Constant Field Values

Contents

org.biojava.*

  • org.biojava.nbio.aaproperties.profeat.convertor.Convertor 
    Modifier and Type Constant Field Value
    public static final char group1 49
    public static final char group2 50
    public static final char group3 51
    public static final char unknownGroup 48
  • 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"