removing chime source files from mother project.

[mothur.git] / binsequencecommand.cpp

diff --git a/binsequencecommand.cpp b/binsequencecommand.cpp
index 3f9378fbdb4650078cf27091326c0dc5e87c993a..2117daff4f2558e26bcf0008666f87bee0180f4d 100644 (file)
--- a/binsequencecommand.cpp
+++ b/binsequencecommand.cpp
@@ -71,6 +71,7 @@ BinSeqCommand::BinSeqCommand(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();
@@ -137,6 +138,7 @@ BinSeqCommand::BinSeqCommand(string option) {
                                else {  m->mothurOut("You have no current fasta file and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
                        }
                        else if (fastafile == "not open") { abort = true; }     
+                       else { m->setFastaFile(fastafile); }
                        
                        listfile = validParameter.validFile(parameters, "list", true);
                        if (listfile == "not found") {                  
@@ -145,6 +147,7 @@ BinSeqCommand::BinSeqCommand(string option) {
                                else {  m->mothurOut("You have no current list file and the list parameter is required."); m->mothurOutEndLine(); abort = true; }
                        }
                        else if (listfile == "not open") { listfile = ""; abort = true; }       
+                       else { m->setListFile(listfile); }
                        
                        //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"){  
@@ -164,12 +167,19 @@ 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); }
 
                        groupfile = validParameter.validFile(parameters, "group", true);
                        if (groupfile == "not open") { abort = true; }
                        else if (groupfile == "not found") { groupfile = ""; }
+                       else { m->setGroupFile(groupfile); }
+                       
+                       if (namesfile == ""){
+                               vector<string> files; files.push_back(fastafile); 
+                               parser.getNameFile(files);
+                       }
                        
                }
        }
@@ -216,12 +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());
@@ -234,7 +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());
@@ -249,7 +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;
@@ -270,7 +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;  
                }
@@ -279,11 +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; }  
-               
-               delete input;  
-               delete fasta; 
-               if (groupfile != "") {  delete groupMap;   } 
+               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();