added alignment code

[mothur.git] / nastreport.cpp

diff --git a/nastreport.cpp b/nastreport.cpp
new file mode 100644 (file)
index 0000000..67ec702
--- /dev/null
+++ b/nastreport.cpp
@@ -0,0 +1,92 @@
+/*
+ *  nastreport.cpp
+ *  
+ *
+ *  Created by Pat Schloss on 12/19/08.
+ *  Copyright 2008 Patrick D. Schloss. All rights reserved.
+ *
+ */
+
+using namespace std;
+
+#include "sequence.hpp"
+#include "nast.hpp"
+#include "alignment.hpp"
+#include "nastreport.hpp"
+
+/******************************************************************************************************************/
+
+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;
+}
+
+/******************************************************************************************************************/
+
+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();
+}
+
+/******************************************************************************************************************/
+
+void NastReport::setCandidate(Sequence* candSeq){ 
+       queryName = candSeq->getName();
+       queryLength = candSeq->getUnalignLength();
+}
+
+/******************************************************************************************************************/
+
+void NastReport::setTemplate(Sequence* tempSeq){ 
+       templateName = tempSeq->getName();
+       templateLength = tempSeq->getUnalignLength();
+}
+
+/******************************************************************************************************************/
+
+void NastReport::setSearchParameters(string method, float score){
+       searchMethod = method;
+       searchScore = score;
+}
+
+/******************************************************************************************************************/
+
+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);
+}
+
+/******************************************************************************************************************/
+
+void NastReport::setNastParameters(Nast nast){
+
+       longestInsert = nast.getMaxInsertLength();
+       similarityToTemplate = nast.getSimilarityScore();
+       
+}
+
+/******************************************************************************************************************/