changes while testing

[mothur.git] / nmdscommand.cpp

diff --git a/nmdscommand.cpp b/nmdscommand.cpp
index 1d936d458d2edb69e6d49f51d8a79171389ea544..a90ed2965888928f4a90049fe04fe888d773c450 100644 (file)
--- a/nmdscommand.cpp
+++ b/nmdscommand.cpp
@@ -13,15 +13,15 @@
 //**********************************************************************************************************************
 vector<string> NMDSCommand::setParameters(){   
        try {
-               CommandParameter paxes("axes", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(paxes);
-               CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pphylip);
-               CommandParameter pmaxdim("maxdim", "Number", "", "2", "", "", "",false,false); parameters.push_back(pmaxdim);
-               CommandParameter pmindim("mindim", "Number", "", "2", "", "", "",false,false); parameters.push_back(pmindim);
-               CommandParameter piters("iters", "Number", "", "10", "", "", "",false,false); parameters.push_back(piters);
-               CommandParameter pmaxiters("maxiters", "Number", "", "500", "", "", "",false,false); parameters.push_back(pmaxiters);
-               CommandParameter pepsilon("epsilon", "Number", "", "0.000000000001", "", "", "",false,false); parameters.push_back(pepsilon);
-               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+               CommandParameter paxes("axes", "InputTypes", "", "", "none", "none", "none","",false,false,true); parameters.push_back(paxes);
+               CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none","nmds-stress",false,true,true); parameters.push_back(pphylip);
+               CommandParameter pmaxdim("maxdim", "Number", "", "2", "", "", "","",false,false); parameters.push_back(pmaxdim);
+               CommandParameter pmindim("mindim", "Number", "", "2", "", "", "","",false,false); parameters.push_back(pmindim);
+               CommandParameter piters("iters", "Number", "", "10", "", "", "","",false,false); parameters.push_back(piters);
+               CommandParameter pmaxiters("maxiters", "Number", "", "500", "", "", "","",false,false); parameters.push_back(pmaxiters);
+               CommandParameter pepsilon("epsilon", "Number", "", "0.000000000001", "", "", "","",false,false); parameters.push_back(pepsilon);
+               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
                
                vector<string> myArray;
                for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
@@ -54,6 +54,24 @@ string NMDSCommand::getHelpString(){
                exit(1);
        }
 }
+//**********************************************************************************************************************
+string NMDSCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+        
+        if (type == "nmds") {  pattern = "[filename],nmds.axes"; } 
+        else if (type == "stress") {  pattern = "[filename],nmds.stress"; } 
+        else if (type == "iters") {  pattern = "[filename],nmds.iters"; } 
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "NMDSCommand", "getOutputPattern");
+        exit(1);
+    }
+}
+
 //**********************************************************************************************************************
 NMDSCommand::NMDSCommand(){    
        try {
@@ -156,7 +174,7 @@ NMDSCommand::NMDSCommand(string option)  {
                        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 +204,10 @@ 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";
+        map<string, string> variables; 
+        variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(phylipfile));
+               string outputFileName = getOutputFileName("iters",variables);
+               string stressFileName = getOutputFileName("stress",variables);
                outputNames.push_back(outputFileName); outputTypes["iters"].push_back(outputFileName);
                outputNames.push_back(stressFileName); outputTypes["stress"].push_back(stressFileName);
                
@@ -256,7 +276,7 @@ int NMDSCommand::execute(){
                out.close(); out2.close();
                
                //output best config
-               string BestFileName = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + "nmds.axes";
+               string BestFileName = getOutputFileName("nmds",variables);
                outputNames.push_back(BestFileName); outputTypes["nmds"].push_back(BestFileName);
                
                m->mothurOut("\nNumber of dimensions:\t" + toString(bestDim) + "\n");