added multiple processors option for Windows users to align.seqs, dist.seqs, summary...

[mothur.git] / matrixoutputcommand.cpp

diff --git a/matrixoutputcommand.cpp b/matrixoutputcommand.cpp
index 35a45532dc64d8d11ab415e777b3afe67ae94057..f5737c766f61d759bf8fae8c5dba74de73b1ed52 100644 (file)
--- a/matrixoutputcommand.cpp
+++ b/matrixoutputcommand.cpp
@@ -181,7 +181,7 @@ MatrixOutputCommand::MatrixOutputCommand(string option)  {
                        if (groups == "not found") { groups = ""; }
                        else { 
                                m->splitAtDash(groups, Groups);
-                               m->Groups = Groups;
+                               m->setGroups(Groups);
                        }
                        
                        string temp = validParameter.validFile(parameters, "processors", false);        if (temp == "not found"){       temp = m->getProcessors();      }
@@ -330,12 +330,12 @@ int MatrixOutputCommand::execute(){
                        lines[i].end = int (sqrt(float(i+1)/float(processors)) * numGroups);
                }       
                
-               if (m->control_pressed) { delete input; for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } m->Groups.clear(); return 0;  }
+               if (m->control_pressed) { delete input; for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } m->clearGroups(); return 0;  }
                                
                //as long as you are not at the end of the file or done wih the lines you want
                while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
                
-                       if (m->control_pressed) { outputTypes.clear(); delete input; for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } for (int i = 0; i < outputNames.size(); i++) {     m->mothurRemove(outputNames[i]); } m->Groups.clear(); return 0;  }
+                       if (m->control_pressed) { outputTypes.clear(); delete input; for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } for (int i = 0; i < outputNames.size(); i++) {     m->mothurRemove(outputNames[i]); } m->clearGroups(); return 0;  }
                
                        if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){                  
                                m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
@@ -368,7 +368,7 @@ int MatrixOutputCommand::execute(){
                        lookup = input->getSharedRAbundVectors();
                }
                
-               if (m->control_pressed) { outputTypes.clear(); delete input; for (int i = 0; i < outputNames.size(); i++) {     m->mothurRemove(outputNames[i]); } m->Groups.clear(); return 0;  }
+               if (m->control_pressed) { outputTypes.clear(); delete input; for (int i = 0; i < outputNames.size(); i++) {     m->mothurRemove(outputNames[i]); } m->clearGroups(); return 0;  }
 
                //output error messages about any remaining user labels
                set<string>::iterator it;
@@ -383,7 +383,7 @@ int MatrixOutputCommand::execute(){
                        }
                }
                
-               if (m->control_pressed) { outputTypes.clear(); delete input;  for (int i = 0; i < outputNames.size(); i++) {    m->mothurRemove(outputNames[i]); } m->Groups.clear(); return 0;  }
+               if (m->control_pressed) { outputTypes.clear(); delete input;  for (int i = 0; i < outputNames.size(); i++) {    m->mothurRemove(outputNames[i]); } m->clearGroups(); return 0;  }
 
                //run last label if you need to
                if (needToRun == true)  {
@@ -395,10 +395,10 @@ int MatrixOutputCommand::execute(){
                        for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } 
                }
                
-               if (m->control_pressed) { outputTypes.clear();  delete input;  for (int i = 0; i < outputNames.size(); i++) {   m->mothurRemove(outputNames[i]); } m->Groups.clear(); return 0;  }
+               if (m->control_pressed) { outputTypes.clear();  delete input;  for (int i = 0; i < outputNames.size(); i++) {   m->mothurRemove(outputNames[i]); } m->clearGroups(); return 0;  }
                
                //reset groups parameter
-               m->Groups.clear();  
+               m->clearGroups();  
                
                //set phylip file as new current phylipfile
                string current = "";