Examples of addSpan()

Examples of com.affymetrix.genometryImpl.symmetry.MutableSeqSymmetry.addSpan()

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        int acount = gseq.getAnnotationCount();

        SeqSymmetry[] path2view = new SeqSymmetry[1];
        MutableSeqSymmetry viewSym = new SimpleMutableSeqSymmetry();
        viewSym.addSpan(new SimpleSeqSpan(gseq.getMin(), gseq.getMax(), gseq));
        vseq = new BioSeq("view seq", null, gseq.getLength());
        vseq.setBounds(gseq.getMin(), gseq.getMax());

        viewSym.addSpan(new SimpleSeqSpan(vseq.getMin(), vseq.getMax(), vseq));
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Examples of com.affymetrix.genometryImpl.symmetry.MutableSeqSymmetry.addSpan()

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        MutableSeqSymmetry viewSym = new SimpleMutableSeqSymmetry();
        viewSym.addSpan(new SimpleSeqSpan(gseq.getMin(), gseq.getMax(), gseq));
        vseq = new BioSeq("view seq", null, gseq.getLength());
        vseq.setBounds(gseq.getMin(), gseq.getMax());

        viewSym.addSpan(new SimpleSeqSpan(vseq.getMin(), vseq.getMax(), vseq));

        path2view[0] = viewSym;

        for (int i = 0; i < acount; i++) {
            SeqSymmetry asym = gseq.getAnnotation(i);
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Examples of com.affymetrix.genometryImpl.symmetry.MutableSeqSymmetry.addSpan()

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            //   [unless start of exon and the insert is actually at exact beginning of exon]
            if (istart != genStart) {
                MutableSeqSymmetry segSym = new SimpleMutableSeqSymmetry();
                SeqSpan gSpan = new SimpleSeqSpan(genStart, istart, genomic);  // start of insert is end of exon seg
                SeqSpan tSpan = new SimpleSeqSpan(transStart, transEnd, mrna);
                segSym.addSpan(gSpan);
                segSym.addSpan(tSpan);
                exonSym.addChild(segSym);
            }
            // now add exon seg for the current insert
            transStart = transEnd;
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Examples of com.affymetrix.genometryImpl.symmetry.MutableSeqSymmetry.addSpan()

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            if (istart != genStart) {
                MutableSeqSymmetry segSym = new SimpleMutableSeqSymmetry();
                SeqSpan gSpan = new SimpleSeqSpan(genStart, istart, genomic);  // start of insert is end of exon seg
                SeqSpan tSpan = new SimpleSeqSpan(transStart, transEnd, mrna);
                segSym.addSpan(gSpan);
                segSym.addSpan(tSpan);
                exonSym.addChild(segSym);
            }
            // now add exon seg for the current insert
            transStart = transEnd;
            transEnd += ilength;
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Examples of com.affymetrix.genometryImpl.symmetry.MutableSeqSymmetry.addSpan()

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            transStart = transEnd;
            transEnd += ilength;
            SeqSpan insert_tspan = new SimpleSeqSpan(transStart, transEnd, mrna);
            SeqSpan insert_gspan = new SimpleSeqSpan(istart, istart, genomic);
            MutableSeqSymmetry isegSym = new SimpleMutableSeqSymmetry();
            isegSym.addSpan(insert_tspan);
            // experimenting with adding a zero-length placeholder for exon insert relative to genomic
            isegSym.addSpan(insert_gspan);
            exonSym.addChild(isegSym);

            // set current genomic start point for next loop to location of current insert
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Examples of com.affymetrix.genometryImpl.symmetry.MutableSeqSymmetry.addSpan()

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            SeqSpan insert_tspan = new SimpleSeqSpan(transStart, transEnd, mrna);
            SeqSpan insert_gspan = new SimpleSeqSpan(istart, istart, genomic);
            MutableSeqSymmetry isegSym = new SimpleMutableSeqSymmetry();
            isegSym.addSpan(insert_tspan);
            // experimenting with adding a zero-length placeholder for exon insert relative to genomic
            isegSym.addSpan(insert_gspan);
            exonSym.addChild(isegSym);

            // set current genomic start point for next loop to location of current insert
            genStart = istart;
            transStart = transEnd;
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Examples of com.affymetrix.genometryImpl.symmetry.MutableSeqSymmetry.addSpan()

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        //   after finished looping through inserts
        if (genStart != egSpan.getEnd()) {
            SeqSpan gSpan = new SimpleSeqSpan(genStart, egSpan.getEnd(), genomic);
            SeqSpan tSpan = new SimpleSeqSpan(transStart, etSpan.getEnd(), mrna);
            MutableSeqSymmetry endSym = new SimpleMutableSeqSymmetry();
            endSym.addSpan(gSpan);
            endSym.addSpan(tSpan);
            exonSym.addChild(endSym);
        }
    }
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Examples of com.affymetrix.genometryImpl.symmetry.MutableSeqSymmetry.addSpan()

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        if (genStart != egSpan.getEnd()) {
            SeqSpan gSpan = new SimpleSeqSpan(genStart, egSpan.getEnd(), genomic);
            SeqSpan tSpan = new SimpleSeqSpan(transStart, etSpan.getEnd(), mrna);
            MutableSeqSymmetry endSym = new SimpleMutableSeqSymmetry();
            endSym.addSpan(gSpan);
            endSym.addSpan(tSpan);
            exonSym.addChild(endSym);
        }
    }

    /**
 
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Examples of com.affymetrix.genometryImpl.symmetry.SimpleMutableSeqSymmetry.addSpan()

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        int acount = gseq.getAnnotationCount();

        SeqSymmetry[] path2view = new SeqSymmetry[1];
        MutableSeqSymmetry viewSym = new SimpleMutableSeqSymmetry();
        viewSym.addSpan(new SimpleSeqSpan(gseq.getMin(), gseq.getMax(), gseq));
        vseq = new BioSeq("view seq", null, gseq.getLength());
        vseq.setBounds(gseq.getMin(), gseq.getMax());

        viewSym.addSpan(new SimpleSeqSpan(vseq.getMin(), vseq.getMax(), vseq));
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Examples of com.affymetrix.genometryImpl.symmetry.SimpleMutableSeqSymmetry.addSpan()

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        MutableSeqSymmetry viewSym = new SimpleMutableSeqSymmetry();
        viewSym.addSpan(new SimpleSeqSpan(gseq.getMin(), gseq.getMax(), gseq));
        vseq = new BioSeq("view seq", null, gseq.getLength());
        vseq.setBounds(gseq.getMin(), gseq.getMax());

        viewSym.addSpan(new SimpleSeqSpan(vseq.getMin(), vseq.getMax(), vseq));

        path2view[0] = viewSym;

        for (int i = 0; i < acount; i++) {
            SeqSymmetry asym = gseq.getAnnotation(i);
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