Examples of com.affymetrix.genometryImpl.span.SimpleMutableSeqSpan

    private static void copyToMutable(SeqSymmetry sym, MutableSeqSymmetry mut) {
        mut.clear();
        int spanCount = sym.getSpanCount();
        for (int i = 0; i < spanCount; i++) {
            SeqSpan span = sym.getSpan(i);
            SeqSpan newspan = new SimpleMutableSeqSpan(span);
            mut.addSpan(newspan);
        }
        int childCount = sym.getChildCount();
        for (int i = 0; i < childCount; i++) {
            SeqSymmetry child = sym.getChild(i);

                    SeqSymmetry spanSym = processSimSpan(query_seq, chelem);
                    ((SymWithProps) spanSym).setProperty(METHODSTR, method);
                    hitSym.addChild(spanSym);
                    SeqSpan spanSpan = spanSym.getSpan(query_seq);
                    if (hitSpan == null) {
                        hitSpan = new SimpleMutableSeqSpan(spanSpan.getMin(), spanSpan.getMax(), query_seq); 
                    } else {
                        SeqUtils.encompass(hitSpan, spanSpan, (MutableSeqSpan) hitSpan);
                    }
                    //hitSym.setProperty(TYPESTR, "hitspan");
          int start = Integer.valueOf(((SymWithProps)spanSym).getProperty(AA_START).toString());

Related Classes of com.affymetrix.genometryImpl.span.SimpleMutableSeqSpan

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