X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=nastreport.cpp;h=95901a36e8576a01cdc3b313ef8d0b11dc0bd402;hp=799793ece4dda8567d1dcb5a9865a70c9dd45f3e;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=5b7ac70116137b52dd7884b76c5bca660a5fea38

diff --git a/nastreport.cpp b/nastreport.cpp
index 799793e..95901a3 100644
--- a/nastreport.cpp
+++ b/nastreport.cpp
@@ -7,86 +7,206 @@
  *
  */
 
-using namespace std;
-
 #include "sequence.hpp"
 #include "nast.hpp"
 #include "alignment.hpp"
 #include "nastreport.hpp"
 
+
+/******************************************************************************************************************/
+
+NastReport::NastReport() {
+	try {
+		m = MothurOut::getInstance();
+		output = "";
+	}
+	catch(exception& e) {
+		m->errorOut(e, "NastReport", "NastReport");
+		exit(1);
+	}
+}
+/******************************************************************************************************************/
+string NastReport::getHeaders() {
+	try {
+		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;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "NastReport", "getHeaders");
+		exit(1);
+	}
+}
 /******************************************************************************************************************/
 
 NastReport::NastReport(string candidateReportFName) {
-	openOutputFile(candidateReportFName, candidateReportFile);
-	
-	candidateReportFile << "QueryName\tQueryLength\tTemplateName\tTemplateLength\t";
-	candidateReportFile << "SearchMethod\tSearchScore\t";
-	candidateReportFile << "AlignmentMethod\tQueryStart\tQueryEnd\tTemplateStart\tTemplateEnd\t";
-	candidateReportFile << "PairwiseAlignmentLength\tGapsInQuery\tGapsInTemplate\t";
-	candidateReportFile << "LongestInsert\t";
-	candidateReportFile << "SimBtwnQuery&Template" << endl;
+	try {
+		m = MothurOut::getInstance();
+		m->openOutputFile(candidateReportFName, candidateReportFile);
+		
+		candidateReportFile << "QueryName\tQueryLength\tTemplateName\tTemplateLength\t";
+		candidateReportFile << "SearchMethod\tSearchScore\t";
+		candidateReportFile << "AlignmentMethod\tQueryStart\tQueryEnd\tTemplateStart\tTemplateEnd\t";
+		candidateReportFile << "PairwiseAlignmentLength\tGapsInQuery\tGapsInTemplate\t";
+		candidateReportFile << "LongestInsert\t";
+		candidateReportFile << "SimBtwnQuery&Template" << endl;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "NastReport", "NastReport");
+		exit(1);
+	}
+}
+
+/******************************************************************************************************************/
+
+NastReport::~NastReport() {
+	try {
+		candidateReportFile.close();
+	}
+	catch(exception& e) {
+		m->errorOut(e, "NastReport", "~NastReport");
+		exit(1);
+	}
 }
 
 /******************************************************************************************************************/
 
 void NastReport::print(){
-	
-	candidateReportFile << queryName << '\t' << queryLength << '\t' << templateName << '\t' << templateLength << '\t';
-	candidateReportFile << searchMethod << '\t' << setprecision(2) << fixed << searchScore << '\t';
-
-	candidateReportFile << alignmentMethod << '\t' << candidateStartPosition << "\t" << candidateEndPosition << '\t';
-	candidateReportFile << templateStartPosition << "\t" << templateEndPosition << '\t';
-	candidateReportFile << pairwiseAlignmentLength << '\t' << totalGapsInQuery << '\t' << totalGapsInTemplate << '\t';
-	candidateReportFile << longestInsert << '\t';;
-	candidateReportFile << setprecision(2) << similarityToTemplate;
-	
-	candidateReportFile << endl;
-	candidateReportFile.flush();
+	try {
+		candidateReportFile << queryName << '\t' << queryLength << '\t' << templateName << '\t' << templateLength << '\t';
+		candidateReportFile << searchMethod << '\t' << setprecision(2) << fixed << searchScore << '\t';
+
+		candidateReportFile << alignmentMethod << '\t' << candidateStartPosition << "\t" << candidateEndPosition << '\t';
+		candidateReportFile << templateStartPosition << "\t" << templateEndPosition << '\t';
+		candidateReportFile << pairwiseAlignmentLength << '\t' << totalGapsInQuery << '\t' << totalGapsInTemplate << '\t';
+		candidateReportFile << longestInsert << '\t';
+		candidateReportFile << setprecision(2) << similarityToTemplate;
+		
+		candidateReportFile << endl;
+		candidateReportFile.flush();
+	}
+	catch(exception& e) {
+		m->errorOut(e, "NastReport", "print");
+		exit(1);
+	}
+}
+/******************************************************************************************************************/
+
+string NastReport::getReport(){
+	try {
+		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;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "NastReport", "getReport");
+		exit(1);
+	}
 }
 
 /******************************************************************************************************************/
 
 void NastReport::setCandidate(Sequence* candSeq){ 
-	queryName = candSeq->getName();
-	queryLength = candSeq->getNumBases();
+	try {
+		queryName = candSeq->getName();
+		queryLength = candSeq->getNumBases();
+	}
+	catch(exception& e) {
+		m->errorOut(e, "NastReport", "setCandidate");
+		exit(1);
+	}
 }
 
 /******************************************************************************************************************/
 
 void NastReport::setTemplate(Sequence* tempSeq){ 
-	templateName = tempSeq->getName();
-	templateLength = tempSeq->getNumBases();
+	try {
+		templateName = tempSeq->getName();
+		templateLength = tempSeq->getNumBases();
+	}
+	catch(exception& e) {
+		m->errorOut(e, "NastReport", "setTemplate");
+		exit(1);
+	}
 }
 
 /******************************************************************************************************************/
 
 void NastReport::setSearchParameters(string method, float score){
-	searchMethod = method;
-	searchScore = score;
+	try {
+		searchMethod = method;
+		searchScore = score;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "NastReport", "setSearchParameters");
+		exit(1);
+	}
 }
 
 /******************************************************************************************************************/
 
 void NastReport::setAlignmentParameters(string method, Alignment* align){
-	alignmentMethod = method;
-	
-	candidateStartPosition = align->getCandidateStartPos();
-	candidateEndPosition = align->getCandidateEndPos();
-	templateStartPosition = align->getTemplateStartPos();
-	templateEndPosition = align->getTemplateEndPos();
-	pairwiseAlignmentLength = align->getPairwiseLength();
-
-	totalGapsInQuery = pairwiseAlignmentLength - (candidateEndPosition - candidateStartPosition + 1);
-	totalGapsInTemplate = pairwiseAlignmentLength - (templateEndPosition - templateStartPosition + 1);
+	try {
+		alignmentMethod = method;
+		
+		candidateStartPosition = align->getCandidateStartPos();
+		candidateEndPosition = align->getCandidateEndPos();
+		templateStartPosition = align->getTemplateStartPos();
+		templateEndPosition = align->getTemplateEndPos();
+		pairwiseAlignmentLength = align->getPairwiseLength();
+
+		totalGapsInQuery = pairwiseAlignmentLength - (candidateEndPosition - candidateStartPosition + 1);
+		totalGapsInTemplate = pairwiseAlignmentLength - (templateEndPosition - templateStartPosition + 1);
+	}
+	catch(exception& e) {
+		m->errorOut(e, "NastReport", "setAlignmentParameters");
+		exit(1);
+	}
 }
 
 /******************************************************************************************************************/
 
 void NastReport::setNastParameters(Nast nast){
-
-	longestInsert = nast.getMaxInsertLength();
-	similarityToTemplate = nast.getSimilarityScore();
-	
+	try {
+
+		longestInsert = nast.getMaxInsertLength();
+		similarityToTemplate = nast.getSimilarityScore();
+	}
+	catch(exception& e) {
+		m->errorOut(e, "NastReport", "setNastParameters");
+		exit(1);
+	}
 }
 
 /******************************************************************************************************************/