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

• LOCUS_TAG

  protected static final java.lang.String LOCUS_TAG

  See Also:

  Constant Field Values

• DEFINITION_TAG

  protected static final java.lang.String DEFINITION_TAG

  See Also:

  Constant Field Values

• ACCESSION_TAG

  protected static final java.lang.String ACCESSION_TAG

  See Also:

  Constant Field Values

• VERSION_TAG

  protected static final java.lang.String VERSION_TAG

  See Also:

  Constant Field Values

• KEYWORDS_TAG

  protected static final java.lang.String KEYWORDS_TAG

  See Also:

  Constant Field Values

• SOURCE_TAG

  protected static final java.lang.String SOURCE_TAG

  See Also:

  Constant Field Values

• ORGANISM_TAG

  protected static final java.lang.String ORGANISM_TAG

  See Also:

  Constant Field Values

• REFERENCE_TAG

  protected static final java.lang.String REFERENCE_TAG

  See Also:

  Constant Field Values

• AUTHORS_TAG

  protected static final java.lang.String AUTHORS_TAG

  See Also:

  Constant Field Values

• CONSORTIUM_TAG

  protected static final java.lang.String CONSORTIUM_TAG

  See Also:

  Constant Field Values

• TITLE_TAG

  protected static final java.lang.String TITLE_TAG

  See Also:

  Constant Field Values

• JOURNAL_TAG

  protected static final java.lang.String JOURNAL_TAG

  See Also:

  Constant Field Values

• PUBMED_TAG

  protected static final java.lang.String PUBMED_TAG

  See Also:

  Constant Field Values

• MEDLINE_TAG

  protected static final java.lang.String MEDLINE_TAG

  See Also:

  Constant Field Values

• REMARK_TAG

  protected static final java.lang.String REMARK_TAG

  See Also:

  Constant Field Values

• COMMENT_TAG

  protected static final java.lang.String COMMENT_TAG

  See Also:

  Constant Field Values

• FEATURE_TAG

  protected static final java.lang.String FEATURE_TAG

  See Also:

  Constant Field Values

• BASE_COUNT_TAG_FULL

  protected static final java.lang.String BASE_COUNT_TAG_FULL

  See Also:

  Constant Field Values

• BASE_COUNT_TAG

  protected static final java.lang.String BASE_COUNT_TAG

  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()

• getSequenceHeaderParser

  public GenericGenbankHeaderParser<S,​C> getSequenceHeaderParser()

• 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()

• parseFeatures

  public void parseFeatures​(AbstractSequence<C> sequence)

• getCompoundType

  public CompoundSet<?> getCompoundType()