added sequence name to error string in fastq.info. Changed np_shannon to npshannon.

[mothur.git] / summarysharedcommand.cpp

diff --git a/summarysharedcommand.cpp b/summarysharedcommand.cpp
index b3b4b1869f4368c3c7555d5a711e95acb54c9283..7116e46e0f9e96045fc3c60a717ae41819949118 100644 (file)
--- a/summarysharedcommand.cpp
+++ b/summarysharedcommand.cpp
@@ -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"; }
@@ -205,7 +205,7 @@ SummarySharedCommand::SummarySharedCommand(string option)  {
                        
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors); 
+                       m->mothurConvert(temp, processors); 
                        
                        if (abort == 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
@@ -572,8 +572,8 @@ 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";
@@ -596,7 +596,7 @@ int SummarySharedCommand::process(vector<SharedRAbundVector*> thisLookup, string
                                                                }
                                                        }
                                                        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