public Explorer(
RegulatoryRegionService regRegionService,
RegulatoryElementService regElService,
String tempIlpJobDirName)
throws DataFormatException {
this.regulatoryRegionService = regRegionService;
this.regulatoryElementService = regElService;
this.tempIlpJobDirName = tempIlpJobDirName;
positiveCutOffScore = SystemVariables.getInstance().getPositivePatserCutOffScore();
negativeCutOffScore = SystemVariables.getInstance().getNegativePatserCutOffScore();
/////// Statistics
SystemVariables.getInstance().cleanStatistics(); // clean old;
SystemVariables.getInstance()
.setPosSeqNum(regulatoryRegionService.getPositiveRegulatoryRegions().size());
SystemVariables.getInstance()
.setNegSeqNum(regulatoryRegionService.getNegativeRegulatoryRegions().size());
SystemVariables.getInstance()
.appendToExperimentNotes(
"\\n* Number of positive sequences: "
+ regulatoryRegionService.getPositiveRegulatoryRegions().size());
SystemVariables.getInstance()
.appendToExperimentNotes(
"\\n* Number of negative sequences: "
+ regulatoryRegionService.getNegativeRegulatoryRegions().size());
SystemVariables.getInstance()
.appendToExperimentNotes(
"\\n* Patser cut-off score for positive sequences: " + positiveCutOffScore);
SystemVariables.getInstance()
.appendToExperimentNotes(
"\\n* Patser cut-off score for negative sequences: " + negativeCutOffScore);
double[] posNtComposition =
FeaturesTools.getNucleotideComposition(
regulatoryRegionService.getPositiveRegulatoryRegions());
posATcomposition = posNtComposition[0] + posNtComposition[3];
posCGcomposition = posNtComposition[1] + posNtComposition[2];
SystemVariables.getInstance()
.appendToExperimentNotes(
"\\n* A:T and C:G composition of positive sequences: "
+ posATcomposition
+ " "
+ posCGcomposition);
SystemVariables.getInstance().setPosATcomposition(posATcomposition);
SystemVariables.getInstance().setPosCGcomposition(posCGcomposition);
double[] negNtComposition =
FeaturesTools.getNucleotideComposition(
regulatoryRegionService.getNegativeRegulatoryRegions());
negATcomposition = negNtComposition[0] + negNtComposition[3];
negCGcomposition = negNtComposition[1] + negNtComposition[2];
SystemVariables.getInstance()
.appendToExperimentNotes(
"\\n* A:T and C:G composition of negative sequences: "
+ negATcomposition
+ " "
+ negCGcomposition);
SystemVariables.getInstance().setNegATcomposition(negATcomposition);
SystemVariables.getInstance().setNegCGcomposition(negCGcomposition);
}
