Class Embl

All Implemented Interfaces:
Iterable<Feature>

public class Embl extends Features
A class representing the same data as an EMBL file References: http://www.ebi.ac.uk/embl/Documentation/User_manual/usrman.html
Author:
pablocingolani
  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    static final int
     
    static final int
     

    Fields inherited from class org.snpeff.genBank.Features

    COMPLEMENT, debug, JOIN, MAX_LEN_TO_SHOW, ORDER
  • Constructor Summary

    Constructors
    Constructor
    Description
    Embl(String fileName)
    Create a Genbank record from a 'GB' file
    Embl(LineFileIterator lineFileIterator)
    Create a Genbank record from a 'GB' file
  • Method Summary

    Modifier and Type
    Method
    Description
    protected boolean
    Has this line a new feature?
    protected void
    parseFieldLine(String fkey, String valueOri, int fieldLineNum)
    Parse a feature line Line types: ID - identification (begins each entry; 1 per entry) AC - accession number (>=1 per entry) PR - project identifier (0 or 1 per entry) DT - date (2 per entry) DE - description (>=1 per entry) KW - keyword (>=1 per entry) OS - organism species (>=1 per entry) OC - organism classification (>=1 per entry) OG - organelle (0 or 1 per entry) RN - reference number (>=1 per entry) RC - reference comment (>=0 per entry) RP - reference positions (>=1 per entry) RX - reference cross-reference (>=0 per entry) RG - reference group (>=0 per entry) RA - reference author(s) (>=0 per entry) RT - reference title (>=1 per entry) RL - reference location (>=1 per entry) DR - database cross-reference (>=0 per entry) CC - comments or notes (>=0 per entry) AH - assembly header (0 or 1 per entry) AS - assembly information (0 or >=1 per entry) FH - feature table header (2 per entry) FT - feature table data (>=2 per entry) XX - spacer line (many per entry) SQ - sequence header (1 per entry) CO - contig/construct line (0 or >=1 per entry) bb - (blanks) sequence data (>=1 per entry) // - termination line (ends each entry; 1 per entry)
    void
    Load and parse the contents of a data file

    Methods inherited from class java.lang.Object

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

    Methods inherited from interface java.lang.Iterable

    forEach, spliterator
  • Field Details

  • Constructor Details

    • Embl

      public Embl(LineFileIterator lineFileIterator)
      Create a Genbank record from a 'GB' file
      Parameters:
      fileName -
    • Embl

      public Embl(String fileName)
      Create a Genbank record from a 'GB' file
      Parameters:
      fileName -
  • Method Details

    • isNewFeature

      protected boolean isNewFeature(String line)
      Has this line a new feature?
      Specified by:
      isNewFeature in class Features
      Parameters:
      line -
      Returns:
    • parseFieldLine

      protected void parseFieldLine(String fkey, String valueOri, int fieldLineNum)
      Parse a feature line Line types: ID - identification (begins each entry; 1 per entry) AC - accession number (>=1 per entry) PR - project identifier (0 or 1 per entry) DT - date (2 per entry) DE - description (>=1 per entry) KW - keyword (>=1 per entry) OS - organism species (>=1 per entry) OC - organism classification (>=1 per entry) OG - organelle (0 or 1 per entry) RN - reference number (>=1 per entry) RC - reference comment (>=0 per entry) RP - reference positions (>=1 per entry) RX - reference cross-reference (>=0 per entry) RG - reference group (>=0 per entry) RA - reference author(s) (>=0 per entry) RT - reference title (>=1 per entry) RL - reference location (>=1 per entry) DR - database cross-reference (>=0 per entry) CC - comments or notes (>=0 per entry) AH - assembly header (0 or 1 per entry) AS - assembly information (0 or >=1 per entry) FH - feature table header (2 per entry) FT - feature table data (>=2 per entry) XX - spacer line (many per entry) SQ - sequence header (1 per entry) CO - contig/construct line (0 or >=1 per entry) bb - (blanks) sequence data (>=1 per entry) // - termination line (ends each entry; 1 per entry)
    • readFile

      public void readFile()
      Load and parse the contents of a data file
      Specified by:
      readFile in class Features
      Parameters:
      fileName -