Package org.snpeff.genBank

Class Features

  • All Implemented Interfaces:
    java.lang.Iterable<Feature>
    Direct Known Subclasses:
    Embl, GenBank
    public abstract class Features
extends java.lang.Object
implements java.lang.Iterable<Feature>
    A class representing a set of features References: http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
    Author:
    pablocingolani

    • Constructor Detail

      • Features

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

      • Features

        public Features​(java.lang.String fileName)
        Create features from a file

    • Method Detail

      • getAccession

        public java.lang.String getAccession()

      • getDate

        public java.lang.String getDate()

      • getDefinition

        public java.lang.String getDefinition()

      • getDivision

        public java.lang.String getDivision()

      • getFeatures

        public java.util.ArrayList<Feature> getFeatures()

      • getKeywords

        public java.lang.String getKeywords()

      • getLocusName

        public java.lang.String getLocusName()

      • getMoleculeType

        public java.lang.String getMoleculeType()

      • getOrganism

        public java.lang.String getOrganism()

      • getReferences

        public java.util.ArrayList<java.lang.StringBuffer> getReferences()

      • getSequence

        public java.lang.String getSequence()

      • getSequenceLength

        public int getSequenceLength()

      • getShape

        public java.lang.String getShape()

      • getSource

        public java.lang.String getSource()

      • getVersion

        public java.lang.String getVersion()

      • isEmpty

        public boolean isEmpty()

      • isNewFeature

        protected abstract boolean isNewFeature​(java.lang.String line)
        Is there a new feature in this line?

      • iterator

        public java.util.Iterator<Feature> iterator()
        Specified by:
        iterator in interface java.lang.Iterable<Feature>

      • open

        protected void open​(java.lang.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 java.lang.String toString()
        Overrides:
        toString in class java.lang.Object