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