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

[mothur.git] / collectsharedcommand.cpp

diff --git a/collectsharedcommand.cpp b/collectsharedcommand.cpp
index 202883e201561f8851d77c5e6569df33280143c3..f3a320b89e0695483a5124b6336d68cf89179293 100644 (file)
--- a/collectsharedcommand.cpp
+++ b/collectsharedcommand.cpp
@@ -270,11 +270,11 @@ CollectSharedCommand::CollectSharedCommand(string option)  {
                        else { 
                                m->splitAtDash(groups, Groups);
                        }
-                       m->Groups = Groups;
+                       m->setGroups(Groups);
                        
                        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, "all", false);                              if (temp == "not found") { temp = "false"; }
                        all = m->isTrue(temp);
@@ -440,15 +440,19 @@ int CollectSharedCommand::execute(){
                        
                //set users groups
                SharedUtil* util = new SharedUtil();
-               util->setGroups(m->Groups, m->namesOfGroups, "collect");
+               Groups = m->getGroups();
+               vector<string> allGroups = m->getAllGroups();
+               util->setGroups(Groups, allGroups, "collect");
+               m->setGroups(Groups);
+               m->setAllGroups(allGroups);
                delete util;
 
                while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
                        if (m->control_pressed) { 
-                                       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();
                                        for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
                                        delete order; delete input;
-                                       m->Groups.clear();
+                                       m->clearGroups();
                                        return 0;
                        }
 
@@ -493,9 +497,9 @@ int CollectSharedCommand::execute(){
                }
                
                if (m->control_pressed) { 
-                                       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();
                                        for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
-                                       m->Groups.clear();
+                                       m->clearGroups();
                                        delete input;
                                        return 0;
                }
@@ -524,11 +528,11 @@ int CollectSharedCommand::execute(){
                        delete cCurve;
                        
                        if (m->control_pressed) { 
-                               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();
                                for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
                                delete order; 
                                delete input;
-                               m->Groups.clear();
+                               m->clearGroups();
                                return 0;
                        }
 
@@ -538,7 +542,7 @@ int CollectSharedCommand::execute(){
                for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }       
                
                //reset groups parameter
-               m->Groups.clear(); 
+               m->clearGroups(); 
                delete input;
                
                m->mothurOutEndLine();