nastreport.cpp

   1 /*
   2  *  nastreport.cpp
   3  *
   4  *
   5  *  Created by Pat Schloss on 12/19/08.
   6  *  Copyright 2008 Patrick D. Schloss. All rights reserved.
   7  *
   8  */
   9
  10 #include "sequence.hpp"
  11 #include "nast.hpp"
  12 #include "alignment.hpp"
  13 #include "nastreport.hpp"
  14
  15
  16 /******************************************************************************************************************/
  17
  18 NastReport::NastReport() {
  19         try {
  20                 m = MothurOut::getInstance();
  21                 output = "";
  22         }
  23         catch(exception& e) {
  24                 m->errorOut(e, "NastReport", "NastReport");
  25                 exit(1);
  26         }
  27 }
  28 /******************************************************************************************************************/
  29 string NastReport::getHeaders() {
  30         try {
  31                 output = "";
  32
  33                 output += "QueryName\tQueryLength\tTemplateName\tTemplateLength\t";
  34                 output += "SearchMethod\tSearchScore\t";
  35                 output += "AlignmentMethod\tQueryStart\tQueryEnd\tTemplateStart\tTemplateEnd\t";
  36                 output += "PairwiseAlignmentLength\tGapsInQuery\tGapsInTemplate\t";
  37                 output += "LongestInsert\t";
  38                 output += "SimBtwnQuery&Template\n";
  39
  40                 return output;
  41         }
  42         catch(exception& e) {
  43                 m->errorOut(e, "NastReport", "getHeaders");
  44                 exit(1);
  45         }
  46 }
  47 /******************************************************************************************************************/
  48
  49 NastReport::NastReport(string candidateReportFName) {
  50         try {
  51                 m = MothurOut::getInstance();
  52                 m->openOutputFile(candidateReportFName, candidateReportFile);
  53
  54                 candidateReportFile << "QueryName\tQueryLength\tTemplateName\tTemplateLength\t";
  55                 candidateReportFile << "SearchMethod\tSearchScore\t";
  56                 candidateReportFile << "AlignmentMethod\tQueryStart\tQueryEnd\tTemplateStart\tTemplateEnd\t";
  57                 candidateReportFile << "PairwiseAlignmentLength\tGapsInQuery\tGapsInTemplate\t";
  58                 candidateReportFile << "LongestInsert\t";
  59                 candidateReportFile << "SimBtwnQuery&Template" << endl;
  60         }
  61         catch(exception& e) {
  62                 m->errorOut(e, "NastReport", "NastReport");
  63                 exit(1);
  64         }
  65 }
  66
  67 /******************************************************************************************************************/
  68
  69 NastReport::~NastReport() {
  70         try {
  71                 candidateReportFile.close();
  72         }
  73         catch(exception& e) {
  74                 m->errorOut(e, "NastReport", "~NastReport");
  75                 exit(1);
  76         }
  77 }
  78
  79 /******************************************************************************************************************/
  80
  81 void NastReport::print(){
  82         try {
  83                 candidateReportFile << queryName << '\t' << queryLength << '\t' << templateName << '\t' << templateLength << '\t';
  84                 candidateReportFile << searchMethod << '\t' << setprecision(2) << fixed << searchScore << '\t';
  85
  86                 candidateReportFile << alignmentMethod << '\t' << candidateStartPosition << "\t" << candidateEndPosition << '\t';
  87                 candidateReportFile << templateStartPosition << "\t" << templateEndPosition << '\t';
  88                 candidateReportFile << pairwiseAlignmentLength << '\t' << totalGapsInQuery << '\t' << totalGapsInTemplate << '\t';
  89                 candidateReportFile << longestInsert << '\t';
  90                 candidateReportFile << setprecision(2) << similarityToTemplate;
  91
  92                 candidateReportFile << endl;
  93                 candidateReportFile.flush();
  94         }
  95         catch(exception& e) {
  96                 m->errorOut(e, "NastReport", "print");
  97                 exit(1);
  98         }
  99 }
 100 /******************************************************************************************************************/
 101
 102 string NastReport::getReport(){
 103         try {
 104                 output = "";
 105
 106                 output += queryName + '\t' + toString(queryLength) + '\t' + templateName + '\t' + toString(templateLength) + '\t';
 107
 108                 string temp = toString(searchScore);
 109                 int pos = temp.find_last_of('.');  //find deicmal point if their is one
 110
 111                 //if there is a decimal
 112                 if (pos != -1) { temp = temp.substr(0, pos+3); } //set precision to 2 places
 113                 else{   temp += ".00";  }
 114
 115                 output += searchMethod + '\t' + temp + '\t';
 116                 output += alignmentMethod + '\t' + toString(candidateStartPosition) + "\t" + toString(candidateEndPosition) + '\t';
 117                 output += toString(templateStartPosition) + "\t" + toString(templateEndPosition) + '\t';
 118                 output += toString(pairwiseAlignmentLength) + '\t' + toString(totalGapsInQuery) + '\t' + toString(totalGapsInTemplate) + '\t';
 119                 output += toString(longestInsert) + '\t';
 120
 121                 temp = toString(similarityToTemplate);
 122                 pos = temp.find_last_of('.');  //find deicmal point if their is one
 123
 124                 //if there is a decimal
 125                 if (pos != -1) { temp = temp.substr(0, pos+3); } //set precision to 2 places
 126                 else{   temp += ".00";  }
 127
 128                 output += temp + '\n';
 129
 130                 return output;
 131         }
 132         catch(exception& e) {
 133                 m->errorOut(e, "NastReport", "getReport");
 134                 exit(1);
 135         }
 136 }
 137
 138 /******************************************************************************************************************/
 139
 140 void NastReport::setCandidate(Sequence* candSeq){
 141         try {
 142                 queryName = candSeq->getName();
 143                 queryLength = candSeq->getNumBases();
 144         }
 145         catch(exception& e) {
 146                 m->errorOut(e, "NastReport", "setCandidate");
 147                 exit(1);
 148         }
 149 }
 150
 151 /******************************************************************************************************************/
 152
 153 void NastReport::setTemplate(Sequence* tempSeq){
 154         try {
 155                 templateName = tempSeq->getName();
 156                 templateLength = tempSeq->getNumBases();
 157         }
 158         catch(exception& e) {
 159                 m->errorOut(e, "NastReport", "setTemplate");
 160                 exit(1);
 161         }
 162 }
 163
 164 /******************************************************************************************************************/
 165
 166 void NastReport::setSearchParameters(string method, float score){
 167         try {
 168                 searchMethod = method;
 169                 searchScore = score;
 170         }
 171         catch(exception& e) {
 172                 m->errorOut(e, "NastReport", "setSearchParameters");
 173                 exit(1);
 174         }
 175 }
 176
 177 /******************************************************************************************************************/
 178
 179 void NastReport::setAlignmentParameters(string method, Alignment* align){
 180         try {
 181                 alignmentMethod = method;
 182
 183                 candidateStartPosition = align->getCandidateStartPos();
 184                 candidateEndPosition = align->getCandidateEndPos();
 185                 templateStartPosition = align->getTemplateStartPos();
 186                 templateEndPosition = align->getTemplateEndPos();
 187                 pairwiseAlignmentLength = align->getPairwiseLength();
 188
 189                 totalGapsInQuery = pairwiseAlignmentLength - (candidateEndPosition - candidateStartPosition + 1);
 190                 totalGapsInTemplate = pairwiseAlignmentLength - (templateEndPosition - templateStartPosition + 1);
 191         }
 192         catch(exception& e) {
 193                 m->errorOut(e, "NastReport", "setAlignmentParameters");
 194                 exit(1);
 195         }
 196 }
 197
 198 /******************************************************************************************************************/
 199
 200 void NastReport::setNastParameters(Nast nast){
 201         try {
 202
 203                 longestInsert = nast.getMaxInsertLength();
 204                 similarityToTemplate = nast.getSimilarityScore();
 205         }
 206         catch(exception& e) {
 207                 m->errorOut(e, "NastReport", "setNastParameters");
 208                 exit(1);
 209         }
 210 }
 211
 212 /******************************************************************************************************************/