X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=nmdscommand.cpp;h=1d936d458d2edb69e6d49f51d8a79171389ea544;hb=8dd3c225255d7084e3aff8740aa4f1f1cabb367a;hp=8fa0145ea7e97081000ee99337309861a0f8c7a9;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/nmdscommand.cpp b/nmdscommand.cpp
index 8fa0145..1d936d4 100644
--- a/nmdscommand.cpp
+++ b/nmdscommand.cpp
@@ -46,7 +46,7 @@ string NMDSCommand::getHelpString(){
 		helpString += "The iters parameter allows you to select the number of random configuration to try. Default=10\n"; 
 		helpString += "The epsilon parameter allows you to select set an acceptable stopping point. Default=1e-12.\n"; 
 		helpString += "Example nmds(phylip=yourDistanceFile).\n";
-		helpString += "Note: No spaces between parameter labels (i.e. phylip), '=' and parameters (i.e.yourDistanceFile).\n\n";
+		helpString += "Note: No spaces between parameter labels (i.e. phylip), '=' and parameters (i.e.yourDistanceFile).\n";
 		return helpString;
 	}
 	catch(exception& e) {
@@ -77,6 +77,7 @@ NMDSCommand::NMDSCommand(string option)  {
 		
 		//allow user to run help
 		if(option == "help") { help(); abort = true; calledHelp = true; }
+		else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 		
 		else {
 			vector<string> myArray = setParameters();
@@ -127,7 +128,7 @@ NMDSCommand::NMDSCommand(string option)  {
 				phylipfile = m->getPhylipFile(); 
 				if (phylipfile != "") { m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
 				else { 	m->mothurOut("You have no current phylip file and the phylip parameter is required."); m->mothurOutEndLine(); abort = true; }
-			}	
+			}else { m->setPhylipFile(phylipfile); }	
 			
 			axesfile = validParameter.validFile(parameters, "axes", true);
 			if (axesfile == "not open") { axesfile = ""; abort = true; }
@@ -140,19 +141,19 @@ NMDSCommand::NMDSCommand(string option)  {
 			}
 			
 			string temp = validParameter.validFile(parameters, "mindim", false);	if (temp == "not found") {	temp = "2";	}
-			convert(temp, mindim);
+			m->mothurConvert(temp, mindim);
 			
 			temp = validParameter.validFile(parameters, "maxiters", false);	if (temp == "not found") {	temp = "500";	}
-			convert(temp, maxIters);
+			m->mothurConvert(temp, maxIters);
 			
 			temp = validParameter.validFile(parameters, "iters", false);	if (temp == "not found") {	temp = "10";	}
-			convert(temp, iters);
+			m->mothurConvert(temp, iters);
 			
 			temp = validParameter.validFile(parameters, "maxdim", false);	if (temp == "not found") {	temp = "2";	}
-			convert(temp, maxdim);
+			m->mothurConvert(temp, maxdim);
 			
 			temp = validParameter.validFile(parameters, "epsilon", false);	if (temp == "not found") {	temp = "0.000000000001";	}
-			convert(temp, epsilon); 
+			m->mothurConvert(temp, epsilon); 
 			
 			if (mindim < 1) { m->mothurOut("mindim must be at least 1."); m->mothurOutEndLine(); abort = true; }
 			if (maxdim < mindim) { m->mothurOut("maxdim must be greater than mindim."); m->mothurOutEndLine(); abort = true; }
@@ -216,21 +217,21 @@ int NMDSCommand::execute(){
 				vector< vector<double> > thisConfig;
 				if (axesfile == "") {	thisConfig = generateStartingConfiguration(names.size(), i);		}
 				else				{	thisConfig = getConfiguration(axes, i);								}
-				if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) {	remove(outputNames[k].c_str());	} return 0; }
+				if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) {	m->mothurRemove(outputNames[k]);	} return 0; }
 				
 				//calc nmds for this dimension
 				double stress;
 				vector< vector<double> > endConfig = nmdsCalc(matrix, thisConfig, stress);
-				if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) {	remove(outputNames[k].c_str());	} return 0; }
+				if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) {	m->mothurRemove(outputNames[k]);	} return 0; }
 				
 				//calc euclid distances for new config
 				vector< vector<double> > newEuclid = linearCalc.calculateEuclidianDistance(endConfig);
-				if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) {	remove(outputNames[k].c_str());	} return 0; }
+				if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) {	m->mothurRemove(outputNames[k]);	} return 0; }
 				
 				//calc correlation between original distances and euclidean distances from this config
 				double rsquared = linearCalc.calcPearson(newEuclid, matrix);
 				rsquared *= rsquared;
-				if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) {	remove(outputNames[k].c_str());	} return 0; }
+				if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) {	m->mothurRemove(outputNames[k]);	} return 0; }
 				
 				//output results
 				out << "Config" << (j+1) << '\t';
@@ -248,7 +249,7 @@ int NMDSCommand::execute(){
 					bestConfig = endConfig;
 				}
 				
-				if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) {	remove(outputNames[k].c_str());	} return 0; }
+				if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) {	m->mothurRemove(outputNames[k]);	} return 0; }
 			}
 		}
 		
@@ -275,7 +276,7 @@ int NMDSCommand::execute(){
 		
 		outBest.close();
 		
-		if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());	} return 0; }
+		if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);	} return 0; }
 		
 		m->mothurOutEndLine();
 		m->mothurOut("Output File Names: "); m->mothurOutEndLine();