added otu.association command. added calcSpearman, calcKendall and calcPearson functi...

[mothur.git] / binsequencecommand.cpp

diff --git a/binsequencecommand.cpp b/binsequencecommand.cpp
index 8e8ec2bc51362d8b8876d6e3cbb10ef9ff5e167e..2117daff4f2558e26bcf0008666f87bee0180f4d 100644 (file)
--- a/binsequencecommand.cpp
+++ b/binsequencecommand.cpp
@@ -167,7 +167,7 @@ BinSeqCommand::BinSeqCommand(string option) {
                        }
                        
                        namesfile = validParameter.validFile(parameters, "name", true);
-                       if (namesfile == "not open") { abort = true; }  
+                       if (namesfile == "not open") { namesfile = ""; abort = true; }  
                        else if (namesfile == "not found") { namesfile = ""; }
                        else {  m->setNameFile(namesfile); }
 
@@ -176,6 +176,11 @@ BinSeqCommand::BinSeqCommand(string option) {
                        else if (groupfile == "not found") { groupfile = ""; }
                        else { m->setGroupFile(groupfile); }
                        
+                       if (namesfile == ""){
+                               vector<string> files; files.push_back(fastafile); 
+                               parser.getNameFile(files);
+                       }
+                       
                }
        }
        catch(exception& e) {
@@ -221,12 +226,12 @@ int BinSeqCommand::execute(){
                                
                while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
                        
-                       if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str());         } delete input;  delete fasta; if (groupfile != "") {  delete groupMap;   } return 0; } 
+                       if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]);                } delete input;  delete fasta; if (groupfile != "") {  delete groupMap;   } return 0; } 
                        
                        if(allLines == 1 || labels.count(list->getLabel()) == 1){
                                
                                error = process(list);  
-                               if (error == 1) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());         } delete input;  delete fasta; if (groupfile != "") {  delete groupMap;   } return 0; } 
+                               if (error == 1) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);                } delete input;  delete fasta; if (groupfile != "") {  delete groupMap;   } return 0; } 
                                                        
                                processedLabels.insert(list->getLabel());
                                userLabels.erase(list->getLabel());
@@ -239,7 +244,7 @@ int BinSeqCommand::execute(){
                                list = input->getListVector(lastLabel);
                                
                                error = process(list);  
-                               if (error == 1) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());         } delete input;  delete fasta; if (groupfile != "") {  delete groupMap;   } return 0; }
+                               if (error == 1) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);                } delete input;  delete fasta; if (groupfile != "") {  delete groupMap;   } return 0; }
                                                                                                        
                                processedLabels.insert(list->getLabel());
                                userLabels.erase(list->getLabel());
@@ -254,7 +259,7 @@ int BinSeqCommand::execute(){
                        list = input->getListVector();
                }
                
-               if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str());         } delete input;  delete fasta; if (groupfile != "") {  delete groupMap;   } return 0; } 
+               if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]);                } delete input;  delete fasta; if (groupfile != "") {  delete groupMap;   } return 0; } 
 
                //output error messages about any remaining user labels
                set<string>::iterator it;
@@ -275,7 +280,7 @@ int BinSeqCommand::execute(){
                        list = input->getListVector(lastLabel);
                                
                        error = process(list);  
-                       if (error == 1) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());         } delete input;  delete fasta; if (groupfile != "") {  delete groupMap;   } return 0; }
+                       if (error == 1) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);                } delete input;  delete fasta; if (groupfile != "") {  delete groupMap;   } return 0; }
                        
                        delete list;  
                }
@@ -284,7 +289,7 @@ int BinSeqCommand::execute(){
                delete fasta; 
                if (groupfile != "") {  delete groupMap;   } 
                
-               if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str());         }  return 0; }  
+               if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]);                }  return 0; }  
                
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();