*
*/
-using namespace std;
-
#include "sequence.hpp"
#include "nast.hpp"
#include "alignment.hpp"
/******************************************************************************************************************/
+NastReport::~NastReport() {
+ candidateReportFile.close();
+}
+
+/******************************************************************************************************************/
+
void NastReport::print(){
candidateReportFile << queryName << '\t' << queryLength << '\t' << templateName << '\t' << templateLength << '\t';
candidateReportFile << alignmentMethod << '\t' << candidateStartPosition << "\t" << candidateEndPosition << '\t';
candidateReportFile << templateStartPosition << "\t" << templateEndPosition << '\t';
candidateReportFile << pairwiseAlignmentLength << '\t' << totalGapsInQuery << '\t' << totalGapsInTemplate << '\t';
- candidateReportFile << longestInsert << '\t';;
+ candidateReportFile << longestInsert << '\t';
candidateReportFile << setprecision(2) << similarityToTemplate;
candidateReportFile << endl;
void NastReport::setCandidate(Sequence* candSeq){
queryName = candSeq->getName();
- queryLength = candSeq->getUnalignLength();
+ queryLength = candSeq->getNumBases();
}
/******************************************************************************************************************/
void NastReport::setTemplate(Sequence* tempSeq){
templateName = tempSeq->getName();
- templateLength = tempSeq->getUnalignLength();
+ templateLength = tempSeq->getNumBases();
}
/******************************************************************************************************************/