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

[mothur.git] / collectcommand.cpp

diff --git a/collectcommand.cpp b/collectcommand.cpp
index 5549fd121dfca80e5cd4a406084f68803875dc58..e0d62dd5ddd7acd106d18af31de013f6fce9c462 100644 (file)
--- a/collectcommand.cpp
+++ b/collectcommand.cpp
@@ -124,7 +124,8 @@ CollectCommand::CollectCommand(string option)  {
                allLines = 1;
                
                //allow user to run help
-               if(option == "help") { help(); abort = true; }
+               if(option == "help") { help(); calledHelp = true; abort = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();
@@ -210,22 +211,22 @@ CollectCommand::CollectCommand(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 the user changes the output directory command factory will send this info to us in the output parameter 
@@ -271,16 +272,21 @@ CollectCommand::CollectCommand(string option)  {
                                 if (calc == "default")  {  calc = "sobs-chao-ace-jack-shannon-npshannon-simpson";  }
                        }
                        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"; }
-                       convert(temp, freq); 
+                       m->mothurConvert(temp, freq); 
                        
                        temp = validParameter.validFile(parameters, "abund", false);            if (temp == "not found") { temp = "10"; }
-                       convert(temp, abund); 
+                       m->mothurConvert(temp, abund); 
                        
                        temp = validParameter.validFile(parameters, "size", false);                     if (temp == "not found") { temp = "0"; }
-                       convert(temp, size); 
+                       m->mothurConvert(temp, size); 
                }
                
        }
@@ -301,7 +307,7 @@ int CollectCommand::execute(){
        
                for (int p = 0; p < inputFileNames.size(); 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->clearGroups();  return 0; }
                        
                        if (outputDir == "") { outputDir += m->hasPath(inputFileNames[p]); }
                        string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p]));
@@ -407,10 +413,10 @@ int CollectCommand::execute(){
                        
                        if (m->control_pressed) {  
                                for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
-                               for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());         } outputTypes.clear(); 
+                               for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);        } outputTypes.clear(); 
                                delete input;  
                                delete order; 
-                               m->Groups.clear();
+                               m->clearGroups();
                                return 0;
                        }
 
@@ -419,10 +425,10 @@ int CollectCommand::execute(){
                        
                                if (m->control_pressed) { 
                                        for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
-                                       for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());         } outputTypes.clear(); 
+                                       for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);        } outputTypes.clear(); 
                                        delete input;  
                                        delete order; 
-                                       m->Groups.clear();
+                                       m->clearGroups();
                                        return 0;
                                }
 
@@ -468,9 +474,9 @@ int CollectCommand::execute(){
                        
                        if (m->control_pressed) { 
                                        for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
-                                       for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());         } outputTypes.clear(); 
+                                       for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);        } outputTypes.clear(); 
                                        delete input;  
-                                       m->Groups.clear();
+                                       m->clearGroups();
                                        return 0;
                        }
                                
@@ -500,10 +506,10 @@ int CollectCommand::execute(){
                                
                                if (m->control_pressed) { 
                                        for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
-                                       for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());         } outputTypes.clear(); 
+                                       for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);        } outputTypes.clear(); 
                                        delete input;  
                                        delete order;
-                                       m->Groups.clear();
+                                       m->clearGroups();
                                        return 0;
                                }
                                delete order;
@@ -514,7 +520,7 @@ int CollectCommand::execute(){
                        delete input;  
                }
                
-               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();
@@ -545,7 +551,7 @@ vector<string> CollectCommand::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"));
                }