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

[mothur.git] / parsimonycommand.cpp

diff --git a/parsimonycommand.cpp b/parsimonycommand.cpp
index 66f8193e647c94db5bc8ac815bb6eea9796cd138..3752935aac5ad0211c5f9bf5b66ca00dce2b366b 100644 (file)
--- a/parsimonycommand.cpp
+++ b/parsimonycommand.cpp
@@ -126,8 +126,8 @@ ParsimonyCommand::ParsimonyCommand(string option)  {
                        }
                        
                        m->runParse = true;
-                       m->Groups.clear();
-                       m->namesOfGroups.clear();
+                       m->clearGroups();
+                       m->clearAllGroups();
                        m->Treenames.clear();
                        m->names.clear();
                        
@@ -164,10 +164,10 @@ ParsimonyCommand::ParsimonyCommand(string option)  {
                        //check for optional parameter and set defaults
                        // ...at some point should added some additional type checking...
                        groups = validParameter.validFile(parameters, "groups", false);                 
-                       if (groups == "not found") { groups = ""; m->Groups.clear(); }
+                       if (groups == "not found") { groups = ""; m->clearGroups(); }
                        else { 
                                m->splitAtDash(groups, Groups);
-                               m->Groups = Groups;
+                               m->setGroups(Groups);
                        }
                                
                        itersString = validParameter.validFile(parameters, "iters", false);                     if (itersString == "not found") { itersString = "1000"; }
@@ -242,7 +242,7 @@ int ParsimonyCommand::execute() {
                                        if (m->control_pressed) { 
                                                delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
                                                for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } outputTypes.clear();
-                                               m->Groups.clear();
+                                               m->clearGroups();
                                                return 0;
                                        }
                                        
@@ -280,8 +280,11 @@ int ParsimonyCommand::execute() {
                        
                //set users groups to analyze
                util = new SharedUtil();
-               util->setGroups(m->Groups, tmap->namesOfGroups, allGroups, numGroups, "parsimony");     //sets the groups the user wants to analyze
-               util->getCombos(groupComb, m->Groups, numComp);
+               vector<string> mGroups = m->getGroups();
+               vector<string> tGroups = tmap->getNamesOfGroups();
+               util->setGroups(mGroups, tGroups, allGroups, numGroups, "parsimony");   //sets the groups the user wants to analyze
+               util->getCombos(groupComb, mGroups, numComp);
+               m->setGroups(mGroups);
                delete util;
                        
                if (numGroups == 1) { numComp++; groupComb.push_back(allGroups); }
@@ -297,7 +300,7 @@ int ParsimonyCommand::execute() {
                        delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
                        if (randomtree == "") {  outSum.close();  }
                        for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } outputTypes.clear();
-                       m->Groups.clear();
+                       m->clearGroups();
                        return 0;
                }
                        
@@ -322,7 +325,7 @@ int ParsimonyCommand::execute() {
                                        delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
                                        if (randomtree == "") {  outSum.close();  }
                                        for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } outputTypes.clear();
-                                       m->Groups.clear();
+                                       m->clearGroups();
                                        return 0;
                                }
 
@@ -361,7 +364,7 @@ int ParsimonyCommand::execute() {
                                        if (randomtree == "") {  outSum.close();  }
                                        for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } outputTypes.clear();
                                        delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
-                                       m->Groups.clear();
+                                       m->clearGroups();
                                        return 0;
                                }
                                        
@@ -398,7 +401,7 @@ int ParsimonyCommand::execute() {
                                        delete reading; delete pars; delete output; delete randT;
                                        delete tmap; 
                                        for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } outputTypes.clear();
-                                       m->Groups.clear();
+                                       m->clearGroups();
                                        return 0;
                                }
 
@@ -410,7 +413,7 @@ int ParsimonyCommand::execute() {
                                        delete reading; delete pars;  delete output; delete randT;
                                        delete tmap; 
                                        for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } outputTypes.clear();
-                                       m->Groups.clear();
+                                       m->clearGroups();
                                        return 0;
                                }
                        
@@ -467,7 +470,7 @@ int ParsimonyCommand::execute() {
                                delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
                                if (randomtree == "") {  outSum.close();  }
                                for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } outputTypes.clear();
-                               m->Groups.clear();
+                               m->clearGroups();
                                return 0;
                }
                
@@ -480,7 +483,7 @@ int ParsimonyCommand::execute() {
                if (randomtree == "") { printUSummaryFile(); }
                
                //reset groups parameter
-               m->Groups.clear(); 
+               m->clearGroups(); 
                
                delete pars; delete output; 
                delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
@@ -585,6 +588,7 @@ void ParsimonyCommand::getUserInput() {
                count = 1;
                numEachGroup.resize(numGroups, 0);  
                
+               
                for (int i = 1; i <= numGroups; i++) {
                        m->mothurOut("Please enter the number of sequences in group " + toString(i) +  ": ");
                        cin >> num;
@@ -592,7 +596,7 @@ void ParsimonyCommand::getUserInput() {
                                
                        //set tmaps seqsPerGroup
                        tmap->seqsPerGroup[toString(i)] = num;
-                       tmap->namesOfGroups.push_back(toString(i));
+                       tmap->addGroup(toString(i));
                        
                        //set tmaps namesOfSeqs
                        for (int j = 0; j < num; j++) {