X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=phylotypecommand.cpp;h=2d2db08a40ea5e1aa8712902dcd419ddb1ad757a;hb=e0ce7cbc93d7d2fbb753ca694182db092a0ea0e7;hp=e7d12969a73a1a2d6576593fc36ec8eb5a9b1d2a;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/phylotypecommand.cpp b/phylotypecommand.cpp
index e7d1296..2d2db08 100644
--- a/phylotypecommand.cpp
+++ b/phylotypecommand.cpp
@@ -45,7 +45,7 @@ string PhylotypeCommand::getHelpString(){
 		helpString += "For the label parameter, levels count down from the root to keep the output similiar to mothur's other commands which report information from finer resolution to coarser resolutions.\n";
 		helpString += "The phylotype command should be in the following format: \n";
 		helpString += "phylotype(taxonomy=yourTaxonomyFile, cutoff=yourCutoff, label=yourLabels) \n";
-		helpString += "Eaxample: phylotype(taxonomy=amazon.taxonomy, cutoff=5, label=1-3-5).\n\n";
+		helpString += "Eaxample: phylotype(taxonomy=amazon.taxonomy, cutoff=5, label=1-3-5).\n";
 		return helpString;
 	}
 	catch(exception& e) {
@@ -76,6 +76,7 @@ PhylotypeCommand::PhylotypeCommand(string option)  {
 		
 		//allow user to run help
 		if(option == "help") { help(); abort = true; calledHelp = true; }
+		else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 		
 		else {
 			vector<string> myArray = setParameters();
@@ -127,12 +128,13 @@ 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(); }	
+			else { readNamesFile(); m->setNameFile(namefile); }	
 			
 			//if the user changes the output directory command factory will send this info to us in the output parameter 
 			outputDir = validParameter.validFile(parameters, "outputdir", false);		if (outputDir == "not found"){	
@@ -142,7 +144,7 @@ PhylotypeCommand::PhylotypeCommand(string option)  {
 			
 			string temp = validParameter.validFile(parameters, "cutoff", false);
 			if (temp == "not found") { temp = "-1"; }
-			convert(temp, cutoff); 
+			m->mothurConvert(temp, cutoff); 
 			
 			label = validParameter.validFile(parameters, "label", false);			
 			if (label == "not found") { label = ""; allLines = 1; }
@@ -151,6 +153,11 @@ PhylotypeCommand::PhylotypeCommand(string option)  {
 				else { allLines = 1;  }
 			}
 			
+			if (namefile == "") {
+				vector<string> files; files.push_back(taxonomyFileName);
+				parser.getNameFile(files);
+			}
+			
 		}
 	}
 	catch(exception& e) {
@@ -213,7 +220,7 @@ int PhylotypeCommand::execute(){
 			
 			if (m->control_pressed) { 
 				outRabund.close(); outSabund.close(); outList.close();
-				for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  }
+				for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);  }
 				delete tree; return 0; 
 			}
 			
@@ -225,6 +232,7 @@ int PhylotypeCommand::execute(){
 				
 				ListVector list;
 				list.setLabel(level);
+                
 				//go through nodes and build listvector 
 				for (itCurrent = currentNodes.begin(); itCurrent != currentNodes.end(); itCurrent++) {
 			
@@ -237,18 +245,20 @@ 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(names[i] + " is not in your namefile, please correct."); m->mothurOutEndLine(); exit(1);  }
+                                
+                            }else{   name += names[i] + ",";	}
+                        }
 					}
 					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
@@ -284,7 +294,7 @@ int PhylotypeCommand::execute(){
 		delete tree;
 		
 		if (m->control_pressed) { 
-			for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  }
+			for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);  }
 			return 0; 
 		}