InputStream, int), or parse(String, int) before calling this function.

Methods inherited from class java.lang.Object

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

Field Detail

INFINITY

public static final int INFINITY

indicates reading as much as possible, without limits

See Also:

Constant Field Values

Constructor Detail

StockholmFileParser

public StockholmFileParser()

Method Detail

parse

public StockholmStructure parse(String filename)
                         throws IOException,
                                ParserException

Parses a Stockholm file and returns a StockholmStructure object with its content.
This function is meant to be used for single access to specific file and it closes the file after doing its assigned job. Any subsequent call to parseNext(int) will throw an exception or will function with unpredicted behavior.

Parameters:

filename - complete(?) path to the file from where to read the content

Returns:

stockholm file content

Throws:

IOException - when an exception occurred while opening/reading/closing the file+

ParserException - if unexpected format is encountered

parse

public List<StockholmStructure> parse(String filename,
                                      int max)
                               throws IOException,
                                      ParserException

Parses a Stockholm file and returns a StockholmStructure object with its content.
This function doesn't close the file after doing its assigned job; to allow for further calls of parseNext(int).

Parameters:

filename - file from where to read the content. see InputStreamProvider for more details.

max - maximum number of files to read, INFINITY for all.

Returns:

a vector of StockholmStructure containing parsed structures.

Throws:

IOException - when an exception occurred while opening/reading/closing the file.

ParserException - if unexpected format is encountered

See Also:

parseNext(int)

parse

public StockholmStructure parse(InputStream inStream)
                         throws ParserException,
                                IOException

parses InputStream and returns a the first contained alignment in a StockholmStructure object. Used mainly for multiple files within the same input stream, (e.g. when reading from Pfam flat files.
This method leaves the stream open for further calls of parseNext(int).

Parameters:

inStream - the InputStream containing the file to read.

Returns:

a StockholmStructure object representing file contents.

Throws:

IOException

ParserException

See Also:

parseNext(int)

parse

public List<StockholmStructure> parse(InputStream inStream,
                                      int max)
                               throws IOException

parses an InputStream and returns at maximum max objects contained in that file.
This method leaves the stream open for further calls of parse(InputStream, int) (same function) or parseNext(int).

Parameters:

inStream - the stream to parse

max - maximum number of structures to try to parse, INFINITY to try to obtain as much as possible.

Returns:

a List of StockholmStructure objects. If there are no more structures, an empty list is returned.

Throws:

IOException - in case an I/O Exception occurred.

See Also:

parseNext(int)

parseNext

public List<StockholmStructure> parseNext(int max)
                                   throws IOException

Tries to parse and return as maximum as max structures in the last used file or input stream.
Please consider calling either parse(InputStream), parse(InputStream, int), or parse(String, int) before calling this function.

Parameters:

max -

Returns:

Throws:

IOException