Class Features

java.lang.Object
org.snpeff.genBank.Features
All Implemented Interfaces:
Iterable<Feature>
Direct Known Subclasses:
Embl, GenBank

public abstract class Features extends Object implements Iterable<Feature>
A class representing a set of features References: http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
Author:
pablocingolani
  • Field Details

  • Constructor Details

    • Features

      public Features(LineFileIterator lineFileIterator)
      Create features from a file
    • Features

      public Features(String fileName)
      Create features from a file
  • Method Details

    • getAccession

      public String getAccession()
    • getDate

      public String getDate()
    • getDefinition

      public String getDefinition()
    • getDivision

      public String getDivision()
    • getFeatures

      public ArrayList<Feature> getFeatures()
    • getKeywords

      public String getKeywords()
    • getLocusName

      public String getLocusName()
    • getMoleculeType

      public String getMoleculeType()
    • getOrganism

      public String getOrganism()
    • getReferences

      public ArrayList<StringBuffer> getReferences()
    • getSequence

      public String getSequence()
    • getSequenceLength

      public int getSequenceLength()
    • getShape

      public String getShape()
    • getSource

      public String getSource()
    • getVersion

      public String getVersion()
    • isEmpty

      public boolean isEmpty()
    • isNewFeature

      protected abstract boolean isNewFeature(String line)
      Is there a new feature in this line?
    • iterator

      public Iterator<Feature> iterator()
      Specified by:
      iterator in interface Iterable<Feature>
    • open

      protected void open(String fileName)
      Open a file
    • parseFeatures

      protected void parseFeatures()
      Parse features
    • readFile

      protected abstract void readFile()
      Load and parse the contents of a data file previously opened by 'open()' method.
    • toString

      public String toString()
      Overrides:
      toString in class Object