added sequence name to error string in fastq.info. Changed np_shannon to npshannon.

[mothur.git] / phylotypecommand.cpp

diff --git a/phylotypecommand.cpp b/phylotypecommand.cpp
index ef23375df9425f11816acbf8594f46e613e9e148..1d6c391de69c83a86971873577a0df0b21efdbcd 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) {
@@ -215,7 +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; 
                        }
                        
@@ -286,7 +291,7 @@ 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; 
                }