Initial revision

[mothur.git] / readdistphylipfilecommand.cpp

diff --git a/readdistphylipfilecommand.cpp b/readdistphylipfilecommand.cpp
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+++ b/readdistphylipfilecommand.cpp
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+/*
+ *  readdistphylipfilecommand.cpp
+ *  Dotur
+ *
+ *  Created by Sarah Westcott on 1/2/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "readdistphylipfilecommand.h"
+
+//**********************************************************************************************************************
+
+ReadDistPhylipFileCommand::ReadDistPhylipFileCommand(){
+       try {
+               globaldata = GlobalData::getInstance();
+               
+               filename = globaldata->inputFileName;
+                               
+               format = globaldata->getFormat();       
+               read = new ReadPhylipMatrix(filename);  
+               
+               if(globaldata->getPrecision() != ""){
+                       convert(globaldata->getPrecision(), precision); 
+               }
+               
+               if(globaldata->getCutOff() != ""){
+                       convert(globaldata->getCutOff(), cutoff);       
+                       cutoff += (5 / (precision * 10.0));
+               }
+               read->setCutoff(cutoff);
+       
+               if(globaldata->getNameFile() != ""){    
+                       nameMap = new NameAssignment(globaldata->getNameFile());
+                       nameMap->readMap(1,2);
+               }
+               else{
+                       nameMap = NULL;
+               }
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the ReadDistPhylipFileCommand class Function ReadDistPhylipFileCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the ReadDistPhylipFileCommand class function ReadDistPhylipFileCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+}
+
+//**********************************************************************************************************************
+
+ReadDistPhylipFileCommand::~ReadDistPhylipFileCommand(){
+       delete read;
+       delete nameMap;
+}
+
+//**********************************************************************************************************************
+
+int ReadDistPhylipFileCommand::execute(){
+       try {
+               read->read(nameMap);
+               globaldata->setListVector(read->getListVector());
+               globaldata->setSparseMatrix(read->getMatrix());
+               return 0;
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the ReadDistPhylipFileCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the ReadDistPhylipFileCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+}