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

[mothur.git] / unifracunweightedcommand.cpp

diff --git a/unifracunweightedcommand.cpp b/unifracunweightedcommand.cpp
index 1c2db5325311d7b6d6afb52aecee51a75bdd1db8..cc175e17fd74f0d808fc9efa11442f582333e73d 100644 (file)
--- a/unifracunweightedcommand.cpp
+++ b/unifracunweightedcommand.cpp
@@ -134,8 +134,8 @@ UnifracUnweightedCommand::UnifracUnweightedCommand(string option)  {
                        }
                        
                        m->runParse = true;
-                       m->Groups.clear();
-                       m->namesOfGroups.clear();
+                       m->clearGroups();
+                       m->clearAllGroups();
                        m->Treenames.clear();
                        m->names.clear();
                        
@@ -167,7 +167,7 @@ UnifracUnweightedCommand::UnifracUnweightedCommand(string option)  {
                        if (groups == "not found") { groups = ""; }
                        else { 
                                m->splitAtDash(groups, Groups);
-                               m->Groups = Groups;
+                               m->setGroups(Groups);
                        }
                                
                        itersString = validParameter.validFile(parameters, "iters", false);                             if (itersString == "not found") { itersString = "1000"; }
@@ -196,7 +196,7 @@ UnifracUnweightedCommand::UnifracUnweightedCommand(string option)  {
                        if ((phylip) && (Groups.size() == 0)) {
                                groups = "all";
                                m->splitAtDash(groups, Groups);
-                               m->Groups = Groups;
+                               m->setGroups(Groups);
                        }
                }
                
@@ -259,7 +259,7 @@ int UnifracUnweightedCommand::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;
                                }
                                
@@ -282,8 +282,10 @@ int UnifracUnweightedCommand::execute() {
                m->openOutputFile(sumFile, outSum);
                
                util = new SharedUtil();
-               util->setGroups(m->Groups, tmap->namesOfGroups, allGroups, numGroups, "unweighted");    //sets the groups the user wants to analyze
-               util->getCombos(groupComb, m->Groups, numComp);
+               vector<string> Groups = m->getGroups();
+               vector<string> namesGroups = tmap->getNamesOfGroups();
+               util->setGroups(Groups, namesGroups, allGroups, numGroups, "unweighted");       //sets the groups the user wants to analyze
+               util->getCombos(groupComb, Groups, numComp);
                delete util;
        
                if (numGroups == 1) { numComp++; groupComb.push_back(allGroups); }
@@ -403,7 +405,7 @@ int UnifracUnweightedCommand::execute() {
                
 
                outSum.close();
-               m->Groups.clear();
+               m->clearGroups();
                delete tmap; delete unweighted;
                for (int i = 0; i < T.size(); i++) { delete T[i]; }
                
@@ -516,18 +518,18 @@ void UnifracUnweightedCommand::createPhylipFile(int i) {
                
                if ((outputForm == "lt") || (outputForm == "square")) {
                        //output numSeqs
-                       out << m->Groups.size() << endl;
+                       out << m->getNumGroups() << endl;
                }
                
                //make matrix with scores in it
-               vector< vector<float> > dists;  dists.resize(m->Groups.size());
-               for (int i = 0; i < m->Groups.size(); i++) {
-                       dists[i].resize(m->Groups.size(), 0.0);
+               vector< vector<float> > dists;  dists.resize(m->getNumGroups());
+               for (int i = 0; i < m->getNumGroups(); i++) {
+                       dists[i].resize(m->getNumGroups(), 0.0);
                }
                
                //flip it so you can print it
                int count = 0;
-               for (int r=0; r<m->Groups.size(); r++) { 
+               for (int r=0; r<m->getNumGroups(); r++) { 
                        for (int l = 0; l < r; l++) {
                                dists[r][l] = utreeScores[count][0];
                                dists[l][r] = utreeScores[count][0];
@@ -536,9 +538,9 @@ void UnifracUnweightedCommand::createPhylipFile(int i) {
                }
                
                //output to file
-               for (int r=0; r<m->Groups.size(); r++) { 
+               for (int r=0; r<m->getNumGroups(); r++) { 
                        //output name
-                       string name = m->Groups[r];
+                       string name = (m->getGroups())[r];
                        if (name.length() < 10) { //pad with spaces to make compatible
                                while (name.length() < 10) {  name += " ";  }
                        }
@@ -553,12 +555,12 @@ void UnifracUnweightedCommand::createPhylipFile(int i) {
                                out << name << '\t';
                                
                                //output distances
-                               for (int l = 0; l < m->Groups.size(); l++) {    out << dists[r][l] << '\t';  }
+                               for (int l = 0; l < m->getNumGroups(); l++) {   out << dists[r][l] << '\t';  }
                                out << endl;
                        }else{
                                //output distances
                                for (int l = 0; l < r; l++) {   
-                                       string otherName = m->Groups[l];
+                                       string otherName = (m->getGroups())[l];
                                        if (otherName.length() < 10) { //pad with spaces to make compatible
                                                while (otherName.length() < 10) {  otherName += " ";  }
                                        }