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

 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

Description

static final int

INFINITY

indicates reading as much as possible, without limits
Constructor Summary

Constructors

Constructor

Description

StockholmFileParser()
Method Summary

Modifier and Type

Method

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 Details
- INFINITY
  
  public static final int INFINITY
  
  indicates reading as much as possible, without limits
  See Also:
  
  Constant Field Values
Constructor Details
- StockholmFileParser
  
  public StockholmFileParser()
Method Details
- 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

Class StockholmFileParser

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Details

INFINITY

Constructor Details

StockholmFileParser

Method Details

parse

parse

parse

parse

parseNext