removed make count from make.contigs

[mothur.git] / phylotypecommand.cpp

diff --git a/phylotypecommand.cpp b/phylotypecommand.cpp
index 00f960bbbab8d07ecbee08dc01b78907c60c0185..fbc7c6003989044eba397ba7d8d6d58fa37c768a 100644 (file)
--- 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