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Constant Field Values

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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.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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