Examples of Landscape2DBuffer

Examples of fork.lib.math.applied.buffer.Landscape2DBuffer

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        String[] chrs= gb.getUnsortedChromosomeList();
        for( int i=0; i<chrs.length ; i++ ){
            String chr= chrs[i];
            if(lbf.containsChromosome(chr) && lbr.containsChromosome(chr) ){
                Landscape2DBuffer tsf= new Landscape2DBuffer(lbf.getLandscape2DForChromosome(chr));
                Landscape2DBuffer tsr= new Landscape2DBuffer(lbr.getLandscape2DForChromosome(chr));
               
               
                ArrayList<Region> regs= gb.getRegionsForChromosome(chr);
                for( int j=0; j<regs.size() ; j++ ){
                    GenomicRegion gr= (GenomicRegion)regs.get(j);
                    GenomicRegion grlow, grhigh;
                    int low, high;
                    low= (int)gr.low;
                    high= (int)gr.high;
                    grlow= new GenomicRegion(gr.chr, low-side, low+side);
                    grhigh= new GenomicRegion(gr.chr, high-side, high+side);

                   
                    double forl= score(tsf.reloadAndGetList(grlow), grlow);
                    double forh= score(tsf.reloadAndGetList(grhigh), grhigh);
                    double revl= score(tsr.reloadAndGetList(grlow), grlow);
                    double revh= score(tsr.reloadAndGetList(grhigh), grhigh);
                   
                    System.out.println(gr.toUCSCFormat()+"    "+ forl+"  "+ forh+"  "+ revl+"  "+revh);
                    System.out.println();
                }
            }
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Examples of fork.lib.math.applied.buffer.Landscape2DBuffer

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protected void init() throws Exception{
    String[] chrs= gb.getUnsortedChromosomeList();
    for( int i=0; i<chrs.length ; i++ ){
        String chr= chrs[i];
        if(lbf.containsChromosome(chr) && lbr.containsChromosome(chr) ){
            Landscape2DBuffer tsf= new Landscape2DBuffer(lbf.getLandscape2DForChromosome(chr));
            Landscape2DBuffer tsr= new Landscape2DBuffer(lbr.getLandscape2DForChromosome(chr));
            tsf.keepLeft= 500;
            tsr.keepLeft= 500;
           
            ArrayList<Region> regs= gb.getRegionsForChromosome(chr);
            for( int j=0; j<regs.size() ; j++ ){
                GenomicRegion gr= (GenomicRegion)regs.get(j);
                GenomicRegion grlow, grhigh;
                int low, high;
                low= (int)gr.low;
                high= (int)gr.high;
                grlow= new GenomicRegion(gr.chr, low-side, low+side);
                grhigh= new GenomicRegion(gr.chr, high-side, high+side);
               
                double forl= score(tsf.reloadAndGetList(grlow), grlow);
                double forh= score(tsf.reloadAndGetList(grhigh), grhigh);
                double revl= score(tsr.reloadAndGetList(grlow), grlow);
                double revh= score(tsr.reloadAndGetList(grhigh), grhigh);
                Res res= new Res(forl, forh, revl, revh);
                ress.put(gr,res);
                //System.out.println(low+"   "+ high);
                //System.out.println(gr.toUCSCFormat()+"  "+ res.str+"   "+ forl+"  "+ forh+"  "+ revl+"  "+revh);
            }
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