Package fork.lib.bio.anno.genomic

Examples of fork.lib.bio.anno.genomic.LandscapeTransformer


    d.add(lbr.getDistribution());
    double med= Math.ceil( d.median() *1.7 );
    double sd= d.standartDeviation();
    System.out.println("med:  "+med +"    sd:  "+sd);
    //d.print(); System.exit(1);
    new LandscapeTransformer(lbf).subtract(med);
    new LandscapeTransformer(lbr).subtract(med);
   
    System.out.println("subtracted");
   
    LandscapeScoringStrand ls= new LandscapeScoringStrand(lbf, lbr, gb){
        protected double[] scoreStrand(ArrayList<Region> bufs, GenomicRegion gr) throws RegionException{
            return new double[]{Landscape2DBuffer.getArea(bufs, gr)};
        }
    };
    double l= gb.totalLength();
    double a=0;
    for( int i=0; i<ls.getResultEntries().size() ; i++ ){
        a+= ls.getResultEntries().get(i).scores[0];
    }
    fac= a/l/100;
    System.out.println("fac:  "+fac);
    new LandscapeTransformer(lbf).divideBy(fac);
    new LandscapeTransformer(lbr).divideBy(fac);
}
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