public String induceRulesWithTestSet(double testSetPercent) throws DataFormatException { SystemVariables.getInstance() .appendToExperimentNotes("\\n* Total number of PSSM matches in positive sequences: "); // System.out.println("Total number of PSSM matches in positive sequences: "); ArrayList<Feature> posTrainingSet = regulatoryElementService.getRegulatoryElements( regulatoryRegionService.getPositiveRegulatoryRegions(), positiveCutOffScore, posATcomposition, posCGcomposition); SystemVariables.getInstance() .appendToExperimentNotes("\\n* Total number of PSSM matches in negative sequences: "); // System.out.println("Total number of PSSM matches in negative sequences: "); ArrayList<Feature> negTrainingSet = regulatoryElementService.getRegulatoryElements( regulatoryRegionService.getNegativeRegulatoryRegions(), negativeCutOffScore, negATcomposition, negCGcomposition); IlpService formatter = new IlpService(tempIlpJobDirName); formatter.createIlpFilesWithTestSet( regulatoryRegionService.getPositiveRegulatoryRegions(), regulatoryRegionService.getNegativeRegulatoryRegions(), posTrainingSet, negTrainingSet, testSetPercent); String ilpTheory = formatter.runILP(); return ilpTheory; }