fixes while testing 1.33.0

[mothur.git] / anosimcommand.cpp

diff --git a/anosimcommand.cpp b/anosimcommand.cpp
index bd4e6b0683886bd0012e6b222a12592c8e594107..2a688f59b72c4ba9779ea921149254b3e554b788 100644 (file)
--- a/anosimcommand.cpp
+++ b/anosimcommand.cpp
@@ -14,12 +14,12 @@
 //**********************************************************************************************************************
 vector<string> AnosimCommand::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 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","anosim",false,true,true); parameters.push_back(pdesign);
+               CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none","anosim",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);          }
@@ -50,24 +50,19 @@ string AnosimCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
-string AnosimCommand::getOutputFileNameTag(string type, string inputName=""){  
-       try {
-        string outputFileName = "";
-               map<string, vector<string> >::iterator it;
+string AnosimCommand::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 == "anosim") {  outputFileName =  "anosim"; }
-            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, "AnosimCommand", "getOutputFileNameTag");
-               exit(1);
-       }
+        if (type == "anosim") {  pattern = "[filename],anosim"; } //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, "AnosimCommand", "getOutputPattern");
+        exit(1);
+    }
 }
 //**********************************************************************************************************************
 AnosimCommand::AnosimCommand(){        
@@ -207,7 +202,9 @@ int AnosimCommand::execute(){
                
                //create a new filename
                ofstream ANOSIMFile;
-               string ANOSIMFileName = outputDir + m->getRootName(m->getSimpleName(phylipFileName)) + getOutputFileNameTag("anosim");                          
+        map<string, string> variables; variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(phylipFileName));
+               string ANOSIMFileName = getOutputFileName("anosim", variables); 
+        
                m->openOutputFile(ANOSIMFileName, ANOSIMFile);
                outputNames.push_back(ANOSIMFileName); outputTypes["anosim"].push_back(ANOSIMFileName);
                m->mothurOut("\ncomparison\tR-value\tP-value\n");