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/*
* nastreport.cpp
*
*
* Created by Pat Schloss on 12/19/08.
* Copyright 2008 Patrick D. Schloss. All rights reserved.
*
*/
#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) {
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(){
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){
try {
queryName = candSeq->getName();
queryLength = candSeq->getNumBases();
}
catch(exception& e) {
m->errorOut(e, "NastReport", "setCandidate");
exit(1);
}
}
/******************************************************************************************************************/
void NastReport::setTemplate(Sequence* tempSeq){
try {
templateName = tempSeq->getName();
templateLength = tempSeq->getNumBases();
}
catch(exception& e) {
m->errorOut(e, "NastReport", "setTemplate");
exit(1);
}
}
/******************************************************************************************************************/
void NastReport::setSearchParameters(string method, float score){
try {
searchMethod = method;
searchScore = score;
}
catch(exception& e) {
m->errorOut(e, "NastReport", "setSearchParameters");
exit(1);
}
}
/******************************************************************************************************************/
void NastReport::setAlignmentParameters(string method, Alignment* align){
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){
try {
longestInsert = nast.getMaxInsertLength();
similarityToTemplate = nast.getSimilarityScore();
}
catch(exception& e) {
m->errorOut(e, "NastReport", "setNastParameters");
exit(1);
}
}
/******************************************************************************************************************/
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