# Constant Field Values

Contents

- org.biojava.*

org.biojava.*

org.biojava.bibliography.BiblioCriterion
`public static final int` `QUERY_CRITERION` `0`
`public static final int` `SORT_CRITERION` `1`

org.biojava.bibliography.BibRefQuery
`public static final String` `PROP_CRITERIONS` `"criterions"`
`public static final String` `PROP_EXCLUDED_ATTRS` `"excluded"`

org.biojava.bibliography.BibRefSupport
`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
`public static final int` `UNCLASSIFIED` `99`
`public static final int` `UNDEFINED` `-1`

org.biojava.bio.chromatogram.ChromatogramFactory
`public static final int` `ABI_MAGIC` `1094863174`
`public static final int` `SCF_MAGIC` `779314022`

org.biojava.bio.dp.SimpleMarkovModel
`public static final long` `serialVersionUID` `-3043028839927615753L`

org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
`public static final String` `LANE` `"Lane"`

org.biojava.bio.gui.sequence.ImageMap
`public static final String` `CIRCLE` `"circle"`
`public static final String` `POLY` `"poly"`
`public static final String` `RECT` `"rect"`

org.biojava.bio.gui.sequence.OffsetRulerRenderer
`public static final int` `TICKS_DOWN` `1`
`public static final int` `TICKS_UP` `0`

org.biojava.bio.gui.sequence.RulerRenderer
`public static final int` `TICKS_DOWN` `1`
`public static final int` `TICKS_UP` `0`

org.biojava.bio.molbio.RestrictionEnzyme
`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
`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
`public static final String` `SITE_FEATURE_SOURCE` `"regex"`
`public static final String` `SITE_FEATURE_TYPE` `"misc_binding"`

org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
`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.das.DASSequence
`public static final String` `PROPERTY_ANNOTATIONSERVER` `"org.biojava.bio.program.das.annotation_server"`
`public static final String` `PROPERTY_FEATUREID` `"org.biojava.bio.program.das.feature_id"`
`public static final String` `PROPERTY_FEATURELABEL` `"org.biojava.bio.program.das.feature_label"`
`public static final String` `PROPERTY_LINKS` `"org.biojava.bio.program.das.links"`
`public static final String` `PROPERTY_SEQUENCEVERSION` `"org.biojava.bio.program.das.sequence_version"`
`public static final int` `SIZE_THRESHOLD` `500000`

org.biojava.bio.program.gff.GFFEntrySet
`public static final String` `PROPERTY_GFF_SCORE` `"org.biojava.bio.program.gff.gff_feature_score"`

org.biojava.bio.program.homologene.HomologeneBuilder
`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
`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
`public static final String` `DEFAULT` `"PHRED"`
`public static final String` `PROPERTY_DESCRIPTIONLINE` `"description_line"`

org.biojava.bio.program.scf.SCF
`public static final int` `BYTE_MAX_VALUE` `256`
`public static final int` `SHORT_MAX_VALUE` `65536`

org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder
`public static final String` `HOMOLOGY_FEATURE_TYPE` `"homology"`

org.biojava.bio.program.ssbind.SeqSimilarityStAXAdapter
`public static final String` `NAMESPACE` `"http://www.biojava.org"`

org.biojava.bio.program.ssbind.SimilarityPairBuilder
`public static final String` `SIMILARITY_PAIR_FEATURE_TYPE` `"similarity"`

org.biojava.bio.program.tagvalue.StateMachine
`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
`public static final String` `EMPTY_LINE_EOR` `""`

org.biojava.bio.program.xff.XFFFeatureSetHandler
`public static final String` `PROPERTY_XFF_ID` `"org.biojava.bio.program.xff.id"`

org.biojava.bio.program.xff.XFFTools
`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
`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
`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
`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
`public static final String` `KEY_QUERY_ID` `"___QUERY_ID___"`

org.biojava.bio.search.SeqSimilaritySearchSubHit
`public static final String` `QUERY_LABEL` `"Query"`

org.biojava.bio.seq.Feature
`public static final String` `PROPERTY_DATA_KEY` `"internal_data"`

org.biojava.bio.seq.FeatureTypes
`public static final String` `URI_PREFIX` `"uri:biojava.org:types"`

org.biojava.bio.seq.Frame
`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
`protected static final String` `urlBatchSequences` `"http://www.ncbi.nlm.nih.gov:80/entrez/eutils/efetch.fcgi"`

org.biojava.bio.seq.db.NCBISequenceDB
`public static final String` `DB_NUCLEOTIDE` `"nucleotide"`
`public static final String` `DB_PROTEIN` `"protein"`

org.biojava.bio.seq.homol.SimilarityPairFeature
`public static final String` `QUERY_LABEL` `"query"`
`public static final String` `SUBJECT_LABEL` `"subject"`

org.biojava.bio.seq.io.AlignIOConstants
`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
`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
`public static final String` `PROPERTY_EMBL_ACCESSIONS` `"embl_accessions"`

org.biojava.bio.seq.io.FastaAlignmentFormat
`public static final int` `DNA` `1`
`public static final int` `PROTEIN` `2`

org.biojava.bio.seq.io.FastaFormat
`public static final String` `DEFAULT` `"FASTA"`
`public static final String` `PROPERTY_DESCRIPTIONLINE` `"description_line"`

org.biojava.bio.seq.io.GAMEFormat
`public static final String` `DEFAULT` `"GAME1.2"`

org.biojava.bio.seq.io.GenbankFormat
`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
`public static final String` `PROPERTY_GENBANK_ACCESSIONS` `"genbank_accessions"`

org.biojava.bio.seq.io.SeqIOConstants
`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
`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
`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
`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
`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
`public static final String` `INDENT` `" "`

org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter
`public static final String` `XML_ANNOTATIONTYPE_NS` `"http://www.biojava.org/AnnotationType"`

org.biojava.bio.seq.io.filterxml.XMLFilterWriter
`public static final String` `XML_FILTER_NS` `"http://www.biojava.org/FeatureFilter"`

org.biojava.bio.structure.AlphaCTools
`public static final double` `MAX_ANGLE` `180.0`
`public static final double` `MIN_ANGLE` `-180.0`

org.biojava.bio.structure.AminoAcid
`public static final String` `ATOMRECORD` `"ATOM"`
`public static final String` `SEQRESRECORD` `"SEQRES"`

org.biojava.bio.structure.AminoAcidImpl
`public static final String` `type` `"amino"`

org.biojava.bio.structure.Calc
`public static final float` `degreesPerRadian` `57.295780181884766f`
`public static final float` `radiansPerDegree` `0.01745329238474369f`

org.biojava.bio.structure.GroupType
`public static final String` `AMINOACID` `"amino"`
`public static final String` `HETATM` `"hetatm"`
`public static final String` `NUCLEOTIDE` `"nucleotide"`

org.biojava.bio.structure.HetatomImpl
`public static final String` `type` `"hetatm"`

org.biojava.bio.structure.NucleotideImpl
`public static final String` `type` `"nucleotide"`

org.biojava.bio.structure.PDBHeader
`public static final float` `DEFAULT_RESOLUTION` `99.0f`

org.biojava.bio.structure.StructureException
`public static final long` `serialVersionUID` `62946250941673093L`

org.biojava.bio.structure.StructureTools
`public static final String` `caAtomName` `"CA"`

org.biojava.bio.structure.align.ClusterAltAligs
`public static final int` `DEFAULT_CLUSTER_CUTOFF` `95`

org.biojava.bio.structure.gui.BiojavaJmol
`public static final String` `adapter` `"org.jmol.api.JmolAdapter"`
`public static final String` `smartAdapter` `"org.jmol.adapter.smarter.SmarterJmolAdapter"`
`public static final String` `viewer` `"org.jmol.api.JmolSimpleViewer"`

org.biojava.bio.structure.gui.SequenceDisplay
`public static final int` `MAX_SCALE` `10`

org.biojava.bio.structure.gui.util.AlignedPosition
`public static final int` `EQUIVALENT` `1`
`public static final int` `NOT_ALIGNED` `0`

org.biojava.bio.structure.gui.util.PDBDirPanel
`public static final String` `PDB_DIR` `"PDB_DIR"`

org.biojava.bio.structure.gui.util.SequenceScalePanel
`public static final int` `DEFAULT_X_RIGHT_BORDER` `40`
`public static final int` `DEFAULT_X_START` `10`
`public static final int` `DEFAULT_Y_BOTTOM` `16`
`public static final int` `DEFAULT_Y_HEIGHT` `8`
`public static final int` `DEFAULT_Y_START` `0`
`public static final int` `DEFAULT_Y_STEP` `10`
`public static final int` `LINE_HEIGHT` `10`
`public static final int` `MINIMUM_HEIGHT` `20`
`public static final int` `SIZE` `20`

org.biojava.bio.structure.io.PDBFileParser
`public static final int` `ATOM_CA_THRESHOLD` `500000`
`public static final String` `HELIX` `"HELIX"`
`public static final int` `MAX_ATOMS` `700000`
`public static final String` `PDB_AUTHOR_ASSIGNMENT` `"PDB_AUTHOR_ASSIGNMENT"`
`public static final String` `STRAND` `"STRAND"`
`public static final String` `TURN` `"TURN"`

org.biojava.bio.structure.io.PDBParseException
`public static final long` `serialVersionUID` `219047230178423923L`

org.biojava.bio.structure.io.mmcif.SimpleMMcifParser
`public static final String` `FIELD_LINE` `"_"`
`public static final String` `LOOP_END` `"#"`
`public static final String` `LOOP_START` `"loop_"`
`public static final String` `STRING_LIMIT` `";"`

org.biojava.bio.structure.server.FlatFileInstallation
`public static final String` `DEFAUL_CHAIN_FILE` `"chaininfo.txt"`
`public static final String` `DEFAULT_INDEX_FILE` `"pdbinfo.txt"`

org.biojava.bio.symbol.AbstractAlphabet
`public static final long` `serialVersionUID` `-3043128839927615753L`

org.biojava.bio.symbol.SymbolPropertyTable
`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
`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
`public static final char` `DEFAULT_TERM_CHAR` `36`
`public static final int` `TO_A_LEAF` `-1`

org.biojava.directory.SystemRegistry
`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
`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
`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
`public static final int` `PRIME` `1000003`

org.biojava.utils.TypedProperties
`public static final String` `DEFAULT_DELIMITERS` `",;\t"`

org.biojava.utils.candy.CandyFinder
`public static final String` `DEFAULT_FINDER_NAME` `"Default vocabulary finder"`
`public static final String` `PROP_VOCABULARY` `"vocabulary"`

org.biojava.utils.candy.CandyVocabulary
`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
`public static final int` `GZIP_MAGIC` `8075`

org.biojava.utils.process.ExternalProcess
`public static final int` `SLEEP_TIME` `10`
`public static final int` `THREAD_POOL_SIZE` `9`

org.biojavax.*

org.biojavax.bio.db.ncbi.GenbankRichSequenceDB
`protected static final String` `urlBatchSequences` `"http://www.ncbi.nlm.nih.gov:80/entrez/eutils/efetch.fcgi"`

org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB
`protected static final String` `urlBatchSequences` `"http://www.ncbi.nlm.nih.gov:80/entrez/eutils/efetch.fcgi"`

org.biojavax.bio.phylo.io.nexus.CharactersBlock
`public static final String` `CHARACTERS_BLOCK` `"CHARACTERS"`

org.biojavax.bio.phylo.io.nexus.DataBlock
`public static final String` `DATA_BLOCK` `"DATA"`

org.biojavax.bio.phylo.io.nexus.DistancesBlock
`public static final String` `DISTANCES_BLOCK` `"DISTANCES"`

org.biojavax.bio.phylo.io.nexus.NexusBlockParser
`public static final String` `UNKNOWN_BLOCK` `"__UNKNOWN"`

org.biojavax.bio.phylo.io.nexus.TaxaBlock
`public static final String` `TAXA_BLOCK` `"TAXA"`

org.biojavax.bio.phylo.io.nexus.TreesBlock
`public static final String` `TREES_BLOCK` `"TREES"`

org.biojavax.bio.seq.Position
`public static final String` `BETWEEN_BASES` `"^"`
`public static final String` `IN_RANGE` `"."`

org.biojavax.bio.seq.RichSequence.Terms
`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
`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
`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
`public static final String` `FASTA_FORMAT` `"FASTA"`

org.biojavax.bio.seq.io.GenbankFormat
`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
`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
`public static final int` `THRESHOLD_VALUE` `5000`

org.biojavax.bio.seq.io.UniProtCommentParser
`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
`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
`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
`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
`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
`public static final int` `DEFAULT_MAX_CROSS` `2147483647`