#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() {
- candidateReportFile.close();
+ 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);
+ }
}
/******************************************************************************************************************/
projects / mothur.git / blobdiff