/** * parse parameters of all entries * * @param in */ private svm_problem parsePara(ArrayList<TrainingEntry> in, String taxo) { int num = 0; for (TrainingEntry t : in) num += t.NumOfMi(); svm_node[][] data = new svm_node[num][]; int i = 0; for (TrainingEntry mi : in) { pri = mi.getPriRNA(); pri.setPriPara(); for (int j = 0; j < mi.NumOfMi(); j++) { pri.process(mi.getStart(j), mi.getSize(j), mi.getStrand(j)); ps = new ParaSummary(pri, pri.getPreRNA(), pri.getMiRNA()); data[i++] = svm.predictMatrix(mi.getLabel(j), ps.paraMatrix(taxo)); } } return svm.trainMatrix(data); }