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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