forced rarefaction.single to output ending line for all groups. added subsample...

[mothur.git] / phylotypecommand.cpp

diff --git a/phylotypecommand.cpp b/phylotypecommand.cpp
index e6dace8b796103804c16a4de86104cff0b05da4f..2d2db08a40ea5e1aa8712902dcd419ddb1ad757a 100644 (file)
--- a/phylotypecommand.cpp
+++ b/phylotypecommand.cpp
@@ -128,11 +128,11 @@ 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); }     
                        
@@ -144,7 +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; }
@@ -153,6 +153,11 @@ PhylotypeCommand::PhylotypeCommand(string option)  {
                                else { allLines = 1;  }
                        }
                        
+                       if (namefile == "") {
+                               vector<string> files; files.push_back(taxonomyFileName);
+                               parser.getNameFile(files);
+                       }
+                       
                }
        }
        catch(exception& e) {
@@ -227,6 +232,7 @@ int PhylotypeCommand::execute(){
                                
                                ListVector list;
                                list.setLabel(level);
+                
                                //go through nodes and build listvector 
                                for (itCurrent = currentNodes.begin(); itCurrent != currentNodes.end(); itCurrent++) {
                        
@@ -239,18 +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