Constant Field Values

Contents

• org.biojava.*

org.biojava.*

org.biojava.nbio.core.exceptions.Messages

Modifier and Type	Constant Field	Value
public static final String	ENDOFFILE	"end of file"
public static final String	SECTIONKEYNULL	"section key is null"

org.biojava.nbio.core.sequence.io.GenbankSequenceParser<S extends AbstractSequence<C>,C extends Compound>

Modifier and Type	Constant Field	Value
protected static final String	ACCESSION_TAG	"ACCESSION"
protected static final String	AUTHORS_TAG	"AUTHORS"
protected static final String	BASE_COUNT_TAG	"BASE"
protected static final String	BASE_COUNT_TAG_FULL	"BASE COUNT"
protected static final String	COMMENT_TAG	"COMMENT"
protected static final String	CONSORTIUM_TAG	"CONSRTM"
protected static final String	DBLINK	"DBLINK"
protected static final String	DBSOURCE	"DBSOURCE"
protected static final String	DEFINITION_TAG	"DEFINITION"
protected static final String	END_SEQUENCE_TAG	"//"
protected static final String	FEATURE_TAG	"FEATURES"
public static final String	GENBANK_FORMAT	"GENBANK"
protected static final String	JOURNAL_TAG	"JOURNAL"
protected static final String	KEYWORDS_TAG	"KEYWORDS"
protected static final String	LOCUS_TAG	"LOCUS"
protected static final String	MEDLINE_TAG	"MEDLINE"
protected static final String	ORGANISM_TAG	"ORGANISM"
protected static final String	PRIMARY	"PRIMARY"
protected static final String	PUBMED_TAG	"PUBMED"
protected static final String	REFERENCE_TAG	"REFERENCE"
protected static final String	REMARK_TAG	"REMARK"
protected static final String	SOURCE_TAG	"SOURCE"
protected static final String	START_SEQUENCE_TAG	"ORIGIN"
protected static final String	TITLE_TAG	"TITLE"
protected static final String	VERSION_TAG	"VERSION"

org.biojava.nbio.core.sequence.io.GenbankWriterHelper

Modifier and Type	Constant Field	Value
public static final String	CIRCULAR_DNA	"circular"
public static final String	LINEAR_DNA	"linear"

org.biojava.nbio.core.sequence.io.GenericInsdcHeaderFormat<S extends AbstractSequence<C>,C extends Compound>

Modifier and Type	Constant Field	Value
protected static final int	MAX_WIDTH	80
protected static final int	QUALIFIER_INDENT	21
protected static final String	QUALIFIER_INDENT_STR	" "
protected static final String	QUALIFIER_INDENT_TMP	" %s "

org.biojava.nbio.core.sequence.io.IUPACParser

Modifier and Type	Constant Field	Value
public static final String	IUPAC_LOCATION	"org/biojava/nbio/core/sequence/iupac.txt"

org.biojava.nbio.core.sequence.io.template.GenbankHeaderFormatInterface<S extends Sequence<?>,C extends Compound>

Modifier and Type	Constant Field	Value
public static final String	UNKNOWN_DNA	"UNK"

org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader<C extends Compound>

Modifier and Type	Constant Field	Value
public static final String	DEFAULT_UNIPROT_BASE_URL	"https://www.uniprot.org"

org.biojava.nbio.core.sequence.location.InsdcParser

Modifier and Type	Constant Field	Value
protected static final String	locationSplitPattern	",(?=([^\\(|\\)]+\\([^\\(|\\)]+\\))[^\\(|\\)]+)"

org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker<C extends Compound>

Modifier and Type	Constant Field	Value
public static final int	BYTES_PER_INT	32

org.biojava.nbio.core.util.Hashcoder

Modifier and Type	Constant Field	Value
public static final int	PRIME	79
public static final int	SEED	9

org.biojava.nbio.core.util.InputStreamProvider

Modifier and Type	Constant Field	Value
public static final String	CACHE_PROPERTY	"biojava.cache.files"
public static final int	GZIP_MAGIC	8075

org.biojava.nbio.core.util.SequenceTools

Modifier and Type	Constant Field	Value
protected static final String	NUCLEOTIDE_LETTERS	"GCTAUXN"

org.biojava.nbio.core.util.SoftHashMap<K,V>

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_LIMIT	1