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

[mothur.git] / libshuffcommand.cpp

diff --git a/libshuffcommand.cpp b/libshuffcommand.cpp
index 96abbbe995918d779e4cd9086e650b7aa63a8a7b..1e8102f49f40753d239f8188f1a88cc9e3578587 100644 (file)
--- a/libshuffcommand.cpp
+++ b/libshuffcommand.cpp
@@ -165,7 +165,7 @@ LibShuffCommand::LibShuffCommand(string option)  {
                        else { 
                                savegroups = groups;
                                m->splitAtDash(groups, Groups);
-                               m->Groups = Groups;
+                               m->setGroups(Groups);
                        }
                                
                        string temp;
@@ -252,9 +252,9 @@ int LibShuffCommand::execute(){
                //this is needed because when we read the matrix we sort it into groups in alphabetical order
                //the rest of the command and the classes used in this command assume specific order
                /********************************************************************************************/
-               matrix->setGroups(groupMap->namesOfGroups);
+               matrix->setGroups(groupMap->getNamesOfGroups());
                vector<int> sizes;
-               for (int i = 0; i < groupMap->namesOfGroups.size(); i++) {   sizes.push_back(groupMap->getNumSeqs(groupMap->namesOfGroups[i]));  }
+               for (int i = 0; i < (groupMap->getNamesOfGroups()).size(); i++) {   sizes.push_back(groupMap->getNumSeqs((groupMap->getNamesOfGroups())[i]));  }
                matrix->setSizes(sizes);
                        
                        
@@ -268,21 +268,21 @@ int LibShuffCommand::execute(){
                savedDXYValues = form->evaluateAll();
                savedMinValues = form->getSavedMins();
                
-               if (m->control_pressed) {  delete form; m->Groups.clear(); delete matrix; delete groupMap; return 0; }
+               if (m->control_pressed) {  delete form; m->clearGroups(); delete matrix; delete groupMap; return 0; }
        
                pValueCounts.resize(numGroups);
                for(int i=0;i<numGroups;i++){
                        pValueCounts[i].assign(numGroups, 0);
                }
        
-               if (m->control_pressed) {  outputTypes.clear(); delete form; m->Groups.clear(); delete matrix; delete groupMap; return 0; }
+               if (m->control_pressed) {  outputTypes.clear(); delete form; m->clearGroups(); delete matrix; delete groupMap; return 0; }
                                
                Progress* reading = new Progress();
                
                for(int i=0;i<numGroups-1;i++) {
                        for(int j=i+1;j<numGroups;j++) {
                                
-                               if (m->control_pressed) {  outputTypes.clear();  delete form; m->Groups.clear(); delete matrix; delete groupMap; delete reading; return 0; }
+                               if (m->control_pressed) {  outputTypes.clear();  delete form; m->clearGroups(); delete matrix; delete groupMap; delete reading; return 0; }
 
                                reading->newLine(groupNames[i]+'-'+groupNames[j], iters);
                                int spoti = groupMap->groupIndex[groupNames[i]]; //neccessary in case user selects groups so you know where they are in the matrix
@@ -290,13 +290,13 @@ int LibShuffCommand::execute(){
        
                                for(int p=0;p<iters;p++) {      
                                        
-                                       if (m->control_pressed) {  outputTypes.clear(); delete form; m->Groups.clear(); delete matrix; delete groupMap; delete reading; return 0; }
+                                       if (m->control_pressed) {  outputTypes.clear(); delete form; m->clearGroups(); delete matrix; delete groupMap; delete reading; return 0; }
                                        
                                        form->randomizeGroups(spoti,spotj); 
                                        if(form->evaluatePair(spoti,spotj) >= savedDXYValues[spoti][spotj])     {       pValueCounts[i][j]++;   }
                                        if(form->evaluatePair(spotj,spoti) >= savedDXYValues[spotj][spoti])     {       pValueCounts[j][i]++;   }
                                        
-                                       if (m->control_pressed) {  outputTypes.clear(); delete form; m->Groups.clear(); delete matrix; delete groupMap; delete reading; return 0; }
+                                       if (m->control_pressed) {  outputTypes.clear(); delete form; m->clearGroups(); delete matrix; delete groupMap; delete reading; return 0; }
                                        
                                        reading->update(p);                     
                                }
@@ -305,7 +305,7 @@ int LibShuffCommand::execute(){
                        }
                }
                
-               if (m->control_pressed) { outputTypes.clear();  delete form; m->Groups.clear(); delete matrix; delete groupMap; delete reading; return 0; }
+               if (m->control_pressed) { outputTypes.clear();  delete form; m->clearGroups(); delete matrix; delete groupMap; delete reading; return 0; }
        
                reading->finish();
                delete reading;
@@ -315,7 +315,7 @@ int LibShuffCommand::execute(){
                printCoverageFile();
                                
                //clear out users groups
-               m->Groups.clear();
+               m->clearGroups();
                delete form;
                
                delete matrix; delete groupMap;
@@ -492,49 +492,51 @@ int LibShuffCommand::printSummaryFile() {
 
 void LibShuffCommand::setGroups() {
        try {
+               vector<string> myGroups = m->getGroups();
                //if the user has not entered specific groups to analyze then do them all
-               if (m->Groups.size() == 0) {
+               if (m->getNumGroups() == 0) {
                        numGroups = groupMap->getNumGroups();
                        for (int i=0; i < numGroups; i++) { 
-                               m->Groups.push_back(groupMap->namesOfGroups[i]);
+                               myGroups.push_back((groupMap->getNamesOfGroups())[i]);
                        }
                } else {
                        if (savegroups != "all") {
                                //check that groups are valid
-                               for (int i = 0; i < m->Groups.size(); i++) {
-                                       if (groupMap->isValidGroup(m->Groups[i]) != true) {
-                                               m->mothurOut(m->Groups[i] + " is not a valid group, and will be disregarded."); m->mothurOutEndLine();
+                               for (int i = 0; i < myGroups.size(); i++) {
+                                       if (groupMap->isValidGroup(myGroups[i]) != true) {
+                                               m->mothurOut(myGroups[i] + " is not a valid group, and will be disregarded."); m->mothurOutEndLine();
                                                // erase the invalid group from globaldata->Groups
-                                               m->Groups.erase(m->Groups.begin()+i);
+                                               myGroups.erase(myGroups.begin()+i);
                                        }
                                }
                        
                                //if the user only entered invalid groups
-                               if ((m->Groups.size() == 0) || (m->Groups.size() == 1)) { 
+                               if ((myGroups.size() == 0) || (myGroups.size() == 1)) { 
                                        numGroups = groupMap->getNumGroups();
                                        for (int i=0; i < numGroups; i++) { 
-                                               m->Groups.push_back(groupMap->namesOfGroups[i]);
+                                               myGroups.push_back((groupMap->getNamesOfGroups())[i]);
                                        }
                                        m->mothurOut("When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile."); m->mothurOutEndLine();
-                               } else { numGroups = m->Groups.size(); }
+                               } else { numGroups = myGroups.size(); }
                        } else { //users wants all groups
                                numGroups = groupMap->getNumGroups();
-                               m->Groups.clear();
+                               myGroups.clear();
                                for (int i=0; i < numGroups; i++) { 
-                                       m->Groups.push_back(groupMap->namesOfGroups[i]);
+                                       myGroups.push_back((groupMap->getNamesOfGroups())[i]);
                                }
                        }
                }
 
                //sort so labels match
-               sort(m->Groups.begin(), m->Groups.end());
+               sort(myGroups.begin(), myGroups.end());
                
                //sort
-               sort(groupMap->namesOfGroups.begin(), groupMap->namesOfGroups.end());
+               //sort(groupMap->namesOfGroups.begin(), groupMap->namesOfGroups.end());
                
-               for (int i = 0; i < groupMap->namesOfGroups.size(); i++) {  groupMap->groupIndex[groupMap->namesOfGroups[i]] = i;  }
+               for (int i = 0; i < (groupMap->getNamesOfGroups()).size(); i++) {  groupMap->groupIndex[(groupMap->getNamesOfGroups())[i]] = i;  }
 
-               groupNames = m->Groups;
+               groupNames = myGroups;
+               m->setGroups(myGroups);
 
        }
        catch(exception& e) {