Package fork.lib.bio.anno.genomic

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

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    HashMap<GenomicRegion, Double> maps= LandscapeScoringResultEntry.toHashMap(rss, 0);
    GenomicRegionsBuilder gbout= new GenomicRegionsBuilder();
    for(int i=0; i<rsz.size() ; i++){
        LandscapeScoringResultEntry rz= rsz.get(i);
        double vz= rz.scores[0], vs= maps.get(rz.gr);
       
        if(vz>zthr && vs<sthr){
            System.out.println(rz.gr.toUCSCFormat()+"  "+ vz+"  "+ vs);
            gbout.add(rz.gr);
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    LandscapeScoring ls = getScoring();
   
    ArrayList<LandscapeScoringResultEntry> res= ls.getResultEntries();
    vec= new Vector(new double[res.get(0).scores.length]);
    for( int i=0; i<res.size(); i++ ){
        LandscapeScoringResultEntry en= res.get(i);
        /*
        bw.write( ((BedAttribute)en.gr.attribute()).getFieldA() );
        double[] vs= en.scores;
        for( int j=0; j<vs.length; j++ ){
            bw.write("\t"+ (double)Math.round(vs[j]*100)/100);
 
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        Vector vec= new Vector(vs);
        double vf= vec.subset(fl, fh).toDistribution().mean();
        double vt= vec.subset(tl, th).toDistribution().mean();
       
        double[] ft= new double[]{vf, vt};
        ress.add(new LandscapeScoringResultEntry(gr,ft));
    }
   
}
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public void writeToFile(File out) throws Exception{
    GenomicRegionsBuilder gbout= new GenomicRegionsBuilder();
    for( int i=0; i<ress.size() ; i++ ){
        LandscapeScoringResultEntry r=ress.get(i);
        GenomicRegion ge= r.gr;
        Object o= ge.attr==null ? ge.toUCSCFormat() : ge.attr;
        ge.attr= new Object[]{o,
            new Double(r.scores[0]), new Double(r.scores[1])
        };
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            return Landscape2DBuffer.getLandscape(bufs, gr);
        }
    };
    ArrayList<LandscapeScoringResultEntry> ress= ls.getResultEntries();
    for( int i=0; i<ress.size() ; i++ ){
        LandscapeScoringResultEntry res= ress.get(i);
        DirectionalGenomicRegion gr= (DirectionalGenomicRegion)res.gr;
        double[] vs= res.scores;
        int slow= gr.isOnForwardStrand() ? side5: side3,
                shigh= gr.isOnForwardStrand() ? side3 : side5;
        if(vs.length >  (slow+shigh)){
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Related Classes of fork.lib.bio.anno.genomic.LandscapeScoringResultEntry

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  • data.cerevisiae.region.scan.ScanIntra
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  • data.cerevisiae.test.T
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