Constant Field Values


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

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

org.biojava.bio.EcNumber
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 java.lang.String LANE "Lane"

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

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

org.biojava.bio.molbio.RestrictionMapper
public static final java.lang.String SITE_FEATURE_SOURCE "regex"
public static final java.lang.String SITE_FEATURE_TYPE "misc_binding"

org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
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 java.lang.String PROPERTY_ANNOTATIONSERVER "org.biojava.bio.program.das.annotation_server"
public static final java.lang.String PROPERTY_FEATUREID "org.biojava.bio.program.das.feature_id"
public static final java.lang.String PROPERTY_FEATURELABEL "org.biojava.bio.program.das.feature_label"
public static final java.lang.String PROPERTY_LINKS "org.biojava.bio.program.das.links"
public static final java.lang.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 java.lang.String PROPERTY_GFF_SCORE "org.biojava.bio.program.gff.gff_feature_score"

org.biojava.bio.program.homologene.HomologeneBuilder
public static final java.lang.String ACCESSION "Accession"
public static final java.lang.String CURATED "curated"
public static final java.lang.String HOMOID "HomologeneID"
public static final java.lang.String LOCUSID "LocusID"
public static final java.lang.String MULTIPLE "multiple"
public static final java.lang.String PERCENTIDENTITY "PercentIdentity"
public static final java.lang.String REFERENCE "Reference"
public static final java.lang.String SIMILARITYTYPE "SimilarityType"
public static final java.lang.String TAXONID "TaxonID"
public static final java.lang.String TWIN "twin"

org.biojava.bio.program.indexdb.BioStoreFactory
public static final java.lang.String KEYS "secondary_namespaces"
public static final java.lang.String PRIMARY_KEY_NAME "primary_namespace"
public static final java.lang.String SEQUENCE_FORMAT "format"
public static final java.lang.String STORE_NAME "name"

org.biojava.bio.program.phred.PhredFormat
public static final java.lang.String DEFAULT "PHRED"
public static final java.lang.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 java.lang.String HOMOLOGY_FEATURE_TYPE "homology"

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

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

org.biojava.bio.program.tagvalue.StateMachine
protected static final java.lang.String END_RECORD_TAG "__END_RECORD__"
protected static final java.lang.String END_TAG "__END_TAG__"
protected static final java.lang.String MAGICAL_STATE "__MAGICAL__"
protected static final java.lang.String START_RECORD_TAG "__START_RECORD_TAG__"

org.biojava.bio.program.tagvalue.TagValueParser
public static final java.lang.String EMPTY_LINE_EOR ""

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

org.biojava.bio.program.xff.XFFTools
public static final java.lang.String XFF_BIOJAVA_NS "http://www.biojava.org/2001/xff-biojava"
public static final java.lang.String XFF_NS "http://www.bioxml.org/2000/xff"

org.biojava.bio.proteomics.MassCalc
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 java.lang.String ARG_C "Arg-C"
public static final java.lang.String ASP_N "Asp-N"
public static final java.lang.String CHYMOTRYP "Chymotrypsin"
public static final java.lang.String CNBr "CNBr"
public static final java.lang.String GLU_C_BICARB "Glu-C-bicarbonate"
public static final java.lang.String GLU_C_PHOS "Glu-C-phosphate"
public static final java.lang.String LYS_C "Lys-C"
public static final java.lang.String TRYPSIN "Trypsin"

org.biojava.bio.proteomics.ProteaseManager
public static final java.lang.String ARG_C "Arg-C"
public static final java.lang.String ASP_N "Asp-N"
public static final java.lang.String CHYMOTRYP "Chymotrypsin"
public static final java.lang.String CNBr "CNBr"
public static final java.lang.String GLU_C_BICARB "Glu-C-bicarbonate"
public static final java.lang.String GLU_C_PHOS "Glu-C-phosphate"
public static final java.lang.String LYS_C "Lys-C"
public static final java.lang.String TRYPSIN "Trypsin"

org.biojava.bio.search.BlastLikeSearchFilter
public static final java.lang.String KEY_QUERY_ID "___QUERY_ID___"

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

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

org.biojava.bio.seq.FeatureTypes
public static final java.lang.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 java.lang.String urlBatchSequences "http://www.ncbi.nlm.nih.gov:80/entrez/eutils/efetch.fcgi"

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

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

org.biojava.bio.seq.io.EmblProcessor
public static final java.lang.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 java.lang.String DEFAULT "FASTA"
public static final java.lang.String PROPERTY_DESCRIPTIONLINE "description_line"

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

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

org.biojava.bio.seq.io.GenbankProcessor
public static final java.lang.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 java.lang.String PROPERTY_SWISSPROT_ACCESSIONS "swissprot.accessions"
public static final java.lang.String PROPERTY_SWISSPROT_COMMENT "swissprot.comment"
public static final java.lang.String PROPERTY_SWISSPROT_FEATUREATTRIBUTE "swissprot.featureattribute"

org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
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 java.lang.String QUALIFIER "qualifier"
public static final java.lang.String RESULT_PROPERTY "result_property"
public static final java.lang.String SCI_PROPERTY "sci_property"
public static final java.lang.String XREF_PROPERTY "xref_property"

org.biojava.bio.seq.io.agave.AgaveWriter
public static final java.lang.String INDENT " "

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

org.biojava.bio.seq.io.filterxml.XMLFilterWriter
public static final java.lang.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.AminoAcidImpl
public static final java.lang.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.HetatomImpl
public static final java.lang.String type "hetatm"

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

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

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

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

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

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

org.biojava.bio.symbol.SymbolPropertyTable
public static final java.lang.String AVG_MASS "avgMass"
public static final java.lang.String MONO_MASS "monoMass"
public static final java.lang.String PK "pK"

org.biojava.bio.symbol.TranslationTable
public static final java.lang.String ALT_YEAST_NUC "ALTERNATIVE_YEAST_NUCLEAR"
public static final java.lang.String ASCID_MITO "ASCIDIAN_MITOCHONDRIAL"
public static final java.lang.String BACTERIAL "BACTERIAL"
public static final java.lang.String BLEPH_MNUC "BLEPHARISMA_MACRONUCLEAR"
public static final java.lang.String CHLORO_MITO "CHLOROPHYCEAN_MITOCHONDRIAL"
public static final java.lang.String CILIATE_NUC "CILIATE_NUCLEAR"
public static final java.lang.String ECHIN_MITO "ECHINODERM_MITOCHONDRIAL"
public static final java.lang.String EUPL_NUC "EUPLOTID_NUCLEAR"
public static final java.lang.String FWORM_MITO "FLATWORM_MITOCHONDRIAL"
public static final java.lang.String INVERT_MITO "INVERTEBRATE_MITOCHONDRIAL"
public static final java.lang.String MOLD_MITO "MOLD_MITOCHONDRIAL"
public static final java.lang.String SCENE_MITO "SCENEDESMUS_MITOCHONDRIAL"
public static final java.lang.String TREMA_MITO "TREMATODE_MITOCHONDRIAL"
public static final java.lang.String UNIVERSAL "UNIVERSAL"
public static final java.lang.String VERT_MITO "VERTEBRATE_MITOCHONDRIAL"
public static final java.lang.String YEAST_MITO "YEAST_MITOCHONDRIAL"

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

org.biojava.directory.SystemRegistry
public static final java.lang.String CONFIG_FILE "seqdatabase.ini"
public static final java.lang.String CONFIG_LOCATOR "http://www.open-bio.org/registry/seqdatabase.ini"
public static final java.lang.String OBDA_SEARCH_ENV "OBDA_SEARCH_PATH"

org.biojava.utils.ObjectUtil
public static final int PRIME 1000003

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

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

org.biojava.utils.candy.CandyVocabulary
public static final java.lang.String CANDIES_NOT_SORTED "candies_not_sorted"
public static final java.lang.String PROP_CASE_SENSITIVE "vocab_case_sensitive"
public static final java.lang.String PROP_ENTRY_COUNT "entry_count"
public static final java.lang.String PROP_VOCAB_DESC "vocab_description"
public static final java.lang.String PROP_VOCAB_NAME "vocab_name"
public static final java.lang.String PROP_VOCAB_VERSION "vocab_version"
public static final java.lang.String PROP_VOCABULARY "vocabulary"

org.biojava.utils.io.InputStreamProvider
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 java.lang.String urlBatchSequences "http://www.ncbi.nlm.nih.gov:80/entrez/eutils/efetch.fcgi"

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

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

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

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

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

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

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

org.biojavax.bio.seq.RichSequence.Terms
public static final java.lang.String DOI_KEY "DOI"
public static final java.lang.String MEDLINE_KEY "MEDLINE"
public static final java.lang.String PUBMED_KEY "PUBMED"

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

org.biojavax.bio.seq.io.EMBLxmlFormat
protected static final java.lang.String AUTHOR_TAG "author"
protected static final java.lang.String BASEPOSITION_EXTENT_ATTR "extent"
protected static final java.lang.String BASEPOSITION_TAG "basePosition"
protected static final java.lang.String BASEPOSITION_TYPE_ATTR "type"
protected static final java.lang.String CITATION_DATE_ATTR "date"
protected static final java.lang.String CITATION_FIRST_ATTR "first"
protected static final java.lang.String CITATION_ID_ATTR "id"
protected static final java.lang.String CITATION_INSTITUTE_ATTR "institute"
protected static final java.lang.String CITATION_ISSUE_ATTR "issue"
protected static final java.lang.String CITATION_LAST_ATTR "last"
protected static final java.lang.String CITATION_NAME_ATTR "name"
protected static final java.lang.String CITATION_PATENT_ATTR "patentNumber"
protected static final java.lang.String CITATION_PUB_ATTR "publisher"
protected static final java.lang.String CITATION_TAG "citation"
protected static final java.lang.String CITATION_TYPE_ATTR "type"
protected static final java.lang.String CITATION_VOL_ATTR "volume"
protected static final java.lang.String CITATION_YEAR_ATTR "year"
protected static final java.lang.String COMMENT_TAG "comment"
protected static final java.lang.String COMNAME_TAG "preferredCommonName"
protected static final java.lang.String CONSORTIUM_TAG "consortium"
protected static final java.lang.String DBREF_DB_ATTR "db"
protected static final java.lang.String DBREF_PRIMARY_ATTR "primary"
protected static final java.lang.String DBREF_SEC_ATTR "secondary"
protected static final java.lang.String DBREFERENCE_TAG "dbreference"
protected static final java.lang.String DESC_TAG "description"
protected static final java.lang.String EDITOR_TAG "editor"
public static final java.lang.String EMBLXML_FORMAT "EMBLxml"
protected static final java.lang.String ENTRY_ACCESSION_ATTR "accession"
protected static final java.lang.String ENTRY_CREATED_ATTR "created"
protected static final java.lang.String ENTRY_DIVISION_ATTR "division"
protected static final java.lang.String ENTRY_GROUP_TAG "EMBL"
protected static final java.lang.String ENTRY_NAME_ATTR "name"
protected static final java.lang.String ENTRY_RELCREATED_ATTR "releaseCreated"
protected static final java.lang.String ENTRY_RELUPDATED_ATTR "releaseLastUpdated"
protected static final java.lang.String ENTRY_TAG "entry"
protected static final java.lang.String ENTRY_UPDATED_ATTR "lastUpdated"
protected static final java.lang.String ENTRY_VER_ATTR "version"
protected static final java.lang.String FEATURE_NAME_ATTR "name"
protected static final java.lang.String FEATURE_TAG "feature"
protected static final java.lang.String KEYWORD_TAG "keyword"
protected static final java.lang.String LINEAGE_TAG "lineage"
protected static final java.lang.String LOC_ELEMENT_ACC_ATTR "accession"
protected static final java.lang.String LOC_ELEMENT_COMPL_ATTR "complement"
protected static final java.lang.String LOC_ELEMENT_TYPE_ATTR "type"
protected static final java.lang.String LOC_ELEMENT_VER_ATTR "version"
protected static final java.lang.String LOCATION_COMPL_ATTR "complement"
protected static final java.lang.String LOCATION_ELEMENT_TAG "locationElement"
protected static final java.lang.String LOCATION_TAG "location"
protected static final java.lang.String LOCATION_TYPE_ATTR "type"
protected static final java.lang.String LOCATOR_TAG "locator"
protected static final java.lang.String NAMESET_TAG "nameSet"
protected static final java.lang.String ORGANISM_TAG "organism"
protected static final java.lang.String PATENT_TAG "patentApplicant"
protected static final java.lang.String QUALIFIER_NAME_ATTR "name"
protected static final java.lang.String QUALIFIER_TAG "qualifier"
protected static final java.lang.String REF_POS_BEGIN_ATTR "begin"
protected static final java.lang.String REF_POS_END_ATTR "end"
protected static final java.lang.String REFERENCE_POSITION_TAG "refPosition"
protected static final java.lang.String REFERENCE_TAG "reference"
protected static final java.lang.String SCINAME_TAG "scientificName"
protected static final java.lang.String SEC_ACC_TAG "secondaryAccession"
protected static final java.lang.String SEQUENCE_LENGTH_ATTR "length"
protected static final java.lang.String SEQUENCE_TAG "sequence"
protected static final java.lang.String SEQUENCE_TOPOLOGY_ATTR "topology"
protected static final java.lang.String SEQUENCE_TYPE_ATTR "type"
protected static final java.lang.String SEQUENCE_VER_ATTR "version"
protected static final java.lang.String TAXID_TAG "taxId"
protected static final java.lang.String TAXON_TAG "taxon"
protected static final java.lang.String TITLE_TAG "title"

org.biojavax.bio.seq.io.FastaFormat
public static final java.lang.String FASTA_FORMAT "FASTA"

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

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

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

org.biojavax.bio.seq.io.UniProtCommentParser
public static final java.lang.String ALTERNATIVE_PRODUCTS "ALTERNATIVE PRODUCTS"
public static final java.lang.String BIOPHYSICOCHEMICAL_PROPERTIES "BIOPHYSICOCHEMICAL PROPERTIES"
public static final java.lang.String DATABASE "DATABASE"
public static final java.lang.String INTERACTION "INTERACTION"
public static final java.lang.String MASS_SPECTROMETRY "MASS SPECTROMETRY"
public static final java.lang.String PTM "PTM"

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

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

org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
public static final java.lang.String ABBREV_NAME_KEY "abbreviation"
public static final java.lang.String COMMON_NAME_KEY "common"
public static final java.lang.String CONTAINS_PREFIX "Contains:"
public static final java.lang.String FULL_NAME_KEY "full"
public static final java.lang.String GENENAME_KEY "primary"
public static final java.lang.String GENESYNONYM_KEY "synonym"
public static final java.lang.String INCLUDES_PREFIX "Includes:"
public static final java.lang.String LOC_FUZZY_END_KEY "greater than"
public static final java.lang.String LOC_FUZZY_START_KEY "less than"
public static final java.lang.String NCBI_TAXON_KEY "NCBI Taxonomy"
public static final java.lang.String ORDLOCNAME_KEY "ordered locus"
public static final java.lang.String ORFNAME_KEY "ORF"
public static final java.lang.String SCIENTIFIC_NAME_KEY "scientific"
public static final java.lang.String SYNONYM_NAME_KEY "synonym"

org.biojavax.bio.taxa.NCBITaxon
public static final java.lang.String ACRONYM "acronym"
public static final java.lang.String COMMON "common name"
public static final java.lang.String EQUIVALENT "equivalent name"
public static final java.lang.String SCIENTIFIC "scientific name"
public static final java.lang.String SYNONYM "synonym"

org.biojavax.ga.functions.CrossOverFunction
public static final int DEFAULT_MAX_CROSS 2147483647