1.21.0

[mothur.git] / removelineagecommand.cpp

diff --git a/removelineagecommand.cpp b/removelineagecommand.cpp
index 5f5435f8679a9b65bb4799dae9dff30555818d3c..b72f4b669d43b4b44fa1c20df4812155aaff82fc 100644 (file)
--- a/removelineagecommand.cpp
+++ b/removelineagecommand.cpp
@@ -171,14 +171,17 @@ RemoveLineageCommand::RemoveLineageCommand(string option)  {
                        fastafile = validParameter.validFile(parameters, "fasta", true);
                        if (fastafile == "not open") { abort = true; }
                        else if (fastafile == "not found") {  fastafile = "";  }        
+                       else { m->setFastaFile(fastafile); }
                        
                        namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not open") { abort = true; }
                        else if (namefile == "not found") {  namefile = "";  }  
+                       else { m->setNameFile(namefile); }
                        
                        groupfile = validParameter.validFile(parameters, "group", true);
                        if (groupfile == "not open") { abort = true; }
                        else if (groupfile == "not found") {  groupfile = "";  }        
+                       else { m->setGroupFile(groupfile); }
                        
                        alignfile = validParameter.validFile(parameters, "alignreport", true);
                        if (alignfile == "not open") { abort = true; }
@@ -187,6 +190,7 @@ RemoveLineageCommand::RemoveLineageCommand(string option)  {
                        listfile = validParameter.validFile(parameters, "list", true);
                        if (listfile == "not open") { abort = true; }
                        else if (listfile == "not found") {  listfile = "";  }
+                       else { m->setListFile(listfile); }
                        
                        taxfile = validParameter.validFile(parameters, "taxonomy", true);
                        if (taxfile == "not open") { abort = true; }
@@ -194,7 +198,7 @@ RemoveLineageCommand::RemoveLineageCommand(string option)  {
                                taxfile = m->getTaxonomyFile(); 
                                if (taxfile != "") { m->mothurOut("Using " + taxfile + " as input file for the taxonomy parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current taxonomy file and the taxonomy parameter is required."); m->mothurOutEndLine(); abort = true; }
-                       }
+                       }else { m->setTaxonomyFile(taxfile); }
                        
                        string usedDups = "true";
                        string temp = validParameter.validFile(parameters, "dups", false);      
@@ -243,7 +247,7 @@ int RemoveLineageCommand::execute(){
                if (listfile != "")                     {               readList();             }
                
                
-               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; }
                
                if (outputNames.size() != 0) {
                        m->mothurOutEndLine();
@@ -305,7 +309,7 @@ int RemoveLineageCommand::readFasta(){
                bool wroteSomething = false;
                
                while(!in.eof()){
-                       if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
+                       if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
                        
                        Sequence currSeq(in);
                        name = currSeq.getName();
@@ -359,7 +363,7 @@ int RemoveLineageCommand::readList(){
                        
                        //for each bin
                        for (int i = 0; i < list.getNumBins(); i++) {
-                               if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
+                               if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
                        
                                //parse out names that are in accnos file
                                string binnames = list.get(i);
@@ -422,7 +426,7 @@ int RemoveLineageCommand::readName(){
                bool wroteSomething = false;
                
                while(!in.eof()){
-                       if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
+                       if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 
                        in >> firstCol;                         
                        in >> secondCol;                        
@@ -500,7 +504,7 @@ int RemoveLineageCommand::readGroup(){
                bool wroteSomething = false;
                
                while(!in.eof()){
-                       if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
+                       if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
                        
                        in >> name;                             //read from first column
                        in >> group;                    //read from second column
@@ -558,7 +562,7 @@ int RemoveLineageCommand::readTax(){
                
                while(!in.eof()){
 
-                       if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str());  return 0; }
+                       if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 
                        in >> name;                             //read from first column
                        in >> tax;                      //read from second column
@@ -770,7 +774,7 @@ int RemoveLineageCommand::readAlign(){
                out << endl;
                
                while(!in.eof()){
-                       if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
+                       if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
                        
                        in >> name;                             //read from first column