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.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 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.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.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.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.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.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 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.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.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 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 REF_ACCESSION_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 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 ORGANISM_TAG "ORGANISM"
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.SeqAlignReadWrite
public static final int EMBL 3
public static final int FASTA 8
public static final int FASTAALIGN 9
public static final int FASTADNA 1
public static final int FASTAPROTEIN 2
public static final int GENBANK 4
public static final int GENPEPT 6
public static final int MSFDNA 7
public static final int MSFPROTEIN 10
public static final int SWISSPROT 5

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.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 BLEPH_MNUC "BLEPHARISMA_MACRONUCLEAR"
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 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"