Constant Field Values

Contents

org.biojava.*

  • org.biojava.nbio.aaproperties.profeat.convertor.Convertor
    Modifier and Type
    Constant Field
    Value
    public static final char
    group1
    '1'
    public static final char
    group2
    '2'
    public static final char
    group3
    '3'
    public static final char
    unknownGroup
    '0'
  • org.biojava.nbio.core.sequence.location.InsdcParser
    Modifier and Type
    Constant Field
    Value
    protected static final String
    locationSplitPattern
    ",(?=([^\\(|\\)]+\\([^\\(|\\)]+\\))[^\\(|\\)]+)"
  • org.biojava.nbio.genome.parsers.cytoband.CytobandParser
    Modifier and Type
    Constant Field
    Value
    public static final String
    DEFAULT_LOCATION
    "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/cytoBand.txt.gz"
  • org.biojava.nbio.genome.parsers.genename.GeneChromosomePositionParser
    Modifier and Type
    Constant Field
    Value
    public static final String
    DEFAULT_MAPPING_URL
    "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/refFlat.txt.gz"
  • org.biojava.nbio.genome.parsers.genename.GeneNamesParser
    Modifier and Type
    Constant Field
    Value
    public static final String
    DEFAULT_GENENAMES_URL
    "https://www.genenames.org/cgi-bin/download?title=HGNC+output+data&hgnc_dbtag=on&col=gd_app_sym&col=gd_app_name&col=gd_status&col=gd_prev_sym&col=gd_prev_name&col=gd_aliases&col=gd_pub_chrom_map&col=gd_pub_acc_ids&col=md_mim_id&col=gd_pub_refseq_ids&col=md_ensembl_id&col=md_prot_id&col=gd_hgnc_id&status=Approved&status_opt=2&where=((gd_pub_chrom_map%20not%20like%20%27%patch%%27%20and%20gd_pub_chrom_map%20not%20like%20%27%ALT_REF%%27)%20or%20gd_pub_chrom_map%20IS%20NULL)%20and%20gd_locus_group%20%3d%20%27protein-coding%20gene%27&order_by=gd_app_sym_sort&format=text&limit=&submit=submit&.cgifields=&.cgifields=chr&.cgifields=status&.cgifields=hgnc_dbtag"
  • org.biojava.nbio.phosphosite.Dataset
    Modifier and Type
    Constant Field
    Value
    public static final String
    ACETYLATION
    "https://www.phosphosite.org/downloads/Acetylation_site_dataset.gz"
    public static final String
    DISEASE_ASSOC
    "https://www.phosphosite.org/downloads/Disease-associated_sites.gz"
    public static final String
    METHYLATION
    "https://www.phosphosite.org/downloads/Methylation_site_dataset.gz"
    public static final String
    PHOSPHORYLATION
    "https://www.phosphosite.org/downloads/Phosphorylation_site_dataset.gz"
    public static final String
    REGULATORY
    "https://www.phosphosite.org/downloads/Regulatory_sites.gz"
    public static final String
    SUMOYLATION
    "https://www.phosphosite.org/downloads/Sumoylation_site_dataset.gz"
    public static final String
    UBIQUITINATION
    "https://www.phosphosite.org/downloads/Ubiquitination_site_dataset.gz"
  • org.biojava.nbio.structure.align.fatcat.calc.AFPCalculator
    Modifier and Type
    Constant Field
    Value
    public static final boolean
    debug
    false
  • org.biojava.nbio.structure.align.fatcat.calc.AFPChainer
    Modifier and Type
    Constant Field
    Value
    public static final boolean
    debug
    false
  • org.biojava.nbio.structure.align.fatcat.calc.AFPOptimizer
    Modifier and Type
    Constant Field
    Value
    public static final boolean
    debug
    false
  • org.biojava.nbio.structure.align.fatcat.calc.AFPPostProcessor
    Modifier and Type
    Constant Field
    Value
    public static final boolean
    debug
    false
  • org.biojava.nbio.structure.align.fatcat.calc.FatCatAligner
    Modifier and Type
    Constant Field
    Value
    public static final boolean
    debug
    false
    public static final boolean
    printTimeStamps
    false
  • org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
    Modifier and Type
    Constant Field
    Value
    public static final int
    DEFAULT_FRAGLEN
    8
  • org.biojava.nbio.structure.domain.pdp.PDPParameters
    Modifier and Type
    Constant Field
    Value
    public static final float
    CUT_OFF_VALUE
    0.5f
    public static final float
    CUT_OFF_VALUE1
    0.28999999165534973f
    public static final float
    CUT_OFF_VALUE1M
    0.20999999344348907f
    public static final float
    CUT_OFF_VALUE1S
    0.1899999976158142f
    public static final float
    CUT_OFF_VALUE2
    0.4399999976158142f
    public static final float
    DBL
    0.05000000074505806f
    public static final int
    ENDS
    12
    public static final int
    ENDSEND
    9
    public static final int
    MAX_CUTS
    80
    public static final int
    MAXCONT
    900
    public static final int
    MAXDOM
    30
    public static final int
    MAXLEN
    3200
    public static final int
    MAXSIZE
    350
    public static final int
    MIN_DOMAIN_LENGTH
    35
    public static final float
    RG
    0.0f
    public static final float
    RG1
    1.0f
    public static final float
    TD
    25.0f
    public static final float
    TD1
    40.0f
  • org.biojava.nbio.structure.gui.BiojavaJmol
    Modifier and Type
    Constant Field
    Value
    public static final String
    adapter
    "org.jmol.api.JmolAdapter"
    public static final String
    smartAdapter
    "org.jmol.adapter.smarter.SmarterJmolAdapter"
    public static final String
    viewer
    "org.jmol.api.JmolSimpleViewer"
  • org.biojava.nbio.structure.gui.JmolViewerImpl
    Modifier and Type
    Constant Field
    Value
    public static final String
    adapter
    "org.jmol.api.JmolAdapter"
    public static final String
    smartAdapter
    "org.jmol.adapter.smarter.SmarterJmolAdapter"
    public static final String
    viewer
    "org.jmol.api.JmolSimpleViewer"
  • org.biojava.nbio.structure.gui.ScaleableMatrixPanel
    Modifier and Type
    Constant Field
    Value
    protected static final int
    SLIDER_STEPS
    8
  • org.biojava.nbio.structure.gui.SequenceDisplay
    Modifier and Type
    Constant Field
    Value
    public static final int
    MAX_SCALE
    10
  • org.biojava.nbio.ws.hmmer.RemoteHmmerScan
    Modifier and Type
    Constant Field
    Value
    public static final String
    HMMER_SERVICE
    "https://www.ebi.ac.uk/Tools/hmmer/search/hmmscan"