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

[mothur.git] / indicatorcommand.cpp

diff --git a/indicatorcommand.cpp b/indicatorcommand.cpp
index 797f62c8908f0c0bd125c9bc1135a45b83e6d028..40d3bcd26f42ff67b424ee6087bc276ceccbd752 100644 (file)
--- a/indicatorcommand.cpp
+++ b/indicatorcommand.cpp
@@ -96,8 +96,8 @@ IndicatorCommand::IndicatorCommand(string option)  {
                        }
                        
                        m->runParse = true;
-                       m->Groups.clear();
-                       m->namesOfGroups.clear();
+                       m->clearGroups();
+                       m->clearAllGroups();
                        m->Treenames.clear();
                        m->names.clear();
                        
@@ -169,7 +169,7 @@ IndicatorCommand::IndicatorCommand(string option)  {
                        groups = validParameter.validFile(parameters, "groups", false);                 
                        if (groups == "not found") { groups = "";  Groups.push_back("all"); }
                        else { m->splitAtDash(groups, Groups);  }                       
-                       m->Groups = Groups;
+                       m->setGroups(Groups);
                        
                        label = validParameter.validFile(parameters, "label", false);                   
                        if (label == "not found") { label = ""; m->mothurOut("You did not provide a label, I will use the first label in your inputfile."); m->mothurOutEndLine(); label=""; }  
@@ -237,11 +237,14 @@ int IndicatorCommand::execute(){
                        
                        //fill Groups - checks for "all" and for any typo groups
                        SharedUtil* util = new SharedUtil();
-                       util->setGroups(Groups, designMap->namesOfGroups);
+                       vector<string> nameGroups = designMap->getNamesOfGroups();
+                       util->setGroups(Groups, nameGroups);
+                       designMap->setNamesOfGroups(nameGroups);
                        delete util;
                        
                        //loop through the Groups and fill Globaldata's Groups with the design file info
-                       m->Groups = designMap->getNamesSeqs(Groups);
+                       vector<string> namesSeqs = designMap->getNamesSeqs(Groups);
+                       m->setGroups(namesSeqs);
                }
        
                /***************************************************/
@@ -258,7 +261,7 @@ int IndicatorCommand::execute(){
                }
                
                //reset groups if needed
-               if (designfile != "") { m->Groups = Groups; }
+               if (designfile != "") { m->setGroups(Groups); }
                        
                /***************************************************/
                //    reading tree info                                                    //
@@ -273,7 +276,7 @@ int IndicatorCommand::execute(){
                        for (int i = 0; i < m->Treenames.size(); i++) { 
                                //sanity check - is this a group that is not in the sharedfile?
                                if (designfile == "") {
-                                       if (!(m->inUsersGroups(m->Treenames[i], m->namesOfGroups))) {
+                                       if (!(m->inUsersGroups(m->Treenames[i], m->getAllGroups()))) {
                                                m->mothurOut("[ERROR]: " + m->Treenames[i] + " is not a group in your shared or relabund file."); m->mothurOutEndLine();
                                                mismatch = true;
                                        }
@@ -283,7 +286,7 @@ int IndicatorCommand::execute(){
                                        vector<string> myNames = designMap->getNamesSeqs(myGroups);
                                        
                                        for(int k = 0; k < myNames.size(); k++) {
-                                               if (!(m->inUsersGroups(myNames[k], m->namesOfGroups))) {
+                                               if (!(m->inUsersGroups(myNames[k], m->getAllGroups()))) {
                                                        m->mothurOut("[ERROR]: " + myNames[k] + " is not a group in your shared or relabund file."); m->mothurOutEndLine();
                                                        mismatch = true;
                                                }
@@ -323,9 +326,9 @@ int IndicatorCommand::execute(){
                        /***************************************************/
                        //    create ouptut tree - respecting pickedGroups //
                        /***************************************************/
-                       Tree* outputTree = new Tree(m->Groups.size(), treeMap); 
+                       Tree* outputTree = new Tree(m->getNumGroups(), treeMap); 
                        
-                       outputTree->getSubTree(T[0], m->Groups);
+                       outputTree->getSubTree(T[0], m->getGroups());
                        outputTree->assembleTree();
                                
                        //no longer need original tree, we have output tree to use and label
@@ -413,11 +416,11 @@ int IndicatorCommand::GetIndicatorSpecies(){
                        vector<SharedRAbundVector*> subset;
                        
                        //for each grouping
-                       for (int i = 0; i < designMap->namesOfGroups.size(); i++) {
+                       for (int i = 0; i < (designMap->getNamesOfGroups()).size(); i++) {
                                
                                for (int k = 0; k < lookup.size(); k++) {
                                        //are you from this grouping?
-                                       if (designMap->getGroup(lookup[k]->getGroup()) == designMap->namesOfGroups[i]) {
+                                       if (designMap->getGroup(lookup[k]->getGroup()) == (designMap->getNamesOfGroups())[i]) {
                                                subset.push_back(lookup[k]);
                                                groupsAlreadyAdded.insert(lookup[k]->getGroup());
                                        }
@@ -437,10 +440,10 @@ int IndicatorCommand::GetIndicatorSpecies(){
                        vector<SharedRAbundFloatVector*> subset;
                        
                        //for each grouping
-                       for (int i = 0; i < designMap->namesOfGroups.size(); i++) {
+                       for (int i = 0; i < (designMap->getNamesOfGroups()).size(); i++) {
                                for (int k = 0; k < lookupFloat.size(); k++) {
                                        //are you from this grouping?
-                                       if (designMap->getGroup(lookupFloat[k]->getGroup()) == designMap->namesOfGroups[i]) {
+                                       if (designMap->getGroup(lookupFloat[k]->getGroup()) == (designMap->getNamesOfGroups())[i]) {
                                                subset.push_back(lookupFloat[k]);
                                                groupsAlreadyAdded.insert(lookupFloat[k]->getGroup());
                                        }