moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / nastreport.cpp

diff --git a/nastreport.cpp b/nastreport.cpp
deleted file mode 100644 (file)
index 95901a3..0000000
--- a/nastreport.cpp
+++ /dev/null
@@ -1,212 +0,0 @@
-/*
- *  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);
-       }
-}
-
-/******************************************************************************************************************/