Constant Field Values

Contents

• org.biojava.*

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 java.lang.String	PROP_CRITERIONS	"criterions"
public static final java.lang.String	PROP_EXCLUDED_ATTRS	"excluded"

org.biojava.bibliography.BibRefSupport

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

Modifier and Type	Constant Field	Value
public static final java.lang.String	DNA	"dna"
public static final java.lang.String	OFFSETS	"trace-offsets"

org.biojava.bio.chromatogram.ChromatogramFactory

Modifier and Type	Constant Field	Value
public static final int	ABI_MAGIC	1094863174
public static final int	SCF_MAGIC	779314022

org.biojava.bio.dp.SimpleMarkovModel

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

org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer

Modifier and Type	Constant Field	Value
public static final java.lang.String	LANE	"Lane"

org.biojava.bio.gui.sequence.ImageMap

Modifier and Type	Constant Field	Value
public static final java.lang.String	CIRCLE	"circle"
public static final java.lang.String	POLY	"poly"
public static final java.lang.String	RECT	"rect"

org.biojava.bio.gui.sequence.OffsetRulerRenderer

Modifier and Type	Constant Field	Value
public static final int	TICKS_DOWN	1
public static final int	TICKS_UP	0

org.biojava.bio.gui.sequence.RulerRenderer

Modifier and Type	Constant Field	Value
public static final int	TICKS_DOWN	1
public static final int	TICKS_UP	0

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 java.lang.String	REBASE_DATA_KEY	"rebase.data.file"
public static final java.lang.String	REBASE_TAG_COMM	"<7>"
public static final java.lang.String	REBASE_TAG_ISZR	"<2>"
public static final java.lang.String	REBASE_TAG_METH	"<4>"
public static final java.lang.String	REBASE_TAG_NAME	"<1>"
public static final java.lang.String	REBASE_TAG_ORGN	"<5>"
public static final java.lang.String	REBASE_TAG_REFS	"<8>"
public static final java.lang.String	REBASE_TAG_SITE	"<3>"
public static final java.lang.String	REBASE_TAG_SRCE	"<6>"

org.biojava.bio.molbio.RestrictionMapper

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

org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord

Modifier and Type	Constant Field	Value
public static final int	DATA_TYPE_ASCII_ARRAY	2
public static final int	DATA_TYPE_DATE	10
public static final int	DATA_TYPE_FLOAT	7
public static final int	DATA_TYPE_INTEGER	4
public static final int	DATA_TYPE_PSTRING	18
public static final int	DATA_TYPE_TIME	11

org.biojava.bio.program.gff.GFFEntrySet

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

org.biojava.bio.program.indexdb.BioStoreFactory

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

org.biojava.bio.program.phred.PhredFormat

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

org.biojava.bio.program.scf.SCF

Modifier and Type	Constant Field	Value
public static final int	BYTE_MAX_VALUE	256
public static final java.lang.String	PROB_NUC_A	"quality-a"
public static final java.lang.String	PROB_NUC_C	"quality-c"
public static final java.lang.String	PROB_NUC_G	"quality-g"
public static final java.lang.String	PROB_NUC_T	"quality-t"
public static final int	SHORT_MAX_VALUE	65536

org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder

Modifier and Type	Constant Field	Value
public static final java.lang.String	HOMOLOGY_FEATURE_TYPE	"homology"

org.biojava.bio.program.ssbind.SeqSimilarityStAXAdapter

Modifier and Type	Constant Field	Value
public static final java.lang.String	NAMESPACE	"http://www.biojava.org"

org.biojava.bio.program.ssbind.SimilarityPairBuilder

Modifier and Type	Constant Field	Value
public static final java.lang.String	SIMILARITY_PAIR_FEATURE_TYPE	"similarity"

org.biojava.bio.program.tagvalue.StateMachine

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

org.biojava.bio.program.tagvalue.TagValueParser

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

org.biojava.bio.program.xff.XFFFeatureSetHandler

Modifier and Type	Constant Field	Value
public static final java.lang.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 java.lang.String	XFF_BIOJAVA_NS	"http://www.biojava.org/2001/xff-biojava"
public static final java.lang.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 java.lang.String	ARG_C	"Arg-C"
public static final java.lang.String	ASP_N	"Asp-N"
public static final java.lang.String	CHYMOTRYP	"Chymotrypsin"
public static final java.lang.String	CNBr	"CNBr"
public static final java.lang.String	GLU_C_BICARB	"Glu-C-bicarbonate"
public static final java.lang.String	GLU_C_PHOS	"Glu-C-phosphate"
public static final java.lang.String	LYS_C	"Lys-C"
public static final java.lang.String	TRYPSIN	"Trypsin"

org.biojava.bio.proteomics.ProteaseManager

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

org.biojava.bio.search.BlastLikeSearchFilter

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

org.biojava.bio.search.SeqSimilaritySearchSubHit

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

org.biojava.bio.seq.Feature

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

org.biojava.bio.seq.FeatureTypes

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

org.biojava.bio.seq.homol.SimilarityPairFeature

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

org.biojava.bio.seq.io.EmblProcessor

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

org.biojava.bio.seq.io.GAMEFormat

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

org.biojava.bio.seq.io.GenbankFormat

Modifier and Type	Constant Field	Value
protected static final java.lang.String	ACCESSION_TAG	"ACCESSION"
protected static final java.lang.String	AUTHORS_TAG	"AUTHORS"
protected static final java.lang.String	BASE_COUNT_TAG	"BASE"
protected static final java.lang.String	CIRCULAR_TAG	"CIRCULAR"
protected static final java.lang.String	COMMENT_TAG	"COMMENT"
protected static final java.lang.String	COORDINATE_TAG	"COORDINATE"
protected static final java.lang.String	DATE_TAG	"MDAT"
public static final java.lang.String	DEFAULT	"GENBANK"
protected static final java.lang.String	DEFINITION_TAG	"DEFINITION"
protected static final java.lang.String	DIVISION_TAG	"DIVISION"
protected static final java.lang.String	END_SEQUENCE_TAG	"//"
protected static final java.lang.String	FEATURE_FLAG	"FT"
protected static final java.lang.String	FEATURE_LINE_PREFIX	" "
protected static final java.lang.String	FEATURE_TAG	"FEATURES"
protected static final java.lang.String	GI_TAG	"GI"
protected static final java.lang.String	JOURNAL_TAG	"JOURNAL"
protected static final java.lang.String	KEYWORDS_TAG	"KW"
protected static final java.lang.String	LOCUS_TAG	"LOCUS"
protected static final java.lang.String	MEDLINE_TAG	"MEDLINE"
protected static final java.lang.String	ORGANISM_TAG	"ORGANISM"
protected static final java.lang.String	PUBMED_TAG	"PUBMED"
protected static final java.lang.String	REF_ACCESSION_TAG	""
protected static final java.lang.String	REFERENCE_TAG	"REFERENCE"
protected static final java.lang.String	SIZE_TAG	"SIZE"
protected static final java.lang.String	SOURCE_TAG	"SOURCE"
protected static final java.lang.String	START_SEQUENCE_TAG	"ORIGIN"
protected static final java.lang.String	STRAND_NUMBER_TAG	"STRANDS"
protected static final java.lang.String	TITLE_TAG	"TITLE"
protected static final java.lang.String	TYPE_TAG	"TYPE"
protected static final java.lang.String	VERSION_TAG	"VERSION"

org.biojava.bio.seq.io.GenbankProcessor

Modifier and Type	Constant Field	Value
public static final java.lang.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.SequenceDBSequenceBuilder

Modifier and Type	Constant Field	Value
public static final int	ANNOTATE_EXISTING	1
public static final int	CREATE_DUMMYSEQ	2
public static final int	CREATE_REALSEQ	3

org.biojava.bio.seq.io.SwissprotProcessor

Modifier and Type	Constant Field	Value
public static final java.lang.String	PROPERTY_SWISSPROT_ACCESSIONS	"swissprot.accessions"
public static final java.lang.String	PROPERTY_SWISSPROT_COMMENT	"swissprot.comment"
public static final java.lang.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 java.lang.String	QUALIFIER	"qualifier"
public static final java.lang.String	RESULT_PROPERTY	"result_property"
public static final java.lang.String	SCI_PROPERTY	"sci_property"
public static final java.lang.String	XREF_PROPERTY	"xref_property"

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

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

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

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

org.biojava.bio.symbol.TranslationTable

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

org.biojava.bio.symbol.UkkonenSuffixTree

Modifier and Type	Constant Field	Value
public static final char	DEFAULT_TERM_CHAR	36
public static final int	TO_A_LEAF	-1

org.biojava.directory.SystemRegistry

Modifier and Type	Constant Field	Value
public static final java.lang.String	CONFIG_FILE	"seqdatabase.ini"
public static final java.lang.String	CONFIG_LOCATOR	"http://www.open-bio.org/registry/seqdatabase.ini"
public static final java.lang.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 java.lang.String	ALT_ID	"alt_id"
public static final java.lang.String	BROAD_SYNONYM	"broad_synonym"
public static final java.lang.String	COMMENT	"comment"
public static final java.lang.String	DEF	"def"
public static final java.lang.String	DISJOINT_FROM	"disjoint_from"
public static final java.lang.String	EXACT_SYNONYM	"exact_synonym"
public static final java.lang.String	ID_KEY	"id"
public static final java.lang.String	INTERSECTION_OF	"intersection_of"
public static final java.lang.String	IS_A	"is_a"
public static final java.lang.String	IS_OBSOLETE	"is_obsolete"
public static final java.lang.String	NAME	"name"
public static final java.lang.String	NARROW_SYNONYM	"narrow_synonym"
public static final java.lang.String	ONTOLOGY	"ontologys"
public static final java.lang.String	REL_SYNONYM	"related_synonym"
public static final java.lang.String	RELATIONSHIP	"relationship"
public static final java.lang.String	SUBSET	"subset"
public static final java.lang.String	SYNONYM	"synonym"
public static final java.lang.String	TERM	"Term"
public static final java.lang.String	TYPEDEF	"Typedef"
public static final java.lang.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 java.lang.String	DEFAULT_DELIMITERS	",;\t"

org.biojava.utils.bytecode.ByteCode

Modifier and Type	Constant Field	Value
public static final byte	op_aaload	50
public static final byte	op_aastore	83
public static final byte	op_aconst_null	1
public static final byte	op_aload	25
public static final byte	op_aload_0	42
public static final byte	op_aload_1	43
public static final byte	op_aload_2	44
public static final byte	op_aload_3	45
public static final byte	op_anewarray	-67
public static final byte	op_anewarray_quick	-34
public static final byte	op_areturn	-80
public static final byte	op_arraylength	-66
public static final byte	op_astore	58
public static final byte	op_astore_0	75
public static final byte	op_astore_1	76
public static final byte	op_astore_2	77
public static final byte	op_astore_3	78
public static final byte	op_athrow	-65
public static final byte	op_baload	51
public static final byte	op_bastore	84
public static final byte	op_bipush	16
public static final byte	op_breakpoint	-54
public static final byte	op_caload	52
public static final byte	op_castore	85
public static final byte	op_checkcast	-64
public static final byte	op_checkcast_quick	-32
public static final byte	op_d2f	-112
public static final byte	op_d2i	-114
public static final byte	op_d2l	-113
public static final byte	op_dadd	99
public static final byte	op_daload	49
public static final byte	op_dastore	82
public static final byte	op_dcmpg	-104
public static final byte	op_dcmpl	-105
public static final byte	op_dconst_0	14
public static final byte	op_dconst_1	15
public static final byte	op_ddiv	111
public static final byte	op_dload	24
public static final byte	op_dload_0	38
public static final byte	op_dload_1	39
public static final byte	op_dload_2	40
public static final byte	op_dload_3	41
public static final byte	op_dmul	107
public static final byte	op_dneg	119
public static final byte	op_drem	115
public static final byte	op_dreturn	-81
public static final byte	op_dstore	57
public static final byte	op_dstore_0	71
public static final byte	op_dstore_1	72
public static final byte	op_dstore_2	73
public static final byte	op_dstore_3	74
public static final byte	op_dsub	103
public static final byte	op_dup	89
public static final byte	op_dup_x1	90
public static final byte	op_dup_x2	91
public static final byte	op_dup2	92
public static final byte	op_dup2_x1	93
public static final byte	op_dup2_x2	94
public static final byte	op_f2d	-115
public static final byte	op_f2i	-117
public static final byte	op_f2l	-116
public static final byte	op_fadd	98
public static final byte	op_faload	48
public static final byte	op_fastore	81
public static final byte	op_fcmpg	-106
public static final byte	op_fcmpl	-107
public static final byte	op_fconst_0	11
public static final byte	op_fconst_1	12
public static final byte	op_fconst_2	13
public static final byte	op_fdiv	110
public static final byte	op_fload	23
public static final byte	op_fload_0	34
public static final byte	op_fload_1	35
public static final byte	op_fload_2	36
public static final byte	op_fload_3	37
public static final byte	op_fmul	106
public static final byte	op_fneg	118
public static final byte	op_frem	114
public static final byte	op_freturn	-82
public static final byte	op_fstore	56
public static final byte	op_fstore_0	67
public static final byte	op_fstore_1	68
public static final byte	op_fstore_2	69
public static final byte	op_fstore_3	70
public static final byte	op_fsub	102
public static final byte	op_getfield	-76
public static final byte	op_getfield_quick	-50
public static final byte	op_getfield_quick_w	-29
public static final byte	op_getfield2_quick	-48
public static final byte	op_getstatic	-78
public static final byte	op_getstatic_quick	-46
public static final byte	op_getstatic2_quick	-44
public static final byte	op_goto	-89
public static final byte	op_goto_w	-56
public static final byte	op_i2b	-111
public static final byte	op_i2c	-110
public static final byte	op_i2d	-121
public static final byte	op_i2f	-122
public static final byte	op_i2l	-123
public static final byte	op_i2s	-109
public static final byte	op_iadd	96
public static final byte	op_iaload	46
public static final byte	op_iand	126
public static final byte	op_iastore	79
public static final byte	op_iconst_0	3
public static final byte	op_iconst_1	4
public static final byte	op_iconst_2	5
public static final byte	op_iconst_3	6
public static final byte	op_iconst_4	7
public static final byte	op_iconst_5	8
public static final byte	op_iconst_m1	2
public static final byte	op_idiv	108
public static final byte	op_if_acmpeq	-91
public static final byte	op_if_acmpne	-90
public static final byte	op_if_icmpeq	-97
public static final byte	op_if_icmpge	-94
public static final byte	op_if_icmpgt	-93
public static final byte	op_if_icmple	-92
public static final byte	op_if_icmplt	-95
public static final byte	op_if_icmpne	-96
public static final byte	op_ifeq	-103
public static final byte	op_ifge	-100
public static final byte	op_ifgt	-99
public static final byte	op_ifle	-98
public static final byte	op_iflt	-101
public static final byte	op_ifne	-102
public static final byte	op_ifnonnull	-57
public static final byte	op_ifnull	-58
public static final byte	op_iinc	-124
public static final byte	op_iload	21
public static final byte	op_iload_0	26
public static final byte	op_iload_1	27
public static final byte	op_iload_2	28
public static final byte	op_iload_3	29
public static final byte	op_impdep1	-2
public static final byte	op_impdep2	-1
public static final byte	op_imul	104
public static final byte	op_ineg	116
public static final byte	op_instanceof	-63
public static final byte	op_instanceof_quick	-31
public static final byte	op_invokeinterface	-71
public static final byte	op_invokeinterface_quick	-38
public static final byte	op_invokenonvirtual_quick	-41
public static final byte	op_invokespecial	-73
public static final byte	op_invokestatic	-72
public static final byte	op_invokestatic_quick	-39
public static final byte	op_invokesuper_quick	-40
public static final byte	op_invokevirtual	-74
public static final byte	op_invokevirtual_quick	-42
public static final byte	op_invokevirtual_quick_w	-30
public static final byte	op_invokevirtualobject_quick	-37
public static final byte	op_ior	-128
public static final byte	op_irem	112
public static final byte	op_ireturn	-84
public static final byte	op_ishl	120
public static final byte	op_ishr	122
public static final byte	op_istore	54
public static final byte	op_istore_0	59
public static final byte	op_istore_1	60
public static final byte	op_istore_2	61
public static final byte	op_istore_3	62
public static final byte	op_isub	100
public static final byte	op_iushr	124
public static final byte	op_ixor	-126
public static final byte	op_jsr	-88
public static final byte	op_jsr_w	-55
public static final byte	op_l2d	-118
public static final byte	op_l2f	-119
public static final byte	op_l2i	-120
public static final byte	op_ladd	97
public static final byte	op_laload	47
public static final byte	op_land	127
public static final byte	op_lastore	80
public static final byte	op_lcmp	-108
public static final byte	op_lconst_0	9
public static final byte	op_lconst_1	10
public static final byte	op_ldc	18
public static final byte	op_ldc_quick	-53
public static final byte	op_ldc_w	19
public static final byte	op_ldc_w_quick	-52
public static final byte	op_ldc2_w	20
public static final byte	op_ldc2_w_quick	-51
public static final byte	op_ldiv	109
public static final byte	op_lload	22
public static final byte	op_lload_0	30
public static final byte	op_lload_1	31
public static final byte	op_lload_2	32
public static final byte	op_lload_3	33
public static final byte	op_lmul	105
public static final byte	op_lneg	117
public static final byte	op_lookupswitch	-85
public static final byte	op_lor	-127
public static final byte	op_lrem	113
public static final byte	op_lreturn	-83
public static final byte	op_lshl	121
public static final byte	op_lshr	123
public static final byte	op_lstore	55
public static final byte	op_lstore_0	63
public static final byte	op_lstore_1	64
public static final byte	op_lstore_2	65
public static final byte	op_lstore_3	66
public static final byte	op_lsub	101
public static final byte	op_lushr	125
public static final byte	op_lxor	-125
public static final byte	op_monitorenter	-62
public static final byte	op_monitorexit	-61
public static final byte	op_multianewarray	-59
public static final byte	op_multianewarray_quick	-33
public static final byte	op_new	-69
public static final byte	op_new_quick	-35
public static final byte	op_newarray	-68
public static final byte	op_nop	0
public static final byte	op_pop	87
public static final byte	op_pop2	88
public static final byte	op_putfield	-75
public static final byte	op_putfield_quick	-49
public static final byte	op_putfield_quick_w	-28
public static final byte	op_putfield2_quick	-47
public static final byte	op_putstatic	-77
public static final byte	op_putstatic_quick	-45
public static final byte	op_putstatic2_quick	-43
public static final byte	op_ret	-87
public static final byte	op_return	-79
public static final byte	op_saload	53
public static final byte	op_sastore	86
public static final byte	op_sipush	17
public static final byte	op_swap	95
public static final byte	op_tableswitch	-86
public static final byte	op_wide	-60

org.biojava.utils.bytecode.CodeUtils

Modifier and Type	Constant Field	Value
public static final int	ACC_ABSTRACT	1024
public static final int	ACC_FINAL	16
public static final int	ACC_INTERFACE	512
public static final int	ACC_NATIVE	256
public static final int	ACC_PRIVATE	2
public static final int	ACC_PROTECTED	4
public static final int	ACC_PUBLIC	1
public static final int	ACC_STATIC	8
public static final int	ACC_STRICT	2048
public static final int	ACC_SUPER	32
public static final int	ACC_SYNCHRONIZED	32
public static final int	ACC_TRANSIENT	128
public static final int	ACC_VOLATILE	64

org.biojava.utils.candy.CandyFinder

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

org.biojava.utils.candy.CandyVocabulary

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

org.biojava.utils.io.InputStreamProvider

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

org.biojavax.bio.phylo.io.nexus.CharactersBlock

Modifier and Type	Constant Field	Value
public static final java.lang.String	CHARACTERS_BLOCK	"CHARACTERS"

org.biojavax.bio.phylo.io.nexus.DataBlock

Modifier and Type	Constant Field	Value
public static final java.lang.String	DATA_BLOCK	"DATA"

org.biojavax.bio.phylo.io.nexus.DistancesBlock

Modifier and Type	Constant Field	Value
public static final java.lang.String	DISTANCES_BLOCK	"DISTANCES"

org.biojavax.bio.phylo.io.nexus.NexusBlockParser

Modifier and Type	Constant Field	Value
public static final java.lang.String	UNKNOWN_BLOCK	"__UNKNOWN"

org.biojavax.bio.phylo.io.nexus.TaxaBlock

Modifier and Type	Constant Field	Value
public static final java.lang.String	TAXA_BLOCK	"TAXA"

org.biojavax.bio.phylo.io.nexus.TreesBlock

Modifier and Type	Constant Field	Value
public static final java.lang.String	TREES_BLOCK	"TREES"

org.biojavax.bio.seq.Position

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

org.biojavax.bio.seq.RichSequence.Terms

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

org.biojavax.bio.seq.io.EMBLFormat

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

org.biojavax.bio.seq.io.EMBLxmlFormat

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

org.biojavax.bio.seq.io.FastaFormat

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

org.biojavax.bio.seq.io.GenbankFormat

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

org.biojavax.bio.seq.io.INSDseqFormat

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

org.biojavax.bio.seq.io.UniProtFormat

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

org.biojavax.bio.seq.io.UniProtXMLFormat

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

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

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

org.biojavax.bio.taxa.NCBITaxon

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

org.biojavax.ga.functions.CrossOverFunction

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