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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.ImageMap
public static final String CIRCLE "circle"
public static final String POLY "poly"
public static final String RECT "rect"

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.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.proteomics.MassCalc
public static final double Cavg 12.011d
public static final double Cmono 12.0d
public static final double Havg 1.00794d
public static final double Hmono 1.007825d
public static final double Navg 14.00674d
public static final double Nmono 14.003074d
public static final double Oavg 15.9994d
public static final double Omono 15.9949146d

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.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.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 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 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 ORGANISM_TAG "ORGANISM"
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 180.0d
public static final double MIN_ANGLE -180.0d

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

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 BLEPH_MNUC "BLEPHARISMA_MACRONUCLEAR"
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 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.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"

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