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# Constant Field Values

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- 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`

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