Examples of toUCSCFormat()

Examples of fork.lib.bio.anno.genomic.region.DirectionalGenomicRegion.toUCSCFormat()

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        GenomicRegion gr= it.next();
        String seq= get.getSequence(gr);
        fe.appendEntry(new FastaEntry(gr.toUCSCFormat(), seq));
        String cseq = NucleotideSequenceParser.parseSequence(seq).complementary().toString();
        DirectionalGenomicRegion cgr= new DirectionalGenomicRegion(gr.chr, '-', (int)gr.low, (int)gr.high);
        fe.appendEntry(new FastaEntry( cgr.toUCSCFormat(), cseq));
    }
    fe.close();
}

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Examples of fork.lib.bio.anno.genomic.region.GenomicRegion.toUCSCFormat()

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    FastaExporter fe= new FastaExporter(out);
    Iterator<GenomicRegion> it= gb.iterator();
    while(it.hasNext()){
        GenomicRegion gr= it.next();
        String seq= get.getSequence(gr);
        fe.appendEntry(new FastaEntry(gr.toUCSCFormat(), seq));
        String cseq = NucleotideSequenceParser.parseSequence(seq).complementary().toString();
        DirectionalGenomicRegion cgr= new DirectionalGenomicRegion(gr.chr, '-', (int)gr.low, (int)gr.high);
        fe.appendEntry(new FastaEntry( cgr.toUCSCFormat(), cseq));
    }
    fe.close();
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Examples of fork.lib.bio.anno.genomic.region.GenomicRegion.toUCSCFormat()

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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])
        };
        gbout.add(ge);
    }
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