X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=phylotypecommand.cpp;h=fbc7c6003989044eba397ba7d8d6d58fa37c768a;hb=38029939675c5bf5e449eac90f801b35064b3a36;hp=2d2db08a40ea5e1aa8712902dcd419ddb1ad757a;hpb=57b3c96832667c1b70d4d526331f52e3d49e8237;p=mothur.git

diff --git a/phylotypecommand.cpp b/phylotypecommand.cpp
index 2d2db08..fbc7c60 100644
--- a/phylotypecommand.cpp
+++ b/phylotypecommand.cpp
@@ -16,12 +16,12 @@
 //**********************************************************************************************************************
 vector<string> PhylotypeCommand::setParameters(){	
 	try {
-		CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptaxonomy);
-		CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
-		CommandParameter pcutoff("cutoff", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pcutoff);
-		CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
-		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+		CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none","list-rabund-sabund",false,true,true); parameters.push_back(ptaxonomy);
+		CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none","",false,false,true); parameters.push_back(pname);
+		CommandParameter pcutoff("cutoff", "Number", "", "-1", "", "", "","",false,false,true); parameters.push_back(pcutoff);
+		CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+		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);		}
@@ -53,7 +53,23 @@ string PhylotypeCommand::getHelpString(){
 		exit(1);
 	}
 }
-
+//**********************************************************************************************************************
+string PhylotypeCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+        
+        if (type == "list") {  pattern = "[filename],[tag],list"; } 
+        else if (type == "rabund") {  pattern = "[filename],[tag],rabund"; } 
+        else if (type == "sabund") {  pattern = "[filename],[tag],sabund"; }
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "PhylotypeCommand", "getOutputPattern");
+        exit(1);
+    }
+}
 //**********************************************************************************************************************
 PhylotypeCommand::PhylotypeCommand(){	
 	try {
@@ -196,15 +212,17 @@ int PhylotypeCommand::execute(){
 		if (m->control_pressed) { delete tree; return 0; }
 		
 		string fileroot = outputDir + m->getRootName(m->getSimpleName(taxonomyFileName));
-		
-		ofstream outList;
-		string outputListFile = fileroot + "tx.list";
+		map<string, string> variables; 
+        variables["[filename]"] = fileroot;
+        variables["[tag]"] = "tx";
+        ofstream outList;
+		string outputListFile = getOutputFileName("list",variables);
 		m->openOutputFile(outputListFile, outList);
 		ofstream outSabund;
-		string outputSabundFile = fileroot + "tx.sabund";
+		string outputSabundFile = getOutputFileName("sabund",variables);
 		m->openOutputFile(outputSabundFile, outSabund);
 		ofstream outRabund;
-		string outputRabundFile = fileroot + "tx.rabund";
+		string outputRabundFile = getOutputFileName("rabund",variables);
 		m->openOutputFile(outputRabundFile, outRabund);
 		
 		outputNames.push_back(outputListFile); outputTypes["list"].push_back(outputListFile);
@@ -251,11 +269,14 @@ int PhylotypeCommand::execute(){
                                 map<string, string>::iterator itNames = namemap.find(names[i]);  //make sure this name is in namefile
                                 
                                 if (itNames != namemap.end()) {  name += namemap[names[i]] + ",";   } //you found it in namefile
-                                else { m->mothurOut(names[i] + " is not in your namefile, please correct."); m->mothurOutEndLine(); exit(1);  }
+                                else { m->mothurOut("[ERROR]: " + names[i] + " is not in your namefile, please correct."); m->mothurOutEndLine(); m->control_pressed = true;  }
                                 
                             }else{   name += names[i] + ",";	}
                         }
 					}
+                    
+                    if (m->control_pressed) { break; }
+                    
 					name = name.substr(0, name.length()-1);  //rip off extra ','
 					//add bin to list vector
 					if (name != "") { list.push_back(name); } //caused by unknown