X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=metastatscommand.cpp;h=9dff3543f49efa25037ce7fb3dd9eeeebbe8c787;hb=bd27c2b0612942815b7417c79f7ee41f669a2a34;hp=c5d349bc77b685b67a1e3251fa70f15602bb215d;hpb=4884e09a6f1f67f9a57aafcef82e248a1c633956;p=mothur.git

diff --git a/metastatscommand.cpp b/metastatscommand.cpp
index c5d349b..9dff354 100644
--- a/metastatscommand.cpp
+++ b/metastatscommand.cpp
@@ -14,16 +14,16 @@
 //**********************************************************************************************************************
 vector<string> MetaStatsCommand::setParameters(){	
 	try {
-		CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pshared);
-		CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pdesign);
-		CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
-		CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
-		CommandParameter pthreshold("threshold", "Number", "", "0.05", "", "", "",false,false); parameters.push_back(pthreshold);
-		CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
-		CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
-		CommandParameter psets("sets", "String", "", "", "", "", "",false,false); parameters.push_back(psets);
-		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+		CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","metastats",false,true,true); parameters.push_back(pshared);
+		CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pdesign);
+		CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+		CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
+		CommandParameter pthreshold("threshold", "Number", "", "0.05", "", "", "","",false,false); parameters.push_back(pthreshold);
+		CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+		CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+		CommandParameter psets("sets", "String", "", "", "", "", "","",false,false); parameters.push_back(psets);
+		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);		}
@@ -61,6 +61,21 @@ string MetaStatsCommand::getHelpString(){
 	}
 }
 //**********************************************************************************************************************
+string MetaStatsCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+        
+        if (type == "metastats") {  pattern = "[filename],[distance],[group],metastats"; } 
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "MetaStatsCommand", "getOutputPattern");
+        exit(1);
+    }
+}
+//**********************************************************************************************************************
 MetaStatsCommand::MetaStatsCommand(){	
 	try {
 		abort = true; calledHelp = true;
@@ -416,6 +431,9 @@ int MetaStatsCommand::process(vector<SharedRAbundVector*>& thisLookUp){
                     
                     //Close all thread handles and free memory allocations.
                     for(int i=0; i < pDataArray.size(); i++){
+                        if (pDataArray[i]->count != (pDataArray[i]->num)) {
+                            m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->num) + " groups assigned to it, quitting. \n"); m->control_pressed = true; 
+                        }
                         for (int j = 0; j < pDataArray[i]->thisLookUp.size(); j++) {  delete pDataArray[i]->thisLookUp[j];  } 
                         for (int j = 0; j < pDataArray[i]->outputNames.size(); j++) {  
                             outputNames.push_back(pDataArray[i]->outputNames[j]);
@@ -449,7 +467,11 @@ int MetaStatsCommand::driver(int start, int num, vector<SharedRAbundVector*>& th
 			string setB = namesOfGroupCombos[c][1];
 		
 			//get filename
-			string outputFileName = outputDir +  m->getRootName(m->getSimpleName(sharedfile)) + thisLookUp[0]->getLabel() + "." + setA + "-" + setB + ".metastats";
+            map<string, string> variables; 
+            variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile));
+            variables["[distance]"] = thisLookUp[0]->getLabel();
+            variables["[group]"] = setA + "-" + setB;
+			string outputFileName = getOutputFileName("metastats",variables);
 			outputNames.push_back(outputFileName); outputTypes["metastats"].push_back(outputFileName);
 			//int nameLength = outputFileName.length();
 			//char * output = new char[nameLength];