added shared file type to get.groups and remove.groups

[mothur.git] / rarefactcommand.cpp

diff --git a/rarefactcommand.cpp b/rarefactcommand.cpp
index 7f2a1d2e752ce54d971845acdfa8848c4bada8a1..82211144eda568cf86f3ca0684a67c2fe64e0bb3 100644 (file)
--- a/rarefactcommand.cpp
+++ b/rarefactcommand.cpp
@@ -107,7 +107,8 @@ RareFactCommand::RareFactCommand(string option)  {
                allLines = 1;
                                                
                //allow user to run help
-               if(option == "help") { abort = true; calledHelp = true; }
+               if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();
@@ -183,22 +184,22 @@ RareFactCommand::RareFactCommand(string option)  {
                        listfile = validParameter.validFile(parameters, "list", true);
                        if (listfile == "not open") { listfile = ""; abort = true; }
                        else if (listfile == "not found") { listfile = ""; }
-                       else {  format = "list"; inputfile = listfile; }
+                       else {  format = "list"; inputfile = listfile; m->setListFile(listfile); }
                        
                        sabundfile = validParameter.validFile(parameters, "sabund", true);
                        if (sabundfile == "not open") { sabundfile = ""; abort = true; }        
                        else if (sabundfile == "not found") { sabundfile = ""; }
-                       else {  format = "sabund"; inputfile = sabundfile; }
+                       else {  format = "sabund"; inputfile = sabundfile; m->setSabundFile(sabundfile); }
                        
                        rabundfile = validParameter.validFile(parameters, "rabund", true);
                        if (rabundfile == "not open") { rabundfile = ""; abort = true; }        
                        else if (rabundfile == "not found") { rabundfile = ""; }
-                       else {  format = "rabund"; inputfile = rabundfile; }
+                       else {  format = "rabund"; inputfile = rabundfile; m->setRabundFile(rabundfile); }
                        
                        sharedfile = validParameter.validFile(parameters, "shared", true);
                        if (sharedfile == "not open") { sharedfile = ""; abort = true; }        
                        else if (sharedfile == "not found") { sharedfile = ""; }
-                       else {  format = "sharedfile"; inputfile = sharedfile; }
+                       else {  format = "sharedfile"; inputfile = sharedfile; m->setSharedFile(sharedfile); }
                                
                        if ((sharedfile == "") && (listfile == "") && (rabundfile == "") && (sabundfile == "")) { 
                                //is there are current file available for any of these?
@@ -242,6 +243,11 @@ RareFactCommand::RareFactCommand(string option)  {
                                 if (calc == "default")  {  calc = "sobs";  }
                        }
                        m->splitAtDash(calc, Estimators);
+                       if (m->inUsersGroups("citation", Estimators)) { 
+                               ValidCalculators validCalc; validCalc.printCitations(Estimators); 
+                               //remove citation from list of calcs
+                               for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") {  Estimators.erase(Estimators.begin()+i); break; } }
+                       }
 
                        string temp;
                        temp = validParameter.validFile(parameters, "freq", false);                     if (temp == "not found") { temp = "100"; }
@@ -280,7 +286,7 @@ int RareFactCommand::execute(){
                        
                        string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p]));
                                                
-                       if (m->control_pressed) {  outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());         }  m->Groups.clear();  return 0; }
+                       if (m->control_pressed) {  outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);        }  m->Groups.clear();  return 0; }
                        
                        if (inputFileNames.size() > 1) {
                                m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine();
@@ -354,12 +360,12 @@ int RareFactCommand::execute(){
                        set<string> processedLabels;
                        set<string> userLabels = labels;
                        
-                       if (m->control_pressed) { for(int i=0;i<rDisplays.size();i++){  delete rDisplays[i];    }  delete input;  delete order;  for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+                       if (m->control_pressed) { for(int i=0;i<rDisplays.size();i++){  delete rDisplays[i];    }  delete input;  delete order;  for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
                        
                        //as long as you are not at the end of the file or done wih the lines you want
                        while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
                                
-                               if (m->control_pressed) { for(int i=0;i<rDisplays.size();i++){  delete rDisplays[i];    }  delete input;  delete order;  for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+                               if (m->control_pressed) { for(int i=0;i<rDisplays.size();i++){  delete rDisplays[i];    }  delete input;  delete order;  for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
 
                                
                                if(allLines == 1 || labels.count(order->getLabel()) == 1){
@@ -397,7 +403,7 @@ int RareFactCommand::execute(){
                                order = (input->getOrderVector());
                        }
                        
-                       if (m->control_pressed) { for(int i=0;i<rDisplays.size();i++){  delete rDisplays[i];    }  delete input;   for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str()); } return 0; }
+                       if (m->control_pressed) { for(int i=0;i<rDisplays.size();i++){  delete rDisplays[i];    }  delete input;   for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]); } return 0; }
 
                        //output error messages about any remaining user labels
                        set<string>::iterator it;
@@ -412,7 +418,7 @@ int RareFactCommand::execute(){
                                }
                        }
                        
-                       if (m->control_pressed) { for(int i=0;i<rDisplays.size();i++){  delete rDisplays[i];    }  delete input;   for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str()); } return 0; }
+                       if (m->control_pressed) { for(int i=0;i<rDisplays.size();i++){  delete rDisplays[i];    }  delete input;   for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]); } return 0; }
 
                        //run last label if you need to
                        if (needToRun == true)  {
@@ -434,7 +440,7 @@ int RareFactCommand::execute(){
                }
                
                
-               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();
@@ -463,7 +469,7 @@ vector<string> RareFactCommand::parseSharedFile(string filename) {
                
                //clears file before we start to write to it below
                for (int i=0; i<lookup.size(); i++) {
-                       remove((sharedFileRoot + lookup[i]->getGroup() + ".rabund").c_str());
+                       m->mothurRemove((sharedFileRoot + lookup[i]->getGroup() + ".rabund"));
                        filenames.push_back((sharedFileRoot + lookup[i]->getGroup() + ".rabund"));
                }