Class GenbankSequenceParser<S extends AbstractSequence<C>,​C extends Compound>

    • Field Detail

      • mapDB

        public java.util.LinkedHashMap<java.lang.String,​java.util.ArrayList<DBReferenceInfo>> mapDB
      • GENBANK_FORMAT

        public static final java.lang.String GENBANK_FORMAT
        The name of this format
        See Also:
        Constant Field Values
      • BASE_COUNT_TAG_FULL

        protected static final java.lang.String BASE_COUNT_TAG_FULL
        See Also:
        Constant Field Values
      • START_SEQUENCE_TAG

        protected static final java.lang.String START_SEQUENCE_TAG
        See Also:
        Constant Field Values
      • END_SEQUENCE_TAG

        protected static final java.lang.String END_SEQUENCE_TAG
        See Also:
        Constant Field Values
      • lp

        protected static final java.util.regex.Pattern lp
      • vp

        protected static final java.util.regex.Pattern vp
      • refRange

        protected static final java.util.regex.Pattern refRange
      • refp

        protected static final java.util.regex.Pattern refp
      • dbxp

        protected static final java.util.regex.Pattern dbxp
      • locationParser

        protected static final InsdcParser locationParser
      • sectp

        protected static final java.util.regex.Pattern sectp
      • readableFiles

        protected static final java.util.regex.Pattern readableFiles
      • headerLine

        protected static final java.util.regex.Pattern headerLine
    • Constructor Detail

      • GenbankSequenceParser

        public GenbankSequenceParser()
    • Method Detail

      • getSequence

        public java.lang.String getSequence​(java.io.BufferedReader bufferedReader,
                                            int sequenceLength)
                                     throws java.io.IOException
        Specified by:
        getSequence in interface SequenceParserInterface
        Returns:
        Throws:
        java.io.IOException
      • getHeader

        public java.lang.String getHeader()
      • getDatabaseReferences

        public java.util.LinkedHashMap<java.lang.String,​java.util.ArrayList<DBReferenceInfo>> getDatabaseReferences()
      • getKeyWords

        public java.util.ArrayList<java.lang.String> getKeyWords()
      • getFeatures

        public java.util.ArrayList<AbstractFeature> getFeatures​(java.lang.String keyword)
      • getFeatures

        public java.util.HashMap<java.lang.String,​java.util.ArrayList<AbstractFeature>> getFeatures()
      • getCompoundType

        public CompoundSet<?> getCompoundType()