X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=phylotypecommand.cpp;h=fbc7c6003989044eba397ba7d8d6d58fa37c768a;hb=67ea6ccd74dbd64828d31b952808255f206364ff;hp=00f960bbbab8d07ecbee08dc01b78907c60c0185;hpb=0ca63a8165baa0afa459e644ebe140ba496d5ba0;p=mothur.git

diff --git a/phylotypecommand.cpp b/phylotypecommand.cpp
index 00f960b..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 {
@@ -128,11 +144,11 @@ PhylotypeCommand::PhylotypeCommand(string option)  {
 					m->mothurOut("No valid current files. taxonomy is a required parameter."); m->mothurOutEndLine(); 
 					abort = true; 
 				}
-			}else if (taxonomyFileName == "not open") { abort = true; }	
+			}else if (taxonomyFileName == "not open") { taxonomyFileName = ""; abort = true; }	
 			else { m->setTaxonomyFile(taxonomyFileName); }
 			
 			namefile = validParameter.validFile(parameters, "name", true);
-			if (namefile == "not open") { abort = true; }
+			if (namefile == "not open") { namefile = ""; abort = true; }
 			else if (namefile == "not found") { namefile = ""; }
 			else { readNamesFile(); m->setNameFile(namefile); }	
 			
@@ -153,6 +169,11 @@ PhylotypeCommand::PhylotypeCommand(string option)  {
 				else { allLines = 1;  }
 			}
 			
+			if (namefile == "") {
+				vector<string> files; files.push_back(taxonomyFileName);
+				parser.getNameFile(files);
+			}
+			
 		}
 	}
 	catch(exception& e) {
@@ -191,15 +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);
@@ -227,6 +250,7 @@ int PhylotypeCommand::execute(){
 				
 				ListVector list;
 				list.setLabel(level);
+                
 				//go through nodes and build listvector 
 				for (itCurrent = currentNodes.begin(); itCurrent != currentNodes.end(); itCurrent++) {
 			
@@ -239,18 +263,23 @@ int PhylotypeCommand::execute(){
 					//make the names compatable with listvector
 					string name = "";
 					for (int i = 0; i < names.size(); i++) {  
-						if (namefile != "") {	
-							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{   name += names[i] + ",";	}
+                        
+                        if (names[i] != "unknown") {
+                            if (namefile != "") {	
+                                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("[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
-					list.push_back(name);
+					if (name != "") { list.push_back(name); } //caused by unknown
 				}	
 				
 				//print listvector