working on pam

[mothur.git] / homovacommand.cpp

diff --git a/homovacommand.cpp b/homovacommand.cpp
index 6496cea746a1cf6895005564798a4c5cb909f88d..488b68e0b6b69a8eb8e351d39be9ff09193fb36f 100644 (file)
--- a/homovacommand.cpp
+++ b/homovacommand.cpp
@@ -15,13 +15,13 @@
 //**********************************************************************************************************************
 vector<string> HomovaCommand::setParameters(){ 
        try {
-               CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pdesign);
-               CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pphylip);
-        CommandParameter psets("sets", "String", "", "", "", "", "",false,false); parameters.push_back(psets);
-               CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
-               CommandParameter palpha("alpha", "Number", "", "0.05", "", "", "",false,false); parameters.push_back(palpha);
-               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+               CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none","homova",false,true,true); parameters.push_back(pdesign);
+               CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none","homova",false,true,true); parameters.push_back(pphylip);
+        CommandParameter psets("sets", "String", "", "", "", "", "","",false,false); parameters.push_back(psets);
+               CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
+               CommandParameter palpha("alpha", "Number", "", "0.05", "", "", "","",false,false); parameters.push_back(palpha);
+               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);          }
@@ -53,24 +53,19 @@ string HomovaCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
-string HomovaCommand::getOutputFileNameTag(string type, string inputName=""){  
-       try {
-        string outputFileName = "";
-               map<string, vector<string> >::iterator it;
+string HomovaCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
         
-        //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 == "homova")            {   outputFileName =  "homova";   }
-            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, "HomovaCommand", "getOutputFileNameTag");
-               exit(1);
-       }
+        if (type == "homova") {  pattern = "[filename],homova"; } 
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "HomovaCommand", "getOutputPattern");
+        exit(1);
+    }
 }
 //**********************************************************************************************************************
 HomovaCommand::HomovaCommand(){        
@@ -242,7 +237,9 @@ int HomovaCommand::execute(){
                
                //create a new filename
                ofstream HOMOVAFile;
-               string HOMOVAFileName = outputDir + m->getRootName(m->getSimpleName(phylipFileName)) + getOutputFileNameTag("homova");                          
+        map<string, string> variables; 
+               variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(phylipFileName));
+               string HOMOVAFileName = getOutputFileName("homova", variables);                         
                m->openOutputFile(HOMOVAFileName, HOMOVAFile);
                outputNames.push_back(HOMOVAFileName); outputTypes["homova"].push_back(HOMOVAFileName);
                
@@ -311,7 +308,7 @@ double HomovaCommand::runHOMOVA(ofstream& HOMOVAFile, map<string, vector<int> >
                        vector<double> ssWithinRandVector;
                        map<string, vector<int> > randomizedGroup = getRandomizedGroups(groupSampleMap);
                        double bValueRand = calcBValue(randomizedGroup, ssWithinRandVector);
-                       if(bValueRand > bValueOrig){    counter++;      }
+                       if(bValueRand >= bValueOrig){   counter++;      }
                }
                
                double pValue = (double) counter / (double) iters;