# Constant Field Values

Contents

- org.biojava.*

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"`