Package fork.lib.math.algebra.elementary.set.continuous

Examples of fork.lib.math.algebra.elementary.set.continuous.Region

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    for( int k=0; k<chrs.length ; k++ ){
        String chr = chrs[k];
        System.out.print(chr+"  ");
        ArrayList<Region> rs= lbb.getLandscape2DForChromosome(chr).getRegions();
        for( int i=1; i<rs.size() ; i++ ){
            Region r= rs.get(i);
            double val= Double.parseDouble(r.attribute().toString());
            int v= (int) (val-thr);
            if(v>0 ){
                bw.write(chr+"\t"+ (int)r.low+"\t"+ ((int)r.high+1)+"\t"+ v+"\n");
            }
        }
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                        int p= Integer.parseInt(ss[0]);
                        double v= Double.parseDouble(ss[1]);
                        if(p<ps){
                            System.out.println(chr+"  "+ p+"  "+ v);
                        }
                        Region reg= new Region(ps, p);
                        reg.setAttribute(v);
                        lb.add(chr, reg);
                        ps= p+1;
                    }
                }
            }
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    for(int i=0; i<chrs.length ; i++){
        String chr= chrs[i];
        ArrayList<Region> rs= gb.getRegionsForChromosome(chr);
        if(chr.equals("chr10")){
            for(int j=0; j<rs.size() ; j++){
                Region r= rs.get(j);
                if(r.higherThan(117000d)){
                    r.setLowHigh(r.low-310, r.high-310);
                    gbout.add((GenomicRegion)r);
                }else{
                    gbout.add((GenomicRegion)r);
                }
            }
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        for( int j=0; j<arr.length ; j++ ){
            String[] r= arr[j];
            int p= Integer.parseInt(r[0]);
            double v= Double.parseDouble(r[1]);
            if(pp!=0){
                Region reg= new Region(pp, p-1);
                reg.attr= (double)Math.round(pv*res)/res;
                lb.add(chr, reg);
            }
            pp=p; pv=v;
        }
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    GenomicRegionsBuilder gbout= new GenomicRegionsBuilder();
   
    String[] chrs= gb.getChromosomeList();
    for(int i=0; i<chrs.length ; i++){
        String chr= chrs[i];
        Region telr= gbtel.getRegionsForChromosome(chr).get(0);
        int low= (int)telr.low+sublen;
        int high= (int)telr.high-sublen;
        Region eur= new Region(low, high);
        ArrayList<Region> rs= gb.getRegionsForChromosome(chr);
        for(int j=0; j<rs.size() ; j++){
            GenomicRegion r= (GenomicRegion)rs.get(j);
            if(eur.contains(r)){
                r.setValue(0);
            }else{
                r.setValue(1);
            }
           
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        System.out.print(chr+"  ");
        ArrayList<Region> frs= lbf.getLandscape2DForChromosome(chr).getRegions();
        ArrayList<Region> irs= lbi.getLandscape2DForChromosome(chr).getRegions();
        RegionBuffer buf= new RegionBuffer(irs);
        for( int j=0; j<frs.size(); j++ ){
            Region fr= frs.get(j);
            ArrayList<Region> bufrs= buf.reloadAndGetList(fr);
            double ival= RegionBuffer.getOverlap(bufrs, fr) / (fr.getRange()+1);
            double fval= (double)fr.attribute();
            double nv= fval - ival*rat;
           
            //System.out.println(fval+"    "+ ival+"   "+ fr.getRange());
            nv= nv<0 ? 0 : nv;
            fr.setAttribute(nv);
            lbout.add(chr, fr);
        }
        BedGraphExporter be= new BedGraphExporter(lbout);
        be.appendToFile(bw);
    }
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    for( int k=0; k<chrs.length ; k++ ){
        String chr = chrs[k];
        System.out.print(chr+"  ");
        ArrayList<Region> rs= lbb.getLandscape2DForChromosome(chr).getRegions();
        for( int i=1; i<rs.size() ; i++ ){
            Region r= rs.get(i);
            double val= Double.parseDouble(r.attribute().toString());
            if(val>thr){
                double v= val-thr;
                bw.write(chr+"\t"+ (int)r.low+"\t"+ ((int)r.high+1)+"\t"+ (int)v+"\n");
            }
        }
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                        int p= Integer.parseInt(ss[0]);
                        double v= Double.parseDouble(ss[1]);
                        if(p<ps){
                            System.out.println(chr+"  "+ p+"  "+ v);
                        }
                        Region reg= new Region(ps, p);
                        reg.setAttribute(v);
                        lb.add(chr, reg);
                        ps= p+1;
                    }
                }
            }
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        String chr= chrs[i];
        if(lb.containsChromosome(chr)){
            ArrayList<Region> rs= lb.getLandscape2DForChromosome(chr).getRegions();
            double lim= gbchr.getRegionsForChromosome(chr).get(0).high;
            for(int j=0; j<rs.size() ; j++){
                Region r= rs.get(j);
                if( r.lowerThan(lim) ){
                    lbout.add(chr,r);
                }
            }
        }
    }
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protected void init() throws Exception {
    String[] chrs= gb.getChromosomeList();
    for( int i=0; i<chrs.length; i++ ){
        String chr= chrs[i];
        Region r= gb.getRegionsForChromosome(chr).get(0);
        double low = r.low;
        while(low+len< r.high){
            Region win= new Region((double)low, (double)low+len-1);
            gbout.add(new GenomicRegion(chr, win));
            low+=len;
        }
    }
}
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