Class Embl

  • All Implemented Interfaces:
    java.lang.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
    • Constructor Summary

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

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      protected boolean isNewFeature​(java.lang.String line)
      Has this line a new feature?
      protected void parseFieldLine​(java.lang.String fkey, java.lang.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 readFile()
      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
    • Constructor Detail

      • Embl

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

        public Embl​(java.lang.String fileName)
        Create a Genbank record from a 'GB' file
        Parameters:
        fileName -
    • Method Detail

      • isNewFeature

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

        protected void parseFieldLine​(java.lang.String fkey,
                                      java.lang.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 -