X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readdistphylipfilecommand.cpp;fp=readdistphylipfilecommand.cpp;h=90804b220e02180bfe2983decb85edaee15729fa;hb=20a2d0350a737a434c89f303662d64a8eeea7b05;hp=0000000000000000000000000000000000000000;hpb=bbb5879a7e566935c23d63d42bb945072424b939;p=mothur.git

diff --git a/readdistphylipfilecommand.cpp b/readdistphylipfilecommand.cpp
new file mode 100644
index 0000000..90804b2
--- /dev/null
+++ b/readdistphylipfilecommand.cpp
@@ -0,0 +1,75 @@
+/*
+ *  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);
+	}
+}