Constant Field Values

Contents

• org.biojava.*
• org.biojavax.*

org.biojava.*

org.biojava.bibliography.BiblioCriterion

Modifier and Type	Constant Field	Value
public static final int	QUERY_CRITERION	0
public static final int	SORT_CRITERION	1

org.biojava.bibliography.BibRefQuery

Modifier and Type	Constant Field	Value
public static final String	PROP_CRITERIONS	"criterions"
public static final String	PROP_EXCLUDED_ATTRS	"excluded"

org.biojava.bibliography.BibRefSupport

Modifier and Type	Constant Field	Value
public static final String	ATTR_FORMAT	"format"
public static final String	ATTR_PROPERTIES	"properties"
public static final String	ATTR_SCOPE	"scope"
public static final String	ENTRY_PROPERTIES	"entry_properties"
public static final String	GENERIC_PROVIDER	"Provider"
public static final String	INIT_PROP_LOG	"log"
public static final String	INIT_PROP_SUPPORT	"bibrefsupport"
public static final String	JOURNAL_ABBREV	"journal_abbreviations"
public static final String	JOURNAL_TITLES	"journal_titles"
public static final String	LANGUAGES	"languages"
public static final String	PROVIDER_ORGANISATION	"Organisation"
public static final String	PROVIDER_PERSON	"Person"
public static final String	PROVIDER_SERVICE	"Service"
public static final String	REPOSITORY_SUBSETS	"repository_subsets"
public static final String	RESOURCE_TYPES	"resource_types"
public static final String	ROLE_ATTR_QUERYABLE	"queryable"
public static final String	ROLE_ATTR_RETRIEVABLE	"retrievable"
public static final String	SUBJECT_HEADINGS	"subject_headings"
public static final String	TYPE_ARTICLE	"Article"
public static final String	TYPE_BOOK	"Book"
public static final String	TYPE_BOOK_ARTICLE	"BookArticle"
public static final String	TYPE_JOURNAL_ARTICLE	"JournalArticle"
public static final String	TYPE_PATENT	"Patent"
public static final String	TYPE_PROCEEDING	"Proceeding"
public static final String	TYPE_TECH_REPORT	"TechReport"
public static final String	TYPE_THESIS	"Thesis"
public static final String	TYPE_WEB_RESOURCE	"WebResource"

org.biojava.bio.EcNumber

Modifier and Type	Constant Field	Value
public static final int	UNCLASSIFIED	99
public static final int	UNDEFINED	-1

org.biojava.bio.dp.SimpleMarkovModel

Modifier and Type	Constant Field	Value
public static final long	serialVersionUID	-3043028839927615753L

org.biojava.bio.molbio.RestrictionEnzyme

Modifier and Type	Constant Field	Value
public static final int	BLUNT	2
public static final int	CUT_COMPOUND	1
public static final int	CUT_SIMPLE	0
public static final int	OVERHANG_3PRIME	1
public static final int	OVERHANG_5PRIME	0

org.biojava.bio.molbio.RestrictionEnzymeManager

Modifier and Type	Constant Field	Value
public static final String	REBASE_DATA_KEY	"rebase.data.file"
public static final String	REBASE_TAG_COMM	"<7>"
public static final String	REBASE_TAG_ISZR	"<2>"
public static final String	REBASE_TAG_METH	"<4>"
public static final String	REBASE_TAG_NAME	"<1>"
public static final String	REBASE_TAG_ORGN	"<5>"
public static final String	REBASE_TAG_REFS	"<8>"
public static final String	REBASE_TAG_SITE	"<3>"
public static final String	REBASE_TAG_SRCE	"<6>"

org.biojava.bio.molbio.RestrictionMapper

Modifier and Type	Constant Field	Value
public static final String	SITE_FEATURE_SOURCE	"regex"
public static final String	SITE_FEATURE_TYPE	"misc_binding"

org.biojava.bio.program.gff.GFFEntrySet

Modifier and Type	Constant Field	Value
public static final String	PROPERTY_GFF_SCORE	"org.biojava.bio.program.gff.gff_feature_score"

org.biojava.bio.program.homologene.HomologeneBuilder

Modifier and Type	Constant Field	Value
public static final String	ACCESSION	"Accession"
public static final String	CURATED	"curated"
public static final String	HOMOID	"HomologeneID"
public static final String	LOCUSID	"LocusID"
public static final String	MULTIPLE	"multiple"
public static final String	PERCENTIDENTITY	"PercentIdentity"
public static final String	REFERENCE	"Reference"
public static final String	SIMILARITYTYPE	"SimilarityType"
public static final String	TAXONID	"TaxonID"
public static final String	TWIN	"twin"

org.biojava.bio.program.indexdb.BioStoreFactory

Modifier and Type	Constant Field	Value
public static final String	KEYS	"secondary_namespaces"
public static final String	PRIMARY_KEY_NAME	"primary_namespace"
public static final String	SEQUENCE_FORMAT	"format"
public static final String	STORE_NAME	"name"

org.biojava.bio.program.phred.PhredFormat

Modifier and Type	Constant Field	Value
public static final String	DEFAULT	"PHRED"
public static final String	PROPERTY_DESCRIPTIONLINE	"description_line"

org.biojava.bio.program.tagvalue.StateMachine

Modifier and Type	Constant Field	Value
protected static final String	END_RECORD_TAG	"__END_RECORD__"
protected static final String	END_TAG	"__END_TAG__"
protected static final String	MAGICAL_STATE	"__MAGICAL__"
protected static final String	START_RECORD_TAG	"__START_RECORD_TAG__"

org.biojava.bio.program.tagvalue.TagValueParser

Modifier and Type	Constant Field	Value
public static final String	EMPTY_LINE_EOR	""

org.biojava.bio.program.xff.XFFFeatureSetHandler

Modifier and Type	Constant Field	Value
public static final String	PROPERTY_XFF_ID	"org.biojava.bio.program.xff.id"

org.biojava.bio.program.xff.XFFTools

Modifier and Type	Constant Field	Value
public static final String	XFF_BIOJAVA_NS	"http://www.biojava.org/2001/xff-biojava"
public static final String	XFF_NS	"http://www.bioxml.org/2000/xff"

org.biojava.bio.proteomics.MassCalc

Modifier and Type	Constant Field	Value
public static final double	Cavg	12.011
public static final double	Cmono	12.0
public static final double	Havg	1.00794
public static final double	Hmono	1.007825
public static final double	Navg	14.00674
public static final double	Nmono	14.003074
public static final double	Oavg	15.9994
public static final double	Omono	15.9949146

org.biojava.bio.proteomics.Protease

Modifier and Type	Constant Field	Value
public static final String	ARG_C	"Arg-C"
public static final String	ASP_N	"Asp-N"
public static final String	CHYMOTRYP	"Chymotrypsin"
public static final String	CNBr	"CNBr"
public static final String	GLU_C_BICARB	"Glu-C-bicarbonate"
public static final String	GLU_C_PHOS	"Glu-C-phosphate"
public static final String	LYS_C	"Lys-C"
public static final String	TRYPSIN	"Trypsin"

org.biojava.bio.proteomics.ProteaseManager

Modifier and Type	Constant Field	Value
public static final String	ARG_C	"Arg-C"
public static final String	ASP_N	"Asp-N"
public static final String	CHYMOTRYP	"Chymotrypsin"
public static final String	CNBr	"CNBr"
public static final String	GLU_C_BICARB	"Glu-C-bicarbonate"
public static final String	GLU_C_PHOS	"Glu-C-phosphate"
public static final String	LYS_C	"Lys-C"
public static final String	TRYPSIN	"Trypsin"

org.biojava.bio.search.BlastLikeSearchFilter

Modifier and Type	Constant Field	Value
public static final String	KEY_QUERY_ID	"___QUERY_ID___"

org.biojava.bio.search.SeqSimilaritySearchSubHit

Modifier and Type	Constant Field	Value
public static final String	QUERY_LABEL	"Query"

org.biojava.bio.seq.Feature

Modifier and Type	Constant Field	Value
public static final String	PROPERTY_DATA_KEY	"internal_data"

org.biojava.bio.seq.FeatureTypes

Modifier and Type	Constant Field	Value
public static final String	URI_PREFIX	"uri:biojava.org:types"

org.biojava.bio.seq.Frame

Modifier and Type	Constant Field	Value
public static final int	FRAME_0	0
public static final int	FRAME_1	1
public static final int	FRAME_2	2

org.biojava.bio.seq.db.GenbankSequenceDB

Modifier and Type	Constant Field	Value
protected static final String	urlBatchSequences	"https://www.ncbi.nlm.nih.gov:80/entrez/eutils/efetch.fcgi"

org.biojava.bio.seq.db.NCBISequenceDB

Modifier and Type	Constant Field	Value
public static final String	DB_NUCLEOTIDE	"nucleotide"
public static final String	DB_PROTEIN	"protein"

org.biojava.bio.seq.homol.SimilarityPairFeature

Modifier and Type	Constant Field	Value
public static final String	QUERY_LABEL	"query"
public static final String	SUBJECT_LABEL	"subject"

org.biojava.bio.seq.io.AlignIOConstants

Modifier and Type	Constant Field	Value
public static final int	CLUSTAL	103
public static final int	CLUSTAL_AA	524391
public static final int	CLUSTAL_DNA	131175
public static final int	CLUSTAL_RNA	262247
public static final int	FASTA	102
public static final int	FASTA_AA	524390
public static final int	FASTA_DNA	131174
public static final int	FASTA_RNA	262246
public static final int	MSF	104
public static final int	MSF_AA	524392
public static final int	MSF_DNA	131176
public static final int	MSF_RNA	262248
public static final int	RAW	101
public static final int	RAW_AA	524389
public static final int	RAW_DNA	131173
public static final int	RAW_RNA	262245
public static final int	UNKNOWN	100

org.biojava.bio.seq.io.EmblLikeFormat

Modifier and Type	Constant Field	Value
protected static final String	ACCESSION_TAG	"AC"
protected static final String	AUTHORS_TAG	"RA"
protected static final String	CIRCULAR_TAG	"CIRCULAR"
protected static final String	COMMENT_TAG	"CC"
protected static final String	COORDINATE_TAG	"RP"
protected static final String	DATE_TAG	"DT"
public static final String	DEFAULT	"EMBL"
protected static final String	DEFINITION_TAG	"DE"
protected static final String	DIVISION_TAG	"DIVISION"
protected static final String	DR_TAG	"DR"
protected static final String	END_SEQUENCE_TAG	"//"
protected static final String	FEATURE_TABLE_TAG	"FT"
protected static final String	FEATURE_TAG	"FH"
protected static final String	ID_TAG	"ID"
protected static final String	JOURNAL_TAG	"RL"
protected static final String	KEYWORDS_TAG	"KW"
protected static final String	ORGANISM_TAG	"OC"
protected static final String	ORGANISM_XREF_TAG	"OX"
protected static final String	REF_ACCESSION_TAG	"RX"
protected static final String	REF_XREF_TAG	"RX"
protected static final String	REFERENCE_TAG	"RN"
protected static final String	SEPARATOR_TAG	"XX"
protected static final String	SIZE_TAG	"SIZE"
protected static final String	SOURCE_TAG	"OS"
protected static final String	START_SEQUENCE_TAG	"SQ"
protected static final String	STRAND_NUMBER_TAG	"STRANDS"
protected static final String	TITLE_TAG	"RT"
protected static final String	TYPE_TAG	"TYPE"
protected static final String	VERSION_TAG	"SV"

org.biojava.bio.seq.io.EmblProcessor

Modifier and Type	Constant Field	Value
public static final String	PROPERTY_EMBL_ACCESSIONS	"embl_accessions"

org.biojava.bio.seq.io.FastaAlignmentFormat

Modifier and Type	Constant Field	Value
public static final int	DNA	1
public static final int	PROTEIN	2

org.biojava.bio.seq.io.FastaFormat

Modifier and Type	Constant Field	Value
public static final String	DEFAULT	"FASTA"
public static final String	PROPERTY_DESCRIPTIONLINE	"description_line"

org.biojava.bio.seq.io.GAMEFormat

Modifier and Type	Constant Field	Value
public static final String	DEFAULT	"GAME1.2"

org.biojava.bio.seq.io.GenbankFormat

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	CIRCULAR_TAG	"CIRCULAR"
protected static final String	COMMENT_TAG	"COMMENT"
protected static final String	COORDINATE_TAG	"COORDINATE"
protected static final String	DATE_TAG	"MDAT"
public static final String	DEFAULT	"GENBANK"
protected static final String	DEFINITION_TAG	"DEFINITION"
protected static final String	DIVISION_TAG	"DIVISION"
protected static final String	END_SEQUENCE_TAG	"//"
protected static final String	FEATURE_FLAG	"FT"
protected static final String	FEATURE_LINE_PREFIX	" "
protected static final String	FEATURE_TAG	"FEATURES"
protected static final String	GI_TAG	"GI"
protected static final String	JOURNAL_TAG	"JOURNAL"
protected static final String	KEYWORDS_TAG	"KW"
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	PUBMED_TAG	"PUBMED"
protected static final String	REF_ACCESSION_TAG	""
protected static final String	REFERENCE_TAG	"REFERENCE"
protected static final String	SIZE_TAG	"SIZE"
protected static final String	SOURCE_TAG	"SOURCE"
protected static final String	START_SEQUENCE_TAG	"ORIGIN"
protected static final String	STRAND_NUMBER_TAG	"STRANDS"
protected static final String	TITLE_TAG	"TITLE"
protected static final String	TYPE_TAG	"TYPE"
protected static final String	VERSION_TAG	"VERSION"

org.biojava.bio.seq.io.GenbankProcessor

Modifier and Type	Constant Field	Value
public static final String	PROPERTY_GENBANK_ACCESSIONS	"genbank_accessions"

org.biojava.bio.seq.io.SeqIOConstants

Modifier and Type	Constant Field	Value
public static final int	AA	524288
public static final int	AMBIGUOUS	65536
public static final int	DNA	131072
public static final int	EMBL	10
public static final int	EMBL_AA	524298
public static final int	EMBL_DNA	131082
public static final int	EMBL_RNA	262154
public static final int	FASTA	2
public static final int	FASTA_AA	524290
public static final int	FASTA_DNA	131074
public static final int	FASTA_RNA	262146
public static final int	GCG	15
public static final int	GENBANK	12
public static final int	GENBANK_AA	524300
public static final int	GENBANK_DNA	131084
public static final int	GENBANK_RNA	262156
public static final int	GENPEPT	524301
public static final int	GFF	20
public static final int	IG	4
public static final int	INTEGER	1048576
public static final int	NBRF	3
public static final int	PDB	524309
public static final int	PHRED	1179678
public static final int	RAW	1
public static final int	REFSEQ	14
public static final int	REFSEQ_AA	524302
public static final int	REFSEQ_DNA	131086
public static final int	REFSEQ_RNA	262158
public static final int	RNA	262144
public static final int	SWISSPROT	524299
public static final int	UNKNOWN	0

org.biojava.bio.seq.io.SwissprotProcessor

Modifier and Type	Constant Field	Value
public static final String	PROPERTY_SWISSPROT_ACCESSIONS	"swissprot.accessions"
public static final String	PROPERTY_SWISSPROT_COMMENT	"swissprot.comment"
public static final String	PROPERTY_SWISSPROT_FEATUREATTRIBUTE	"swissprot.featureattribute"

org.biojava.bio.seq.io.agave.AGAVEAnnotFilter

Modifier and Type	Constant Field	Value
public static final int	BOTH_FORWARD_COMPLEMENT	0
public static final int	COMPLEMENT	-1
public static final int	FORWARD	1

org.biojava.bio.seq.io.agave.AGAVEProperty

Modifier and Type	Constant Field	Value
public static final String	QUALIFIER	"qualifier"
public static final String	RESULT_PROPERTY	"result_property"
public static final String	SCI_PROPERTY	"sci_property"
public static final String	XREF_PROPERTY	"xref_property"

org.biojava.bio.seq.io.agave.AgaveWriter

Modifier and Type	Constant Field	Value
public static final String	INDENT	" "

org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter

Modifier and Type	Constant Field	Value
public static final String	XML_ANNOTATIONTYPE_NS	"http://www.biojava.org/AnnotationType"

org.biojava.bio.seq.io.filterxml.XMLFilterWriter

Modifier and Type	Constant Field	Value
public static final String	XML_FILTER_NS	"http://www.biojava.org/FeatureFilter"

org.biojava.bio.symbol.AbstractAlphabet

Modifier and Type	Constant Field	Value
public static final long	serialVersionUID	-3043128839927615753L

org.biojava.bio.symbol.SymbolPropertyTable

Modifier and Type	Constant Field	Value
public static final String	AVG_MASS	"avgMass"
public static final String	HYDROPATHICITY	"hydropathicity"
public static final String	MONO_MASS	"monoMass"
public static final String	PK	"pK"
public static final String	PK_Cterm	"pK_Cterm"
public static final String	PK_Nterm	"pK_Nterm"

org.biojava.bio.symbol.TranslationTable

Modifier and Type	Constant Field	Value
public static final String	ALT_YEAST_NUC	"ALTERNATIVE_YEAST_NUCLEAR"
public static final String	ASCID_MITO	"ASCIDIAN_MITOCHONDRIAL"
public static final String	BACTERIAL	"BACTERIAL"
public static final String	BLEPH_MNUC	"BLEPHARISMA_MACRONUCLEAR"
public static final String	CHLORO_MITO	"CHLOROPHYCEAN_MITOCHONDRIAL"
public static final String	CILIATE_NUC	"CILIATE_NUCLEAR"
public static final String	ECHIN_MITO	"ECHINODERM_MITOCHONDRIAL"
public static final String	EUPL_NUC	"EUPLOTID_NUCLEAR"
public static final String	FWORM_MITO	"FLATWORM_MITOCHONDRIAL"
public static final String	INVERT_MITO	"INVERTEBRATE_MITOCHONDRIAL"
public static final String	MOLD_MITO	"MOLD_MITOCHONDRIAL"
public static final String	SCENE_MITO	"SCENEDESMUS_MITOCHONDRIAL"
public static final String	TREMA_MITO	"TREMATODE_MITOCHONDRIAL"
public static final String	UNIVERSAL	"UNIVERSAL"
public static final String	VERT_MITO	"VERTEBRATE_MITOCHONDRIAL"
public static final String	YEAST_MITO	"YEAST_MITOCHONDRIAL"

org.biojava.bio.symbol.UkkonenSuffixTree

Modifier and Type	Constant Field	Value
public static final char	DEFAULT_TERM_CHAR	'$'
public static final int	TO_A_LEAF	-1

org.biojava.directory.SystemRegistry

Modifier and Type	Constant Field	Value
public static final String	CONFIG_FILE	"seqdatabase.ini"
public static final String	CONFIG_LOCATOR	"http://www.open-bio.org/registry/seqdatabase.ini"
public static final String	OBDA_SEARCH_ENV	"OBDA_SEARCH_PATH"

org.biojava.ontology.Synonym

Modifier and Type	Constant Field	Value
public static final int	BROAD_SYNONYM	3
public static final int	EXACT_SYNONYM	1
public static final int	NARROW_SYNONYM	2
public static final int	RELATED_SYNONYM	0
public static final int	UNKNOWN_SCOPE	-1

org.biojava.ontology.obo.OboFileHandler

Modifier and Type	Constant Field	Value
public static final String	ALT_ID	"alt_id"
public static final String	BROAD_SYNONYM	"broad_synonym"
public static final String	COMMENT	"comment"
public static final String	DEF	"def"
public static final String	DISJOINT_FROM	"disjoint_from"
public static final String	EXACT_SYNONYM	"exact_synonym"
public static final String	ID_KEY	"id"
public static final String	INTERSECTION_OF	"intersection_of"
public static final String	IS_A	"is_a"
public static final String	IS_OBSOLETE	"is_obsolete"
public static final String	NAME	"name"
public static final String	NARROW_SYNONYM	"narrow_synonym"
public static final String	ONTOLOGY	"ontologys"
public static final String	REL_SYNONYM	"related_synonym"
public static final String	RELATIONSHIP	"relationship"
public static final String	SUBSET	"subset"
public static final String	SYNONYM	"synonym"
public static final String	TERM	"Term"
public static final String	TYPEDEF	"Typedef"
public static final String	XREF_ANALOG	"xref_analog"

org.biojava.utils.ObjectUtil

Modifier and Type	Constant Field	Value
public static final int	PRIME	1000003

org.biojava.utils.TypedProperties

Modifier and Type	Constant Field	Value
public static final String	DEFAULT_DELIMITERS	",;\t"

org.biojava.utils.candy.CandyFinder

Modifier and Type	Constant Field	Value
public static final String	DEFAULT_FINDER_NAME	"Default vocabulary finder"
public static final String	PROP_VOCABULARY	"vocabulary"

org.biojava.utils.candy.CandyVocabulary

Modifier and Type	Constant Field	Value
public static final String	CANDIES_NOT_SORTED	"candies_not_sorted"
public static final String	PROP_CASE_SENSITIVE	"vocab_case_sensitive"
public static final String	PROP_ENTRY_COUNT	"entry_count"
public static final String	PROP_VOCAB_DESC	"vocab_description"
public static final String	PROP_VOCAB_NAME	"vocab_name"
public static final String	PROP_VOCAB_VERSION	"vocab_version"
public static final String	PROP_VOCABULARY	"vocabulary"

org.biojava.utils.io.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.utils.io.SoftHashMap

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

org.biojava.utils.process.ExternalProcess

Modifier and Type	Constant Field	Value
public static final int	SLEEP_TIME	10
public static final int	THREAD_POOL_SIZE	9

org.biojavax.*

org.biojavax.bio.alignment.RemotePairwiseAlignmentOutputProperties

Modifier and Type	Constant Field	Value
public static final long	serialVersionUID	1L

org.biojavax.bio.alignment.RemotePairwiseAlignmentProperties

Modifier and Type	Constant Field	Value
public static final long	serialVersionUID	1L

org.biojavax.bio.db.ncbi.GenbankRichSequenceDB

Modifier and Type	Constant Field	Value
protected static final String	urlBatchSequences	"https://www.ncbi.nlm.nih.gov:80/entrez/eutils/efetch.fcgi"

org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB

Modifier and Type	Constant Field	Value
protected static final String	urlBatchSequences	"https://www.ncbi.nlm.nih.gov:80/entrez/eutils/efetch.fcgi"

org.biojavax.bio.seq.Position

Modifier and Type	Constant Field	Value
public static final String	BETWEEN_BASES	"^"
public static final String	IN_RANGE	"."

org.biojavax.bio.seq.RichSequence.Terms

Modifier and Type	Constant Field	Value
public static final String	DOI_KEY	"DOI"
public static final String	MEDLINE_KEY	"MEDLINE"
public static final String	PUBMED_KEY	"PUBMED"

org.biojavax.bio.seq.io.EMBLFormat

Modifier and Type	Constant Field	Value
protected static final String	ACCESSION_TAG	"AC"
protected static final String	AUTHORS_TAG	"RA"
protected static final String	COMMENT_TAG	"CC"
protected static final String	CONSORTIUM_TAG	"RG"
protected static final String	CONTIG_TAG	"CO"
protected static final String	DATABASE_XREF_TAG	"DR"
protected static final String	DATE_TAG	"DT"
protected static final String	DEFINITION_TAG	"DE"
protected static final String	DELIMITER_TAG	"XX"
public static final String	EMBL_FORMAT	"EMBL"
public static final String	EMBL_PRE87_FORMAT	"EMBL_PRE87"
protected static final String	END_SEQUENCE_TAG	"//"
protected static final String	FEATURE_HEADER_TAG	"FH"
protected static final String	FEATURE_TAG	"FT"
protected static final String	KEYWORDS_TAG	"KW"
protected static final String	LOCATOR_TAG	"RL"
protected static final String	LOCUS_TAG	"ID"
protected static final String	ORGANELLE_TAG	"OG"
protected static final String	ORGANISM_TAG	"OC"
protected static final String	REFERENCE_POSITION_TAG	"RP"
protected static final String	REFERENCE_TAG	"RN"
protected static final String	REFERENCE_XREF_TAG	"RX"
protected static final String	REMARK_TAG	"RC"
protected static final String	SOURCE_TAG	"OS"
protected static final String	START_SEQUENCE_TAG	"SQ"
protected static final String	TITLE_TAG	"RT"
protected static final String	TPA_TAG	"AH"
protected static final String	VERSION_TAG	"SV"

org.biojavax.bio.seq.io.EMBLxmlFormat

Modifier and Type	Constant Field	Value
protected static final String	AUTHOR_TAG	"author"
protected static final String	BASEPOSITION_TAG	"basePosition"
protected static final String	BASEPOSITION_TYPE_ATTR	"type"
protected static final String	CITATION_DATE_ATTR	"date"
protected static final String	CITATION_FIRST_ATTR	"first"
protected static final String	CITATION_ID_ATTR	"id"
protected static final String	CITATION_INSTITUTE_ATTR	"institute"
protected static final String	CITATION_ISSUE_ATTR	"issue"
protected static final String	CITATION_LAST_ATTR	"last"
protected static final String	CITATION_LOCATION_TAG	"citationLocation"
protected static final String	CITATION_NAME_ATTR	"name"
protected static final String	CITATION_PATENT_ATTR	"patentNumber"
protected static final String	CITATION_PUB_ATTR	"publisher"
protected static final String	CITATION_TAG	"citation"
protected static final String	CITATION_TYPE_ATTR	"type"
protected static final String	CITATION_VOL_ATTR	"volume"
protected static final String	CITATION_YEAR_ATTR	"year"
protected static final String	COMMENT_TAG	"comment"
protected static final String	COMNAME_TAG	"preferredCommonName"
protected static final String	CONSORTIUM_TAG	"consortium"
protected static final String	CONTIG_TAG	"contig"
protected static final String	DBREF_DB_ATTR	"db"
protected static final String	DBREF_PRIMARY_ATTR	"primary"
protected static final String	DBREF_SEC_ATTR	"secondary"
protected static final String	DBREFERENCE_TAG	"dbreference"
protected static final String	DESC_TAG	"description"
protected static final String	EDITOR_TAG	"editor"
public static final String	EMBLXML_FORMAT	"EMBLxml"
protected static final String	ENTRY_ACCESSION_ATTR	"accession"
protected static final String	ENTRY_CREATED_ATTR	"created"
protected static final String	ENTRY_DATACLASS_ATTR	"dataClass"
protected static final String	ENTRY_GROUP_TAG	"EMBL_Services"
protected static final String	ENTRY_RELCREATED_ATTR	"releaseCreated"
protected static final String	ENTRY_RELUPDATED_ATTR	"releaseLastUpdated"
protected static final String	ENTRY_STATUS_ATTR	"status"
protected static final String	ENTRY_STATUS_DATE_ATTR	"statusDate"
protected static final String	ENTRY_SUBACC_ATTR	"submitterAccession"
protected static final String	ENTRY_SUBVER_ATTR	"submitterVersion"
protected static final String	ENTRY_SUBWGSVER_ATTR	"submitterWgsVersion"
protected static final String	ENTRY_TAG	"entry"
protected static final String	ENTRY_TAX_DIVISION_ATTR	"taxonomicDivision"
protected static final String	ENTRY_UPDATED_ATTR	"lastUpdated"
protected static final String	ENTRY_VER_ATTR	"version"
protected static final String	FEATURE_NAME_ATTR	"name"
protected static final String	FEATURE_TAG	"feature"
protected static final String	KEYWORD_TAG	"keyword"
protected static final String	LINEAGE_TAG	"lineage"
protected static final String	LOC_ELEMENT_ACC_ATTR	"accession"
protected static final String	LOC_ELEMENT_COMPL_ATTR	"complement"
protected static final String	LOC_ELEMENT_TYPE_ATTR	"type"
protected static final String	LOC_ELEMENT_VER_ATTR	"version"
protected static final String	LOCATION_COMPL_ATTR	"complement"
protected static final String	LOCATION_ELEMENT_TAG	"locationElement"
protected static final String	LOCATION_TAG	"location"
protected static final String	LOCATION_TYPE_ATTR	"type"
protected static final String	LOCATOR_TAG	"locator"
protected static final String	ORGANELLE_TAG	"organelle"
protected static final String	ORGANISM_TAG	"organism"
protected static final String	PATENT_TAG	"patentApplicant"
protected static final String	PROJ_ACC_TAG	"projectAccession"
protected static final String	QUALIFIER_NAME_ATTR	"name"
protected static final String	QUALIFIER_TAG	"qualifier"
protected static final String	REF_POS_BEGIN_ATTR	"begin"
protected static final String	REF_POS_END_ATTR	"end"
protected static final String	REFERENCE_TAG	"reference"
protected static final String	SCINAME_TAG	"scientificName"
protected static final String	SEC_ACC_TAG	"secondaryAccession"
protected static final String	SEQUENCE_LENGTH_ATTR	"length"
protected static final String	SEQUENCE_TAG	"sequence"
protected static final String	SEQUENCE_TOPOLOGY_ATTR	"topology"
protected static final String	SEQUENCE_TYPE_ATTR	"type"
protected static final String	SEQUENCE_VER_ATTR	"version"
protected static final String	TAXID_TAG	"taxId"
protected static final String	TAXON_TAG	"taxon"
protected static final String	TITLE_TAG	"title"

org.biojavax.bio.seq.io.FastaFormat

Modifier and Type	Constant Field	Value
public static final String	FASTA_FORMAT	"FASTA"

org.biojavax.bio.seq.io.GenbankFormat

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	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	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.biojavax.bio.seq.io.INSDseqFormat

Modifier and Type	Constant Field	Value
protected static final String	ACC_VERSION_TAG	"INSDSeq_accession-version"
protected static final String	ACCESSION_TAG	"INSDSeq_primary-accession"
protected static final String	AUTHOR_TAG	"INSDAuthor"
protected static final String	AUTHORS_GROUP_TAG	"INSDReference_authors"
protected static final String	COMMENT_TAG	"INSDSeq_comment"
protected static final String	CONSORTIUM_TAG	"INSDReference_consortium"
protected static final String	CONTIG_TAG	"INSDSeq_contig"
protected static final String	CREATE_DATE_TAG	"INSDSeq_create-date"
protected static final String	CREATE_REL_TAG	"INSDSeq_create-release"
protected static final String	DATABASE_XREF_TAG	"INSDSeq_database-reference"
protected static final String	DEFINITION_TAG	"INSDSeq_definition"
protected static final String	DIVISION_TAG	"INSDSeq_division"
protected static final String	FEATURE_ACCESSION_TAG	"INSDInterval_accession"
protected static final String	FEATURE_FROM_TAG	"INSDInterval_from"
protected static final String	FEATURE_INTERBP_TAG	"INSDInterval_interbp"
protected static final String	FEATURE_INTERVAL_TAG	"INSDInterval"
protected static final String	FEATURE_INTERVALS_GROUP_TAG	"INSDFeature_intervals"
protected static final String	FEATURE_ISCOMP_TAG	"INSDInterval_iscomp"
protected static final String	FEATURE_KEY_TAG	"INSDFeature_key"
protected static final String	FEATURE_LOC_TAG	"INSDFeature_location"
protected static final String	FEATURE_OPERATOR_TAG	"INSDFeature_operator"
protected static final String	FEATURE_PARTIAL3_TAG	"INSDFeature_partial3"
protected static final String	FEATURE_PARTIAL5_TAG	"INSDFeature_partial5"
protected static final String	FEATURE_POINT_TAG	"INSDInterval_point"
protected static final String	FEATURE_TAG	"INSDFeature"
protected static final String	FEATURE_TO_TAG	"INSDInterval_to"
protected static final String	FEATUREQUAL_NAME_TAG	"INSDQualifier_name"
protected static final String	FEATUREQUAL_TAG	"INSDQualifier"
protected static final String	FEATUREQUAL_VALUE_TAG	"INSDQualifier_value"
protected static final String	FEATUREQUALS_GROUP_TAG	"INSDFeature_quals"
protected static final String	FEATURES_GROUP_TAG	"INSDSeq_feature-table"
public static final String	INSDSEQ_FORMAT	"INSDseq"
protected static final String	INSDSEQ_TAG	"INSDSeq"
protected static final String	INSDSEQS_GROUP_TAG	"INSDSet"
protected static final String	JOURNAL_TAG	"INSDReference_journal"
protected static final String	KEYWORD_TAG	"INSDKeyword"
protected static final String	KEYWORDS_GROUP_TAG	"INSDSeq_keywords"
protected static final String	LENGTH_TAG	"INSDSeq_length"
protected static final String	LOCUS_TAG	"INSDSeq_locus"
protected static final String	MOLTYPE_TAG	"INSDSeq_moltype"
protected static final String	ORGANISM_TAG	"INSDSeq_organism"
protected static final String	OTHER_SEQID_TAG	"INSDSeqid"
protected static final String	OTHER_SEQIDS_GROUP_TAG	"INSDSeq_other-seqids"
protected static final String	PUBMED_TAG	"INSDReference_pubmed"
protected static final String	REFERENCE_LOCATION_TAG	"INSDReference_reference"
protected static final String	REFERENCE_POSITION_TAG	"INSDReference_position"
protected static final String	REFERENCE_TAG	"INSDReference"
protected static final String	REFERENCES_GROUP_TAG	"INSDSeq_references"
protected static final String	REMARK_TAG	"INSDReference_remark"
protected static final String	SECONDARY_ACCESSION_TAG	"INSDSecondary-accn"
protected static final String	SECONDARY_ACCESSIONS_GROUP_TAG	"INSDSeq_secondary-accessions"
protected static final String	SEQUENCE_TAG	"INSDSeq_sequence"
protected static final String	SOURCE_TAG	"INSDSeq_source"
protected static final String	STRANDED_TAG	"INSDSeq_strandedness"
protected static final String	TAXONOMY_TAG	"INSDSeq_taxonomy"
protected static final String	TITLE_TAG	"INSDReference_title"
protected static final String	TOPOLOGY_TAG	"INSDSeq_topology"
protected static final String	UPDATE_DATE_TAG	"INSDSeq_update-date"
protected static final String	UPDATE_REL_TAG	"INSDSeq_update-release"
protected static final String	XREF_DBNAME_TAG	"INSDXref_dbname"
protected static final String	XREF_ID_TAG	"INSDXref_id"
protected static final String	XREF_TAG	"INSDXref"

org.biojavax.bio.seq.io.RichSequenceBuilderFactory

Modifier and Type	Constant Field	Value
public static final int	THRESHOLD_VALUE	5000

org.biojavax.bio.seq.io.UniProtCommentParser

Modifier and Type	Constant Field	Value
public static final String	ALTERNATIVE_PRODUCTS	"ALTERNATIVE PRODUCTS"
public static final String	BIOPHYSICOCHEMICAL_PROPERTIES	"BIOPHYSICOCHEMICAL PROPERTIES"
public static final String	DATABASE	"DATABASE"
public static final String	INTERACTION	"INTERACTION"
public static final String	MASS_SPECTROMETRY	"MASS SPECTROMETRY"
public static final String	PTM	"PTM"
public static final String	SEQUENCE_CAUTION	"SEQUENCE CAUTION"

org.biojavax.bio.seq.io.UniProtFormat

Modifier and Type	Constant Field	Value
protected static final String	ACCESSION_TAG	"AC"
protected static final String	AUTHORS_TAG	"RA"
protected static final String	COMMENT_TAG	"CC"
protected static final String	CONSORTIUM_TAG	"RG"
protected static final String	DATABASE_XREF_TAG	"DR"
protected static final String	DATE_TAG	"DT"
protected static final String	DEFINITION_TAG	"DE"
protected static final String	END_SEQUENCE_TAG	"//"
protected static final String	FEATURE_TAG	"FT"
protected static final String	GENE_TAG	"GN"
protected static final String	KEYWORDS_TAG	"KW"
protected static final String	LOCATION_TAG	"RL"
protected static final String	LOCUS_TAG	"ID"
protected static final String	ORGANELLE_TAG	"OG"
protected static final String	ORGANISM_TAG	"OC"
protected static final String	PROTEIN_EXIST_TAG	"PE"
protected static final String	RC_LINE_TAG	"RC"
protected static final String	REFERENCE_TAG	"RN"
protected static final String	REFERENCE_XREF_TAG	"RX"
protected static final String	RP_LINE_TAG	"RP"
protected static final String	SOURCE_TAG	"OS"
protected static final String	START_SEQUENCE_TAG	"SQ"
protected static final String	TAXON_TAG	"OX"
protected static final String	TITLE_TAG	"RT"
public static final String	UNIPROT_FORMAT	"UniProt"

org.biojavax.bio.seq.io.UniProtXMLFormat

Modifier and Type	Constant Field	Value
protected static final String	ACCESSION_TAG	"accession"
protected static final String	AUTHOR_LIST_TAG	"authorList"
protected static final String	CITATION_TAG	"citation"
protected static final String	COMMENT_ABS_MAX_TAG	"max"
protected static final String	COMMENT_ABSORPTION_TAG	"absorption"
protected static final String	COMMENT_ERROR_ATTR	"error"
protected static final String	COMMENT_EVENT_TAG	"event"
protected static final String	COMMENT_EXPERIMENTS_TAG	"experiments"
protected static final String	COMMENT_INTERACT_INTACT_ATTR	"intactId"
protected static final String	COMMENT_INTERACT_LABEL_TAG	"label"
protected static final String	COMMENT_INTERACTANT_TAG	"interactant"
protected static final String	COMMENT_ISOFORM_TAG	"isoform"
protected static final String	COMMENT_KIN_KM_TAG	"KM"
protected static final String	COMMENT_KIN_VMAX_TAG	"VMax"
protected static final String	COMMENT_KINETICS_TAG	"kinetics"
protected static final String	COMMENT_LINK_TAG	"link"
protected static final String	COMMENT_LINK_URI_ATTR	"uri"
protected static final String	COMMENT_LOCTYPE_ATTR	"locationType"
protected static final String	COMMENT_MASS_ATTR	"mass"
protected static final String	COMMENT_METHOD_ATTR	"method"
protected static final String	COMMENT_ORGANISMS_TAG	"organismsDiffer"
protected static final String	COMMENT_PH_TAG	"phDependence"
protected static final String	COMMENT_REDOX_TAG	"redoxPotential"
protected static final String	COMMENT_TAG	"comment"
protected static final String	COMMENT_TEMPERATURE_TAG	"temperatureDependence"
protected static final String	COMPONENT_TAG	"component"
protected static final String	CONSORTIUM_TAG	"consortium"
protected static final String	COPYRIGHT_TAG	"copyright"
protected static final String	DBXREF_TAG	"dbReference"
protected static final String	DOMAIN_TAG	"domain"
protected static final String	EDITOR_LIST_TAG	"editorList"
protected static final String	ENTRY_CREATED_ATTR	"created"
protected static final String	ENTRY_GROUP_TAG	"uniprot"
protected static final String	ENTRY_NAMESPACE_ATTR	"dataset"
protected static final String	ENTRY_TAG	"entry"
protected static final String	ENTRY_UPDATED_ATTR	"modified"
protected static final String	ENTRY_VERSION_ATTR	"version"
protected static final String	EVIDENCE_ATTR	"evidence"
protected static final String	EVIDENCE_ATTRIBUTE_ATTR	"attribute"
protected static final String	EVIDENCE_CATEGORY_ATTR	"category"
protected static final String	EVIDENCE_DATE_ATTR	"date"
protected static final String	EVIDENCE_TAG	"evidence"
protected static final String	FEATURE_DESC_ATTR	"description"
protected static final String	FEATURE_ORIGINAL_TAG	"original"
protected static final String	FEATURE_TAG	"feature"
protected static final String	FEATURE_VARIATION_TAG	"variation"
protected static final String	GENE_TAG	"gene"
protected static final String	GENELOCATION_NAME_TAG	"name"
protected static final String	GENELOCATION_TAG	"geneLocation"
protected static final String	ID_ATTR	"id"
protected static final String	ID_TAG	"id"
protected static final String	KEY_ATTR	"key"
protected static final String	KEYWORD_TAG	"keyword"
protected static final String	LINEAGE_TAG	"lineage"
protected static final String	LOCATION_BEGIN_TAG	"begin"
protected static final String	LOCATION_END_TAG	"end"
protected static final String	LOCATION_POSITION_ATTR	"position"
protected static final String	LOCATION_POSITION_TAG	"position"
protected static final String	LOCATION_SEQ_ATTR	"sequence"
protected static final String	LOCATION_TAG	"location"
protected static final String	LOCATOR_TAG	"locator"
protected static final String	NAME_ATTR	"name"
protected static final String	NAME_TAG	"name"
protected static final String	NOTE_TAG	"note"
protected static final String	ORGANISM_TAG	"organism"
protected static final String	PERSON_TAG	"person"
protected static final String	PROPERTY_TAG	"property"
protected static final String	PROTEIN_EXISTS_TAG	"proteinExistence"
protected static final String	PROTEIN_TAG	"protein"
protected static final String	PROTEIN_TYPE_ATTR	"type"
protected static final String	RC_LINE_TAG	"source"
protected static final String	RC_PLASMID_TAG	"plasmid"
protected static final String	RC_SPECIES_TAG	"species"
protected static final String	RC_STRAIN_TAG	"strain"
protected static final String	RC_TISSUE_TAG	"tissue"
protected static final String	RC_TRANSP_TAG	"transposon"
protected static final String	REF_ATTR	"ref"
protected static final String	REFERENCE_TAG	"reference"
protected static final String	RP_LINE_TAG	"scope"
protected static final String	SEQUENCE_CHECKSUM_ATTR	"checksum"
protected static final String	SEQUENCE_LENGTH_ATTR	"length"
protected static final String	SEQUENCE_MASS_ATTR	"mass"
protected static final String	SEQUENCE_MODIFIED_ATTR	"modified"
protected static final String	SEQUENCE_TAG	"sequence"
protected static final String	SEQUENCE_VERSION_ATTR	"version"
protected static final String	STATUS_ATTR	"value"
protected static final String	TAXON_TAG	"taxon"
protected static final String	TEXT_TAG	"text"
protected static final String	TITLE_TAG	"title"
protected static final String	TYPE_ATTR	"type"
public static final String	UNIPROTXML_FORMAT	"UniProtXML"
protected static final String	VALUE_ATTR	"value"

org.biojavax.bio.seq.io.UniProtXMLFormat.Terms

Modifier and Type	Constant Field	Value
public static final String	ABBREV_NAME_KEY	"abbreviation"
public static final String	COMMON_NAME_KEY	"common"
public static final String	CONTAINS_PREFIX	"Contains:"
public static final String	FULL_NAME_KEY	"full"
public static final String	GENENAME_KEY	"primary"
public static final String	GENESYNONYM_KEY	"synonym"
public static final String	INCLUDES_PREFIX	"Includes:"
public static final String	LOC_FUZZY_END_KEY	"greater than"
public static final String	LOC_FUZZY_START_KEY	"less than"
public static final String	NCBI_TAXON_KEY	"NCBI Taxonomy"
public static final String	ORDLOCNAME_KEY	"ordered locus"
public static final String	ORFNAME_KEY	"ORF"
public static final String	SCIENTIFIC_NAME_KEY	"scientific"
public static final String	SYNONYM_NAME_KEY	"synonym"

org.biojavax.bio.taxa.NCBITaxon

Modifier and Type	Constant Field	Value
public static final String	ACRONYM	"acronym"
public static final String	COMMON	"common name"
public static final String	EQUIVALENT	"equivalent name"
public static final String	SCIENTIFIC	"scientific name"
public static final String	SYNONYM	"synonym"

org.biojavax.ga.functions.CrossOverFunction

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_MAX_CROSS	2147483647