Package org.snpeff.genBank

Class GenBank

java.lang.Object
org.snpeff.genBank.Features
org.snpeff.genBank.GenBank
All Implemented Interfaces:
Iterable<Feature>
public class GenBank extends Features
A class representing the same data as a GenBank file (a 'GB' file) References: http://www.insdc.org/documents/feature-table http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord
Author:
pablocingolani

  • Field Details

    • FEATURE_NAME_FIELD_LEN

      public static final int FEATURE_NAME_FIELD_LEN
      See Also:

  • Constructor Details

    • GenBank

      public GenBank(LineFileIterator lineFileIterator)

    • GenBank

      public GenBank(String fileName)
      Create a Genbank record from a 'GB' file

  • Method Details

    • isNewFeature

      protected boolean isNewFeature(String line)
      Has this line a new feature?
      Specified by:
      isNewFeature in class Features

    • parseFieldLine

      protected void parseFieldLine(String name, String valueOri, int fieldLineNum, int fileLineNum)
      Parse a feature line

    • readFile

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