X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=nastreport.cpp;h=132886bd55be4e9a57aa52816cfc49bcfb98eb42;hb=86b6cc7ce1ec7fce12cdfdd6225de4dee7cfbdbf;hp=67ec702fdd122b732b0f7e0598fe54f791a121c8;hpb=526a868606faa50caf86e7399f7554c0335b39e5;p=mothur.git

diff --git a/nastreport.cpp b/nastreport.cpp
index 67ec702..132886b 100644
--- a/nastreport.cpp
+++ b/nastreport.cpp
@@ -7,13 +7,30 @@
  *
  */
 
-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) {
@@ -29,6 +46,12 @@ NastReport::NastReport(string candidateReportFName) {
 
 /******************************************************************************************************************/
 
+NastReport::~NastReport() {
+	candidateReportFile.close();
+}
+
+/******************************************************************************************************************/
+
 void NastReport::print(){
 	
 	candidateReportFile << queryName << '\t' << queryLength << '\t' << templateName << '\t' << templateLength << '\t';
@@ -37,25 +60,57 @@ void NastReport::print(){
 	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();
 }
 
 /******************************************************************************************************************/