rewrote metastats command in c++, added mothurRemove function to handle ~ error....

[mothur.git] / removegroupscommand.cpp

diff --git a/removegroupscommand.cpp b/removegroupscommand.cpp
index e0943cf0cb52f2c2ba3faf7fe8a5e2add7281597..c9908fbc715f33eb33f75ff2005d51c9347678ff 100644 (file)
--- a/removegroupscommand.cpp
+++ b/removegroupscommand.cpp
@@ -79,6 +79,7 @@ RemoveGroupsCommand::RemoveGroupsCommand(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();
@@ -165,14 +166,17 @@ RemoveGroupsCommand::RemoveGroupsCommand(string option)  {
                        accnosfile = validParameter.validFile(parameters, "accnos", true);
                        if (accnosfile == "not open") { abort = true; }
                        else if (accnosfile == "not found") {  accnosfile = ""; }       
+                       else { m->setAccnosFile(accnosfile); }
                        
                        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; }
@@ -181,15 +185,17 @@ RemoveGroupsCommand::RemoveGroupsCommand(string option)  {
                                groupfile = m->getGroupFile(); 
                                if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current groupfile and the group parameter is required."); m->mothurOutEndLine(); abort = true; }
-                       }       
+                       }else { m->setGroupFile(groupfile); }   
                        
                        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; }
                        else if (taxfile == "not found") {  taxfile = "";  }
+                       else { m->setTaxonomyFile(taxfile); }
                        
                        groups = validParameter.validFile(parameters, "groups", false);                 
                        if (groups == "not found") { groups = ""; }
@@ -239,10 +245,10 @@ int RemoveGroupsCommand::execute(){
                if (listfile != "")                     {               readList();             }
                if (taxfile != "")                      {               readTax();              }
                
-               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->mothurOut("Removed " + toString(names.size()) + " sequences. From the groups: "); m->mothurOutEndLine();
-               for (int i = 0; i < Groups.size(); i++) {       m->mothurOut(Groups[i]); m->mothurOut(" contains " + toString(groupMap->getNumSeqs(Groups[i])) + " sequences."); m->mothurOutEndLine(); }
+               for (int i = 0; i < Groups.size(); i++) {       m->mothurOut(Groups[i]); m->mothurOut("\t" + toString(groupMap->getNumSeqs(Groups[i]))); m->mothurOutEndLine(); }
                m->mothurOutEndLine();
                
                if (outputNames.size() != 0) {
@@ -305,7 +311,7 @@ int RemoveGroupsCommand::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();
@@ -360,7 +366,7 @@ int RemoveGroupsCommand::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);
@@ -423,7 +429,7 @@ int RemoveGroupsCommand::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;         m->gobble(in);          
                        in >> secondCol;                        
@@ -499,7 +505,7 @@ int RemoveGroupsCommand::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
@@ -541,7 +547,7 @@ int RemoveGroupsCommand::readTax(){
                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 >> tax;                      //read from second column