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 a9ca4d01260340fbdc08ccf423c6022f8dd5abbc..cc175e17fd74f0d808fc9efa11442f582333e73d 100644 (file)
--- a/unifracunweightedcommand.cpp
+++ b/unifracunweightedcommand.cpp
@@ -80,6 +80,7 @@ UnifracUnweightedCommand::UnifracUnweightedCommand(string option)  {
                        
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();
@@ -133,8 +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();
                        
@@ -145,16 +146,18 @@ UnifracUnweightedCommand::UnifracUnweightedCommand(string option)  {
                                treefile = m->getTreeFile(); 
                                if (treefile != "") { m->mothurOut("Using " + treefile + " as input file for the tree parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current tree file and the tree parameter is required."); m->mothurOutEndLine(); abort = true; }                                                               
-                       }       
+                       }else { m->setTreeFile(treefile); }     
                        
                        //check for required parameters
                        groupfile = validParameter.validFile(parameters, "group", true);
                        if (groupfile == "not open") { abort = true; }
                        else if (groupfile == "not found") { groupfile = ""; }
+                       else { m->setGroupFile(groupfile); }
                        
                        namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not open") { abort = true; }
                        else if (namefile == "not found") { namefile = ""; }
+                       else { m->setNameFile(namefile); }
                        
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = ""; }
                        
@@ -164,7 +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"; }
@@ -193,7 +196,7 @@ UnifracUnweightedCommand::UnifracUnweightedCommand(string option)  {
                        if ((phylip) && (Groups.size() == 0)) {
                                groups = "all";
                                m->splitAtDash(groups, Groups);
-                               m->Groups = Groups;
+                               m->setGroups(Groups);
                        }
                }
                
@@ -255,8 +258,8 @@ 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++) {  remove(outputNames[i].c_str()); } outputTypes.clear();
-                                       m->Groups.clear();
+                                       for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } outputTypes.clear();
+                                       m->clearGroups();
                                        return 0;
                                }
                                
@@ -279,8 +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); }
@@ -295,8 +300,10 @@ int UnifracUnweightedCommand::execute() {
                
                if (numComp < processors) { processors = numComp;  }
                
-               outSum << "Tree#" << '\t' << "Groups" << '\t'  <<  "UWScore" <<'\t' << "UWSig" <<  endl;
-               m->mothurOut("Tree#\tGroups\tUWScore\tUWSig"); m->mothurOutEndLine();
+               outSum << "Tree#" << '\t' << "Groups" << '\t'  <<  "UWScore" <<'\t';
+               m->mothurOut("Tree#\tGroups\tUWScore\t");
+               if (random) { outSum << "UWSig"; m->mothurOut("UWSig"); }
+               outSum << endl; m->mothurOutEndLine();
         
                //get pscores for users trees
                for (int i = 0; i < T.size(); i++) {
@@ -304,7 +311,7 @@ int UnifracUnweightedCommand::execute() {
                                delete tmap; delete unweighted;
                                for (int i = 0; i < T.size(); i++) { delete T[i]; }
                                outSum.close();
-                               for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  }
+                               for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  }
                                return 0; 
                        }
                        
@@ -326,7 +333,7 @@ int UnifracUnweightedCommand::execute() {
                        userData = unweighted->getValues(T[i], processors, outputDir);  //userData[0] = unweightedscore
                
                        if (m->control_pressed) { delete tmap; delete unweighted;
-                               for (int i = 0; i < T.size(); i++) { delete T[i]; }if (random) { delete output;  } outSum.close();  for (int i = 0; i < outputNames.size(); i++) {      remove(outputNames[i].c_str());  }return 0; }
+                               for (int i = 0; i < T.size(); i++) { delete T[i]; }if (random) { delete output;  } outSum.close();  for (int i = 0; i < outputNames.size(); i++) {      m->mothurRemove(outputNames[i]);  }return 0; }
                        
                        //output scores for each combination
                        for(int k = 0; k < numComp; k++) {
@@ -344,7 +351,7 @@ int UnifracUnweightedCommand::execute() {
                                randomData = unweighted->getValues(T[i], "", "", processors, outputDir);
                                
                                if (m->control_pressed) { delete tmap; delete unweighted;
-                                       for (int i = 0; i < T.size(); i++) { delete T[i]; }if (random) { delete output;  } outSum.close(); for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str());  } return 0; }
+                                       for (int i = 0; i < T.size(); i++) { delete T[i]; }if (random) { delete output;  } outSum.close(); for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]);  } return 0; }
                        
                                for(int k = 0; k < numComp; k++) {      
                                        //add trees unweighted score to map of scores
@@ -382,7 +389,7 @@ int UnifracUnweightedCommand::execute() {
                        }
                        
                        if (m->control_pressed) { delete tmap; delete unweighted;
-                               for (int i = 0; i < T.size(); i++) { delete T[i]; }if (random) { delete output;  } outSum.close(); for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str());  } return 0;  }
+                               for (int i = 0; i < T.size(); i++) { delete T[i]; }if (random) { delete output;  } outSum.close(); for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]);  } return 0;  }
                        
                        //print output files
                        printUWSummaryFile(i);
@@ -398,11 +405,11 @@ 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]; }
                
-               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  }      return 0; }
+               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);  }     return 0; }
                
                m->mothurOut("It took " + toString(time(NULL) - start) + " secs to run unifrac.unweighted."); m->mothurOutEndLine();
                
@@ -482,9 +489,9 @@ void UnifracUnweightedCommand::printUWSummaryFile(int i) {
                                        m->mothurOutJustToLog(groupComb[a]  + "\t" + toString(utreeScores[a][0])  + "\t<" + toString((1/float(iters))) + "\n"); 
                                }
                        }else{
-                               outSum << setprecision(6) << groupComb[a]  << '\t' << utreeScores[a][0] << '\t' << "0.00" << endl;
-                               cout << setprecision(6)  << groupComb[a]  << '\t' << utreeScores[a][0] << '\t' << "0.00" << endl; 
-                               m->mothurOutJustToLog(groupComb[a]  + "\t" + toString(utreeScores[a][0])  + "\t0.00\n");
+                               outSum << setprecision(6) << groupComb[a]  << '\t' << utreeScores[a][0]  << endl;
+                               cout << setprecision(6)  << groupComb[a]  << '\t' << utreeScores[a][0]  << endl; 
+                               m->mothurOutJustToLog(groupComb[a]  + "\t" + toString(utreeScores[a][0]) + "\n");
                        }
                }
                
@@ -511,18 +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];
@@ -531,9 +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 += " ";  }
                        }
@@ -548,12 +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 += " ";  }
                                        }