Package com.affymetrix.genometryImpl.symmetry

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

280
281
282
283
284
285
286
287
288
289
290
        hitSym.setProperty("num_spans", prop);
        hitSym.setProperty(TYPESTR, "simHit");
    hitSym.setProperty(AA_START, String.valueOf(aa_start));
    hitSym.setProperty(AA_END, String.valueOf(aa_end));
    hitSym.setProperty(AA_LENGTH, String.valueOf(aa_end - aa_start));
        hitSym.addSpan(hitSpan);
        hitSym.setID("");
        query_seq.addAnnotation(hitSym);
    }

    /**
 
View Full Code Here
436
437
438
439
440
441
442
443
444
445
446
        }
        NodeList children = elem.getChildNodes();
        SeqSpan span = new SimpleSeqSpan(start, end, genomic);

        TypeContainerAnnot m2gSym = new TypeContainerAnnot(elem.getAttribute("method"));
        m2gSym.addSpan(span);
        addDescriptors(elem, m2gSym);
        m2gSym.setProperty(TYPESTR, "mRNA");
        boolean forward = (span.isForward());

View Full Code Here
768
769
770
771
772
773
774
775
776
777
778
        prot_hash.put(protein_id, protein);
        SeqSpan pspan = new SimpleSeqSpan(protein.getMin(), protein.getMax(), protein);
        if (DEBUG) {
            System.err.println("protein: length = " + pspan.getLength());
        }
        m2pSym.addSpan(mspan);
        m2pSym.addSpan(pspan);

        m2pSym.setID("");
        protein.addAnnotation(m2pSym);
        mrna.addAnnotation(m2pSym);
View Full Code Here
769
770
771
772
773
774
775
776
777
778
779
        SeqSpan pspan = new SimpleSeqSpan(protein.getMin(), protein.getMax(), protein);
        if (DEBUG) {
            System.err.println("protein: length = " + pspan.getLength());
        }
        m2pSym.addSpan(mspan);
        m2pSym.addSpan(pspan);

        m2pSym.setID("");
        protein.addAnnotation(m2pSym);
        mrna.addAnnotation(m2pSym);
View Full Code Here
TOP
Copyright © 2018 www.massapi.com. All rights reserved.
All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.