Class Feature

  • All Implemented Interfaces:
    java.lang.Iterable<FeatureCoordinates>

    public class Feature
    extends java.lang.Object
    implements java.lang.Iterable<FeatureCoordinates>
    A feature in a GenBank or EMBL file
    Author:
    pablocingolani
    • Field Detail

      • COMPLEMENT_STRING

        public static final java.lang.String COMPLEMENT_STRING
        See Also:
        Constant Field Values
    • Constructor Detail

      • Feature

        public Feature​(Feature.Type type,
                       java.lang.String def)
      • Feature

        public Feature​(Feature.Type type,
                       java.lang.String def,
                       int start,
                       int end,
                       boolean complement,
                       int lineNum)
    • Method Detail

      • get

        public java.lang.String get​(java.lang.String name)
        Get a qualifier by name
      • getAasequence

        public java.lang.String getAasequence()
        Get translated amino acid sequence
      • getEnd

        public int getEnd()
      • getGeneId

        public java.lang.String getGeneId()
      • getGeneName

        public java.lang.String getGeneName()
        Get gene name from feature
      • getStart

        public int getStart()
      • getTranscriptId

        public java.lang.String getTranscriptId()
        Create a transcript ID based on a feature
      • hasMultipleCoordinates

        public boolean hasMultipleCoordinates()
      • isComplement

        public boolean isComplement()
      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object