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

[mothur.git] / summarysharedcommand.cpp

diff --git a/summarysharedcommand.cpp b/summarysharedcommand.cpp
index 8e162eed63a4f1a4b5ca026dcb09bb60f2b31743..c8d112fd3031d4995e4675a3dbe3d4daf91aebf9 100644 (file)
--- a/summarysharedcommand.cpp
+++ b/summarysharedcommand.cpp
@@ -56,7 +56,7 @@ vector<string> SummarySharedCommand::setParameters(){
                CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pshared);
                CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
                CommandParameter pdistance("distance", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pdistance);
-               CommandParameter pcalc("calc", "Multiple", "sharedchao-sharedsobs-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-whittaker-sharednseqs-ochiai-anderberg-skulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-structchi2-hamming-gower-memchi2-memchord-memeuclidean-mempearson", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan", "", "", "",true,false); parameters.push_back(pcalc);
+               CommandParameter pcalc("calc", "Multiple", "sharedchao-sharedsobs-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-whittaker-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-structchi2-hamming-gower-memchi2-memchord-memeuclidean-mempearson", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan", "", "", "",true,false); parameters.push_back(pcalc);
                CommandParameter pall("all", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pall);
                CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
                CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
@@ -161,7 +161,7 @@ SummarySharedCommand::SummarySharedCommand(string option)  {
                                sharedfile = m->getSharedFile(); 
                                if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
-                       }
+                       }else { m->setSharedFile(sharedfile); }
                        
                        
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
@@ -194,7 +194,7 @@ SummarySharedCommand::SummarySharedCommand(string option)  {
                        if (groups == "not found") { groups = ""; }
                        else { 
                                m->splitAtDash(groups, Groups);
-                               m->Groups = Groups;
+                               m->setGroups(Groups);
                        }
                        
                        string temp = validParameter.validFile(parameters, "all", false);                               if (temp == "not found") { temp = "false"; }
@@ -364,23 +364,23 @@ int SummarySharedCommand::execute(){
                        for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
                        
                        //close files and clean up
-                       remove(outputFileName.c_str());
-                       if (mult == true) { remove(outAllFileName.c_str());  }
+                       m->mothurRemove(outputFileName);
+                       if (mult == true) { m->mothurRemove(outAllFileName);  }
                        return 0;
                //if you only have 2 groups you don't need a .sharedmultiple file
                }else if ((lookup.size() == 2) && (mult == true)) { 
                        mult = false;
-                       remove(outAllFileName.c_str());
+                       m->mothurRemove(outAllFileName);
                        outputNames.pop_back();
                }
                
                if (m->control_pressed) {
-                       if (mult) {  remove(outAllFileName.c_str());  }
-                       remove(outputFileName.c_str()); 
+                       if (mult) {  m->mothurRemove(outAllFileName);  }
+                       m->mothurRemove(outputFileName); 
                        delete input;
                        for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
                        for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }
-                       m->Groups.clear(); 
+                       m->clearGroups(); 
                        return 0;
                }
                /******************************************************/
@@ -388,7 +388,7 @@ int SummarySharedCommand::execute(){
                
                /******************************************************/
                //comparison breakup to be used by different processes later
-               numGroups = m->Groups.size();
+               numGroups = m->getNumGroups();
                lines.resize(processors);
                for (int i = 0; i < processors; i++) {
                        lines[i].start = int (sqrt(float(i)/float(processors)) * numGroups);
@@ -403,12 +403,12 @@ int SummarySharedCommand::execute(){
                //as long as you are not at the end of the file or done wih the lines you want
                while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
                        if (m->control_pressed) {
-                               if (mult) {  remove(outAllFileName.c_str());  }
-                               remove(outputFileName.c_str()); 
+                               if (mult) {  m->mothurRemove(outAllFileName);  }
+                               m->mothurRemove(outputFileName); 
                                delete input; 
                                for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
                                for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }
-                               m->Groups.clear(); 
+                               m->clearGroups(); 
                                return 0;
                        }
 
@@ -446,11 +446,11 @@ int SummarySharedCommand::execute(){
                }
                
                if (m->control_pressed) {
-                       if (mult) { remove(outAllFileName.c_str());  }
-                       remove(outputFileName.c_str()); 
+                       if (mult) { m->mothurRemove(outAllFileName);  }
+                       m->mothurRemove(outputFileName); 
                        delete input; 
                        for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }
-                       m->Groups.clear(); 
+                       m->clearGroups(); 
                        return 0;
                }
 
@@ -479,14 +479,14 @@ int SummarySharedCommand::execute(){
                
                                
                //reset groups parameter
-               m->Groups.clear();  
+               m->clearGroups();  
                
                for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }
                delete input;  
                
                if (m->control_pressed) {
-                       remove(outAllFileName.c_str());  
-                       remove(outputFileName.c_str()); 
+                       m->mothurRemove(outAllFileName);  
+                       m->mothurRemove(outputFileName); 
                        return 0;
                }
                
@@ -515,10 +515,10 @@ int SummarySharedCommand::process(vector<SharedRAbundVector*> thisLookup, string
                                if(processors == 1){
                                        driver(thisLookup, 0, numGroups, sumFileName+".temp", sumAllFileName+".temp", calcDists);
                                        m->appendFiles((sumFileName + ".temp"), sumFileName);
-                                       remove((sumFileName + ".temp").c_str());
+                                       m->mothurRemove((sumFileName + ".temp"));
                                        if (mult) {
                                                m->appendFiles((sumAllFileName + ".temp"), sumAllFileName);
-                                               remove((sumAllFileName + ".temp").c_str());
+                                               m->mothurRemove((sumAllFileName + ".temp"));
                                        }
                                }else{
                                        int process = 1;
@@ -561,7 +561,7 @@ int SummarySharedCommand::process(vector<SharedRAbundVector*> thisLookup, string
                                        //parent do your part
                                        driver(thisLookup, lines[0].start, lines[0].end, sumFileName + toString(getpid()) + ".temp", sumAllFileName + toString(getpid()) + ".temp", calcDists);   
                                        m->appendFiles((sumFileName + toString(getpid()) + ".temp"), sumFileName);
-                                       remove((sumFileName + toString(getpid()) + ".temp").c_str());
+                                       m->mothurRemove((sumFileName + toString(getpid()) + ".temp"));
                                        if (mult) { m->appendFiles((sumAllFileName + toString(getpid()) + ".temp"), sumAllFileName); }
                                                
                                        //force parent to wait until all the processes are done
@@ -572,15 +572,15 @@ int SummarySharedCommand::process(vector<SharedRAbundVector*> thisLookup, string
                                        
                                        for (int i = 0; i < processIDS.size(); i++) {
                                                m->appendFiles((sumFileName + toString(processIDS[i]) + ".temp"), sumFileName);
-                                               remove((sumFileName + toString(processIDS[i]) + ".temp").c_str());
-                                               if (mult) {     remove((sumAllFileName + toString(processIDS[i]) + ".temp").c_str());   }
+                                               m->mothurRemove((sumFileName + toString(processIDS[i]) + ".temp"));
+                                               if (mult) {     m->mothurRemove((sumAllFileName + toString(processIDS[i]) + ".temp"));  }
                                                
                                                if (createPhylip) {
                                                        string tempdistFileName = m->getRootName(m->getSimpleName(sumFileName)) + toString(processIDS[i]) +  ".dist";
                                                        ifstream intemp;
                                                        m->openInputFile(tempdistFileName, intemp);
                                                        
-                                                       for (int i = 0; i < calcDists.size(); i++) {
+                                                       for (int k = 0; k < calcDists.size(); k++) {
                                                                int size = 0;
                                                                intemp >> size; m->gobble(intemp);
                                                                        
@@ -592,11 +592,11 @@ int SummarySharedCommand::process(vector<SharedRAbundVector*> thisLookup, string
                                                                        intemp >> seq1 >> seq2 >> dist;   m->gobble(intemp);
                                                                        
                                                                        seqDist tempDist(seq1, seq2, dist);
-                                                                       calcDists[i].push_back(tempDist);
+                                                                       calcDists[k].push_back(tempDist);
                                                                }
                                                        }
                                                        intemp.close();
-                                                       remove(tempdistFileName.c_str());
+                                                       m->mothurRemove(tempdistFileName);
                                                }
                                        }
 
@@ -604,10 +604,10 @@ int SummarySharedCommand::process(vector<SharedRAbundVector*> thisLookup, string
                        #else
                                driver(thisLookup, 0, numGroups, (sumFileName + ".temp"), (sumAllFileName + ".temp"), calcDists);
                                m->appendFiles((sumFileName + ".temp"), sumFileName);
-                               remove((sumFileName + ".temp").c_str());
+                               m->mothurRemove((sumFileName + ".temp"));
                                if (mult) {
                                        m->appendFiles((sumAllFileName + ".temp"), sumAllFileName);
-                                       remove((sumAllFileName + ".temp").c_str());
+                                       m->mothurRemove((sumAllFileName + ".temp"));
                                }
                        #endif
                        
@@ -733,7 +733,7 @@ int SummarySharedCommand::driver(vector<SharedRAbundVector*> thisLookup, int sta
                                        outputFileHandle << '\t';
                                        sumCalculators[i]->print(outputFileHandle);
                                        
-                                       seqDist temp(l, k, (1.0 - tempdata[0]));
+                                       seqDist temp(l, k, tempdata[0]);
                                        calcDists[i].push_back(temp);
                                }
                                outputFileHandle << endl;