fixed phylip convert for cluster.split command

[mothur.git] / nastreport.cpp

diff --git a/nastreport.cpp b/nastreport.cpp
index 67ec702fdd122b732b0f7e0598fe54f791a121c8..132886bd55be4e9a57aa52816cfc49bcfb98eb42 100644 (file)
--- a/nastreport.cpp
+++ b/nastreport.cpp
@@ -7,13 +7,30 @@
  *
  */
 
-using namespace std;
-
 #include "sequence.hpp"
 #include "nast.hpp"
 #include "alignment.hpp"
 #include "nastreport.hpp"
 
+
+/******************************************************************************************************************/
+
+NastReport::NastReport() {
+       output = "";
+}
+/******************************************************************************************************************/
+string NastReport::getHeaders() {
+       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;
+}
 /******************************************************************************************************************/
 
 NastReport::NastReport(string candidateReportFName) {
@@ -29,6 +46,12 @@ NastReport::NastReport(string candidateReportFName) {
 
 /******************************************************************************************************************/
 
+NastReport::~NastReport() {
+       candidateReportFile.close();
+}
+
+/******************************************************************************************************************/
+
 void NastReport::print(){
        
        candidateReportFile << queryName << '\t' << queryLength << '\t' << templateName << '\t' << templateLength << '\t';
@@ -37,25 +60,57 @@ void NastReport::print(){
        candidateReportFile << alignmentMethod << '\t' << candidateStartPosition << "\t" << candidateEndPosition << '\t';
        candidateReportFile << templateStartPosition << "\t" << templateEndPosition << '\t';
        candidateReportFile << pairwiseAlignmentLength << '\t' << totalGapsInQuery << '\t' << totalGapsInTemplate << '\t';
-       candidateReportFile << longestInsert << '\t';;
+       candidateReportFile << longestInsert << '\t';
        candidateReportFile << setprecision(2) << similarityToTemplate;
        
        candidateReportFile << endl;
        candidateReportFile.flush();
 }
+/******************************************************************************************************************/
+
+string NastReport::getReport(){
+       
+       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;
+}
 
 /******************************************************************************************************************/
 
 void NastReport::setCandidate(Sequence* candSeq){ 
        queryName = candSeq->getName();
-       queryLength = candSeq->getUnalignLength();
+       queryLength = candSeq->getNumBases();
 }
 
 /******************************************************************************************************************/
 
 void NastReport::setTemplate(Sequence* tempSeq){ 
        templateName = tempSeq->getName();
-       templateLength = tempSeq->getUnalignLength();
+       templateLength = tempSeq->getNumBases();
 }
 
 /******************************************************************************************************************/