structureScoringMatrix, new AffineGapGlobalSequenceAlignment(
10, 10, RnaAlphabet.getInstance(),
new AffineGapScoringMatrix(
"matrix/NUC-Affine-sim-RIBOSUM85-60.matrix",
RnaAlphabet.getInstance())),
new LocalSequenceAlignment(10, 10, RnaAlphabet.getInstance(),
new ScoringMatrix("matrix/NUC-sim-RIBOSUM85-60.matrix",
RnaAlphabet.getInstance())));
StemStructure str1 = new StemStructure(">1", new CharBuffer(
"AGAGGUAAAAUGCAUCU"), new CharBuffer("((..(((...)))..))"));