*
*/
-using namespace std;
-
#include "sequence.hpp"
#include "nast.hpp"
#include "alignment.hpp"
#include "nastreport.hpp"
+
+/******************************************************************************************************************/
+
+NastReport::NastReport() {
+ output = "";
+}
+/******************************************************************************************************************/
+string NastReport::getHeaders() {
+ output = "";
+
+ output += "QueryName\tQueryLength\tTemplateName\tTemplateLength\t";
+ output += "SearchMethod\tSearchScore\t";
+ output += "AlignmentMethod\tQueryStart\tQueryEnd\tTemplateStart\tTemplateEnd\t";
+ output += "PairwiseAlignmentLength\tGapsInQuery\tGapsInTemplate\t";
+ output += "LongestInsert\t";
+ output += "SimBtwnQuery&Template\n";
+
+ return output;
+}
/******************************************************************************************************************/
NastReport::NastReport(string candidateReportFName) {
/******************************************************************************************************************/
+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;
candidateReportFile.flush();
}
+/******************************************************************************************************************/
+
+string NastReport::getReport(){
+
+ output = "";
+
+ output += queryName + '\t' + toString(queryLength) + '\t' + templateName + '\t' + toString(templateLength) + '\t';
+
+ string temp = toString(searchScore);
+ int pos = temp.find_last_of('.'); //find deicmal point if their is one
+
+ //if there is a decimal
+ if (pos != -1) { temp = temp.substr(0, pos+3); } //set precision to 2 places
+ else{ temp += ".00"; }
+
+ output += searchMethod + '\t' + temp + '\t';
+ output += alignmentMethod + '\t' + toString(candidateStartPosition) + "\t" + toString(candidateEndPosition) + '\t';
+ output += toString(templateStartPosition) + "\t" + toString(templateEndPosition) + '\t';
+ output += toString(pairwiseAlignmentLength) + '\t' + toString(totalGapsInQuery) + '\t' + toString(totalGapsInTemplate) + '\t';
+ output += toString(longestInsert) + '\t';
+
+ temp = toString(similarityToTemplate);
+ pos = temp.find_last_of('.'); //find deicmal point if their is one
+
+ //if there is a decimal
+ if (pos != -1) { temp = temp.substr(0, pos+3); } //set precision to 2 places
+ else{ temp += ".00"; }
+
+ output += temp + '\n';
+
+ return output;
+}
/******************************************************************************************************************/
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();
}
/******************************************************************************************************************/