changes while testing

[mothur.git] / amovacommand.cpp

diff --git a/amovacommand.cpp b/amovacommand.cpp
index f36027f9acb625ab9c02e906a90d5716aa66aa58..492a096f76cc1de12514731f66514e8d632c0c5f 100644 (file)
--- a/amovacommand.cpp
+++ b/amovacommand.cpp
@@ -16,13 +16,13 @@
 //**********************************************************************************************************************
 vector<string> AmovaCommand::setParameters(){  
        try {
-               CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pdesign);
-        CommandParameter psets("sets", "String", "", "", "", "", "",false,false); parameters.push_back(psets);
-               CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pphylip);
-               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","amova",false,true,true); parameters.push_back(pdesign);
+        CommandParameter psets("sets", "String", "", "", "", "", "","",false,false); parameters.push_back(psets);
+               CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none","amova",false,true,true); parameters.push_back(pphylip);
+               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);          }
@@ -54,24 +54,19 @@ string AmovaCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
-string AmovaCommand::getOutputFileNameTag(string type, string inputName=""){   
-       try {
-        string tag = "";
-               map<string, vector<string> >::iterator it;
+string AmovaCommand::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 == "amova") {  tag = "amova"; }
-            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file.\n");  }
-        }
-        return tag;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "AmovaCommand", "getOutputFileNameTag");
-               exit(1);
-       }
+        if (type == "amova") {  pattern = "[filename],amova"; } //makes file like: amazon.align
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "AmovaCommand", "getOutputPattern");
+        exit(1);
+    }
 }
 //**********************************************************************************************************************
 AmovaCommand::AmovaCommand(){  
@@ -241,7 +236,9 @@ int AmovaCommand::execute(){
                
                //create a new filename
                ofstream AMOVAFile;
-               string AMOVAFileName = outputDir + m->getRootName(m->getSimpleName(phylipFileName)) + getOutputFileNameTag("amova");                            
+        map<string, string> variables; variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(phylipFileName));
+               string AMOVAFileName = getOutputFileName("amova", variables);   
+        
                m->openOutputFile(AMOVAFileName, AMOVAFile);
                outputNames.push_back(AMOVAFileName); outputTypes["amova"].push_back(AMOVAFileName);
                
@@ -310,7 +307,7 @@ double AmovaCommand::runAMOVA(ofstream& AMOVAFile, map<string, vector<int> > gro
                for(int i=0;i<iters;i++){
                        map<string, vector<int> > randomizedGroup = getRandomizedGroups(groupSampleMap);
                        double ssWithinRand = calcSSWithin(randomizedGroup);
-                       if(ssWithinRand < ssWithinOrig){        counter++;      }
+                       if(ssWithinRand <= ssWithinOrig){       counter++;      }
                }
                
                double pValue = (double)counter / (double) iters;