Constant Field Values

Contents

org.biojava.*

  • org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer 
    Modifier and Type Constant Field Value
    public static final java.lang.String LANE "Lane"
  • org.biojava.bio.gui.sequence.ImageMap 
    Modifier and Type Constant Field Value
    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.OffsetRulerRenderer 
    Modifier and Type Constant Field Value
    public static final int TICKS_DOWN 1
    public static final int TICKS_UP 0
  • org.biojava.bio.gui.sequence.RulerRenderer 
    Modifier and Type Constant Field Value
    public static final int TICKS_DOWN 1
    public static final int TICKS_UP 0
  • org.biojava.bio.program.gff.GFFEntrySet 
    Modifier and Type Constant Field Value
    public static final java.lang.String PROPERTY_GFF_SCORE "org.biojava.bio.program.gff.gff_feature_score"
  • org.biojava.bio.program.homologene.HomologeneBuilder 
    Modifier and Type Constant Field Value
    public static final java.lang.String ACCESSION "Accession"
    public static final java.lang.String CURATED "curated"
    public static final java.lang.String HOMOID "HomologeneID"
    public static final java.lang.String LOCUSID "LocusID"
    public static final java.lang.String MULTIPLE "multiple"
    public static final java.lang.String PERCENTIDENTITY "PercentIdentity"
    public static final java.lang.String REFERENCE "Reference"
    public static final java.lang.String SIMILARITYTYPE "SimilarityType"
    public static final java.lang.String TAXONID "TaxonID"
    public static final java.lang.String TWIN "twin"
  • org.biojava.bio.program.indexdb.BioStoreFactory 
    Modifier and Type Constant Field Value
    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 
    Modifier and Type Constant Field Value
    public static final java.lang.String DEFAULT "PHRED"
    public static final java.lang.String PROPERTY_DESCRIPTIONLINE "description_line"
  • org.biojava.bio.program.tagvalue.StateMachine 
    Modifier and Type Constant Field Value
    protected static final java.lang.String END_RECORD_TAG "__END_RECORD__"
    protected static final java.lang.String END_TAG "__END_TAG__"
    protected static final java.lang.String MAGICAL_STATE "__MAGICAL__"
    protected static final java.lang.String START_RECORD_TAG "__START_RECORD_TAG__"
  • org.biojava.bio.program.tagvalue.TagValueParser 
    Modifier and Type Constant Field Value
    public static final java.lang.String EMPTY_LINE_EOR ""
  • org.biojava.bio.program.xff.XFFFeatureSetHandler 
    Modifier and Type Constant Field Value
    public static final java.lang.String PROPERTY_XFF_ID "org.biojava.bio.program.xff.id"
  • org.biojava.bio.program.xff.XFFTools 
    Modifier and Type Constant Field Value
    public static final java.lang.String XFF_BIOJAVA_NS "http://www.biojava.org/2001/xff-biojava"
    public static final java.lang.String XFF_NS "http://www.bioxml.org/2000/xff"
  • org.biojava.bio.proteomics.MassCalc 
    Modifier and Type Constant Field Value
    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 
    Modifier and Type Constant Field Value
    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 
    Modifier and Type Constant Field Value
    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.seq.Feature 
    Modifier and Type Constant Field Value
    public static final java.lang.String PROPERTY_DATA_KEY "internal_data"
  • org.biojava.bio.seq.FeatureTypes 
    Modifier and Type Constant Field Value
    public static final java.lang.String URI_PREFIX "uri:biojava.org:types"
  • org.biojava.bio.seq.Frame 
    Modifier and Type Constant Field Value
    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 
    Modifier and Type Constant Field Value
    protected static final java.lang.String urlBatchSequences "http://www.ncbi.nlm.nih.gov:80/entrez/eutils/efetch.fcgi"
  • org.biojava.bio.seq.db.NCBISequenceDB 
    Modifier and Type Constant Field Value
    public static final java.lang.String DB_NUCLEOTIDE "nucleotide"
    public static final java.lang.String DB_PROTEIN "protein"
  • org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter 
    Modifier and Type Constant Field Value
    public static final java.lang.String XML_ANNOTATIONTYPE_NS "http://www.biojava.org/AnnotationType"
  • org.biojava.bio.seq.io.filterxml.XMLFilterWriter 
    Modifier and Type Constant Field Value
    public static final java.lang.String XML_FILTER_NS "http://www.biojava.org/FeatureFilter"
  • org.biojava.bio.structure.AlphaCTools 
    Modifier and Type Constant Field Value
    public static final double MAX_ANGLE 180.0
    public static final double MIN_ANGLE -180.0
  • org.biojava.bio.structure.AminoAcid 
    Modifier and Type Constant Field Value
    public static final java.lang.String ATOMRECORD "ATOM"
    public static final java.lang.String SEQRESRECORD "SEQRES"
  • org.biojava.bio.structure.AminoAcidImpl 
    Modifier and Type Constant Field Value
    public static final java.lang.String type "amino"
  • org.biojava.bio.structure.Calc 
    Modifier and Type Constant Field Value
    public static final float degreesPerRadian 57.295780181884766f
    public static final float radiansPerDegree 0.01745329238474369f
  • org.biojava.bio.structure.GroupType 
    Modifier and Type Constant Field Value
    public static final java.lang.String AMINOACID "amino"
    public static final java.lang.String HETATM "hetatm"
    public static final java.lang.String NUCLEOTIDE "nucleotide"
  • org.biojava.bio.structure.HetatomImpl 
    Modifier and Type Constant Field Value
    public static final java.lang.String type "hetatm"
  • org.biojava.bio.structure.NucleotideImpl 
    Modifier and Type Constant Field Value
    public static final java.lang.String type "nucleotide"
  • org.biojava.bio.structure.PDBHeader 
    Modifier and Type Constant Field Value
    public static final float DEFAULT_RESOLUTION 99.0f
  • org.biojava.bio.structure.StructureException 
    Modifier and Type Constant Field Value
    public static final long serialVersionUID 62946250941673093L
  • org.biojava.bio.structure.StructureTools 
    Modifier and Type Constant Field Value
    public static final java.lang.String caAtomName "CA"
  • org.biojava.bio.structure.gui.BiojavaJmol 
    Modifier and Type Constant Field Value
    public static final java.lang.String adapter "org.jmol.api.JmolAdapter"
    public static final java.lang.String smartAdapter "org.jmol.adapter.smarter.SmarterJmolAdapter"
    public static final java.lang.String viewer "org.jmol.api.JmolSimpleViewer"
  • org.biojava.bio.structure.gui.SequenceDisplay 
    Modifier and Type Constant Field Value
    public static final int MAX_SCALE 10
  • org.biojava.bio.structure.io.PDBFileParser 
    Modifier and Type Constant Field Value
    public static final int ATOM_CA_THRESHOLD 500000
    public static final java.lang.String HELIX "HELIX"
    public static final int MAX_ATOMS 700000
    public static final java.lang.String PDB_AUTHOR_ASSIGNMENT "PDB_AUTHOR_ASSIGNMENT"
    public static final java.lang.String STRAND "STRAND"
    public static final java.lang.String TURN "TURN"
  • org.biojava.bio.structure.io.PDBParseException 
    Modifier and Type Constant Field Value
    public static final long serialVersionUID 219047230178423923L
  • org.biojava.bio.structure.io.mmcif.SimpleMMcifParser 
    Modifier and Type Constant Field Value
    public static final java.lang.String FIELD_LINE "_"
    public static final java.lang.String LOOP_END "#"
    public static final java.lang.String LOOP_START "loop_"
    public static final java.lang.String STRING_LIMIT ";"
  • org.biojava.bio.symbol.AbstractAlphabet 
    Modifier and Type Constant Field Value
    public static final long serialVersionUID -3043128839927615753L
  • org.biojava.bio.symbol.SymbolPropertyTable 
    Modifier and Type Constant Field Value
    public static final java.lang.String AVG_MASS "avgMass"
    public static final java.lang.String HYDROPATHICITY "hydropathicity"
    public static final java.lang.String MONO_MASS "monoMass"
    public static final java.lang.String PK "pK"
    public static final java.lang.String PK_Cterm "pK_Cterm"
    public static final java.lang.String PK_Nterm "pK_Nterm"
  • org.biojava.bio.symbol.TranslationTable 
    Modifier and Type Constant Field Value
    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 BACTERIAL "BACTERIAL"
    public static final java.lang.String BLEPH_MNUC "BLEPHARISMA_MACRONUCLEAR"
    public static final java.lang.String CHLORO_MITO "CHLOROPHYCEAN_MITOCHONDRIAL"
    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 SCENE_MITO "SCENEDESMUS_MITOCHONDRIAL"
    public static final java.lang.String TREMA_MITO "TREMATODE_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 
    Modifier and Type Constant Field Value
    public static final char DEFAULT_TERM_CHAR 36
    public static final int TO_A_LEAF -1
  • org.biojava.directory.SystemRegistry 
    Modifier and Type Constant Field Value
    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.ontology.obo.OboFileHandler 
    Modifier and Type Constant Field Value
    public static final java.lang.String ALT_ID "alt_id"
    public static final java.lang.String BROAD_SYNONYM "broad_synonym"
    public static final java.lang.String COMMENT "comment"
    public static final java.lang.String DEF "def"
    public static final java.lang.String DISJOINT_FROM "disjoint_from"
    public static final java.lang.String EXACT_SYNONYM "exact_synonym"
    public static final java.lang.String ID_KEY "id"
    public static final java.lang.String INTERSECTION_OF "intersection_of"
    public static final java.lang.String IS_A "is_a"
    public static final java.lang.String IS_OBSOLETE "is_obsolete"
    public static final java.lang.String NAME "name"
    public static final java.lang.String NARROW_SYNONYM "narrow_synonym"
    public static final java.lang.String ONTOLOGY "ontologys"
    public static final java.lang.String REL_SYNONYM "related_synonym"
    public static final java.lang.String RELATIONSHIP "relationship"
    public static final java.lang.String SUBSET "subset"
    public static final java.lang.String SYNONYM "synonym"
    public static final java.lang.String TERM "Term"
    public static final java.lang.String TYPEDEF "Typedef"
    public static final java.lang.String XREF_ANALOG "xref_analog"
  • org.biojava.utils.ObjectUtil 
    Modifier and Type Constant Field Value
    public static final int PRIME 1000003
  • org.biojava.utils.TypedProperties 
    Modifier and Type Constant Field Value
    public static final java.lang.String DEFAULT_DELIMITERS ",;\t"

org.biojavax.*

  • org.biojavax.bio.db.ncbi.GenbankRichSequenceDB 
    Modifier and Type Constant Field Value
    protected static final java.lang.String urlBatchSequences "http://www.ncbi.nlm.nih.gov:80/entrez/eutils/efetch.fcgi"
  • org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB 
    Modifier and Type Constant Field Value
    protected static final java.lang.String urlBatchSequences "http://www.ncbi.nlm.nih.gov:80/entrez/eutils/efetch.fcgi"
  • org.biojavax.bio.seq.Position 
    Modifier and Type Constant Field Value
    public static final java.lang.String BETWEEN_BASES "^"
    public static final java.lang.String IN_RANGE "."
  • org.biojavax.bio.seq.RichSequence.Terms 
    Modifier and Type Constant Field Value
    public static final java.lang.String DOI_KEY "DOI"
    public static final java.lang.String MEDLINE_KEY "MEDLINE"
    public static final java.lang.String PUBMED_KEY "PUBMED"
  • org.biojavax.bio.taxa.NCBITaxon 
    Modifier and Type Constant Field Value
    public static final java.lang.String ACRONYM "acronym"
    public static final java.lang.String COMMON "common name"
    public static final java.lang.String EQUIVALENT "equivalent name"
    public static final java.lang.String SCIENTIFIC "scientific name"
    public static final java.lang.String SYNONYM "synonym"