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

[mothur.git] / phylodiversitycommand.cpp

diff --git a/phylodiversitycommand.cpp b/phylodiversitycommand.cpp
index d273e1dd3f4aab843190aceb4888e547a8bd81f5..ca0d02aca04b0a737d45c29b44cb02c2925ff257 100644 (file)
--- a/phylodiversitycommand.cpp
+++ b/phylodiversitycommand.cpp
@@ -137,8 +137,8 @@ PhyloDiversityCommand::PhyloDiversityCommand(string option)  {
                        }
                        
                        m->runParse = true;
-                       m->Groups.clear();
-                       m->namesOfGroups.clear();
+                       m->clearGroups();
+                       m->clearAllGroups();
                        m->Treenames.clear();
                        m->names.clear();
                        
@@ -193,7 +193,7 @@ PhyloDiversityCommand::PhyloDiversityCommand(string option)  {
                        if (groups == "not found") { groups = "";  }
                        else { 
                                m->splitAtDash(groups, Groups);
-                               m->Groups = Groups;
+                               m->setGroups(Groups);
                        }
                        
                        if ((!collect) && (!rarefy) && (!summary)) { m->mothurOut("No outputs selected. You must set either collect, rarefy or summary to true, summary=T by default."); m->mothurOutEndLine(); abort=true; }
@@ -258,7 +258,7 @@ int PhyloDiversityCommand::execute(){
                                if (m->control_pressed) { 
                                        delete tmap; for (int i = 0; i < trees.size(); i++) { delete trees[i]; }
                                        for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } outputTypes.clear();
-                                       m->Groups.clear();
+                                       m->clearGroups();
                                        return 0;
                                }
                                
@@ -277,11 +277,14 @@ int PhyloDiversityCommand::execute(){
                }
                
                SharedUtil* util = new SharedUtil();
-               util->setGroups(m->Groups, tmap->namesOfGroups, "phylo.diversity");     //sets the groups the user wants to analyze
+               vector<string> mGroups = m->getGroups();
+               vector<string> tGroups = tmap->getNamesOfGroups();
+               util->setGroups(mGroups, tGroups, "phylo.diversity");   //sets the groups the user wants to analyze
                delete util;
                
                //incase the user had some mismatches between the tree and group files we don't want group xxx to be analyzed
-               for (int i = 0; i < m->Groups.size(); i++) { if (m->Groups[i] == "xxx") { m->Groups.erase(m->Groups.begin()+i);  break; }  }
+               for (int i = 0; i < mGroups.size(); i++) { if (mGroups[i] == "xxx") { mGroups.erase(mGroups.begin()+i);  break; }  }
+               m->setGroups(mGroups);
                 
                vector<string> outputNames;
                
@@ -304,7 +307,7 @@ int PhyloDiversityCommand::execute(){
                        //create a vector containing indexes of leaf nodes, randomize it, select nodes to send to calculator
                        vector<int> randomLeaf;
                        for (int j = 0; j < numLeafNodes; j++) {  
-                               if (m->inUsersGroups(trees[i]->tree[j].getGroup(), m->Groups) == true) { //is this a node from the group the user selected.
+                               if (m->inUsersGroups(trees[i]->tree[j].getGroup(), mGroups) == true) { //is this a node from the group the user selected.
                                        randomLeaf.push_back(j); 
                                }
                        }
@@ -319,15 +322,15 @@ int PhyloDiversityCommand::execute(){
                        
                        //find largest group total 
                        int largestGroup = 0;
-                       for (int j = 0; j < m->Groups.size(); j++) {  
-                               if (tmap->seqsPerGroup[m->Groups[j]] > largestGroup) { largestGroup = tmap->seqsPerGroup[m->Groups[j]]; }
+                       for (int j = 0; j < mGroups.size(); j++) {  
+                               if (tmap->seqsPerGroup[mGroups[j]] > largestGroup) { largestGroup = tmap->seqsPerGroup[mGroups[j]]; }
                                
                                //initialize diversity
-                               diversity[m->Groups[j]].resize(tmap->seqsPerGroup[m->Groups[j]]+1, 0.0);                //numSampled
+                               diversity[mGroups[j]].resize(tmap->seqsPerGroup[mGroups[j]]+1, 0.0);            //numSampled
                                                                                                                                                                                                                        //groupA                0.0                     0.0
                                                                                                                                                                                                                        
                                //initialize sumDiversity
-                               sumDiversity[m->Groups[j]].resize(tmap->seqsPerGroup[m->Groups[j]]+1, 0.0);
+                               sumDiversity[mGroups[j]].resize(tmap->seqsPerGroup[mGroups[j]]+1, 0.0);
                        }       
 
                        //convert freq percentage to number
@@ -341,8 +344,8 @@ int PhyloDiversityCommand::execute(){
                        if(largestGroup % increment != 0){      numSampledList.insert(largestGroup);   }
                        
                        //add other groups ending points
-                       for (int j = 0; j < m->Groups.size(); j++) {  
-                               if (numSampledList.count(diversity[m->Groups[j]].size()-1) == 0) {  numSampledList.insert(diversity[m->Groups[j]].size()-1); }
+                       for (int j = 0; j < mGroups.size(); j++) {  
+                               if (numSampledList.count(diversity[mGroups[j]].size()-1) == 0) {  numSampledList.insert(diversity[mGroups[j]].size()-1); }
                        }
                        
                        #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
@@ -484,6 +487,7 @@ int PhyloDiversityCommand::createProcesses(vector<int>& procIters, Tree* t, map<
 int PhyloDiversityCommand::driver(Tree* t, map< string, vector<float> >& div, map<string, vector<float> >& sumDiv, int numIters, int increment, vector<int>& randomLeaf, set<int>& numSampledList, ofstream& outCollect, ofstream& outSum, bool doSumCollect){
        try {
                int numLeafNodes = randomLeaf.size();
+               vector<string> mGroups = m->getGroups();
        
                for (int l = 0; l < numIters; l++) {
                                random_shuffle(randomLeaf.begin(), randomLeaf.end());
@@ -491,7 +495,7 @@ int PhyloDiversityCommand::driver(Tree* t, map< string, vector<float> >& div, ma
                                //initialize counts
                                map<string, int> counts;
                                map< string, set<int> > countedBranch;  
-                               for (int j = 0; j < m->Groups.size(); j++) {  counts[m->Groups[j]] = 0; countedBranch[m->Groups[j]].insert(-2);  }  //add dummy index to initialize countedBranch sets
+                               for (int j = 0; j < mGroups.size(); j++) {  counts[mGroups[j]] = 0; countedBranch[mGroups[j]].insert(-2);  }  //add dummy index to initialize countedBranch sets
                                
                                for(int k = 0; k < numLeafNodes; k++){
                                                
@@ -522,9 +526,9 @@ int PhyloDiversityCommand::driver(Tree* t, map< string, vector<float> >& div, ma
                                
                                if (rarefy) {
                                        //add this diversity to the sum
-                                       for (int j = 0; j < m->Groups.size(); j++) {  
-                                               for (int g = 0; g < div[m->Groups[j]].size(); g++) {
-                                                       sumDiv[m->Groups[j]][g] += div[m->Groups[j]][g];
+                                       for (int j = 0; j < mGroups.size(); j++) {  
+                                               for (int g = 0; g < div[mGroups[j]].size(); g++) {
+                                                       sumDiv[mGroups[j]][g] += div[mGroups[j]][g];
                                                }
                                        }
                                }
@@ -550,15 +554,16 @@ void PhyloDiversityCommand::printSumData(map< string, vector<float> >& div, ofst
                out << "Groups\tnumSampled\tphyloDiversity" << endl;
                
                out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
-                       
-               for (int j = 0; j < m->Groups.size(); j++) {
-                       int numSampled = (div[m->Groups[j]].size()-1);
-                       out << m->Groups[j] << '\t' << numSampled << '\t';
+               
+               vector<string> mGroups = m->getGroups();
+               for (int j = 0; j < mGroups.size(); j++) {
+                       int numSampled = (div[mGroups[j]].size()-1);
+                       out << mGroups[j] << '\t' << numSampled << '\t';
                
                         
                        float score;
-                       if (scale)      {  score = (div[m->Groups[j]][numSampled] / (float)numIters) / (float)numSampled;       }
-                       else            {       score = div[m->Groups[j]][numSampled] / (float)numIters;        }
+                       if (scale)      {  score = (div[mGroups[j]][numSampled] / (float)numIters) / (float)numSampled; }
+                       else            {       score = div[mGroups[j]][numSampled] / (float)numIters;  }
                                
                        out << setprecision(4) << score << endl;
                }
@@ -577,7 +582,8 @@ void PhyloDiversityCommand::printData(set<int>& num, map< string, vector<float>
        try {
                
                out << "numSampled\t";
-               for (int i = 0; i < m->Groups.size(); i++) { out << m->Groups[i] << '\t';  }
+               vector<string> mGroups = m->getGroups();
+               for (int i = 0; i < mGroups.size(); i++) { out << mGroups[i] << '\t';  }
                out << endl;
                
                out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
@@ -586,12 +592,12 @@ void PhyloDiversityCommand::printData(set<int>& num, map< string, vector<float>
                        int numSampled = *it;
                        
                        out << numSampled << '\t';  
-                       
-                       for (int j = 0; j < m->Groups.size(); j++) {
-                               if (numSampled < div[m->Groups[j]].size()) { 
+               
+                       for (int j = 0; j < mGroups.size(); j++) {
+                               if (numSampled < div[mGroups[j]].size()) { 
                                        float score;
-                                       if (scale)      {  score = (div[m->Groups[j]][numSampled] / (float)numIters) / (float)numSampled;       }
-                                       else            {       score = div[m->Groups[j]][numSampled] / (float)numIters;        }
+                                       if (scale)      {  score = (div[mGroups[j]][numSampled] / (float)numIters) / (float)numSampled; }
+                                       else            {       score = div[mGroups[j]][numSampled] / (float)numIters;  }
 
                                        out << setprecision(4) << score << '\t';
                                }else { out << "NA" << '\t'; }