X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=nmdscommand.cpp;h=900f50bd43ffb2aaee98f279023e684bb8d7c00d;hb=6ede3bf5c0a9eedb23f24577a97da81ab3e1f7df;hp=4567dbba1e7b0b16e88f496307ef3cb7ff3a8650;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77;p=mothur.git

diff --git a/nmdscommand.cpp b/nmdscommand.cpp
index 4567dbb..900f50b 100644
--- a/nmdscommand.cpp
+++ b/nmdscommand.cpp
@@ -55,6 +55,28 @@ string NMDSCommand::getHelpString(){
 	}
 }
 //**********************************************************************************************************************
+string NMDSCommand::getOutputFileNameTag(string type, string inputName=""){	
+	try {
+        string outputFileName = "";
+		map<string, vector<string> >::iterator it;
+        
+        //is this a type this command creates
+        it = outputTypes.find(type);
+        if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+        else {
+            if (type == "nmds") {  outputFileName =  "nmds.axes"; }
+            else if (type == "stress") {  outputFileName =  "nmds.stress"; }
+            else if (type == "iters") {  outputFileName =  "nmds.iters"; }
+            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
+        }
+        return outputFileName;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "NMDSCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
 NMDSCommand::NMDSCommand(){	
 	try {
 		abort = true; calledHelp = true; 
@@ -128,7 +150,7 @@ 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; }
@@ -141,22 +163,22 @@ 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; }
+			if (maxdim < mindim) { maxdim = mindim; }
 		}
 		
 	}
@@ -186,8 +208,8 @@ int NMDSCommand::execute(){
 		vector< vector<double> > axes;
 		if (axesfile != "") {  axes = readAxes(names);		}
 		
-		string outputFileName = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + "nmds.iters";
-		string stressFileName = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + "nmds.stress";
+		string outputFileName = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + getOutputFileNameTag("iters");
+		string stressFileName = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + getOutputFileNameTag("stress");
 		outputNames.push_back(outputFileName); outputTypes["iters"].push_back(outputFileName);
 		outputNames.push_back(stressFileName); outputTypes["stress"].push_back(stressFileName);
 		
@@ -217,21 +239,21 @@ 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';
@@ -249,14 +271,14 @@ 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; }
 			}
 		}
 		
 		out.close(); out2.close();
 		
 		//output best config
-		string BestFileName = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + "nmds.axes";
+		string BestFileName = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + getOutputFileNameTag("nmds");
 		outputNames.push_back(BestFileName); outputTypes["nmds"].push_back(BestFileName);
 		
 		m->mothurOut("\nNumber of dimensions:\t" + toString(bestDim) + "\n");
@@ -276,7 +298,7 @@ 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();