fixed phylo.diversity and made trim.seqs with allfiles=T open one file at a time.

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 1f8dc579a986350d51d88f3be2e84cd9617f90d7..56fd8c54b53aaff9f4e43e8e694fc71f6987fd7c 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -481,22 +481,40 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                }
                
                ofstream outGroups;
-               vector<ofstream*> fastaFileNames;
-               vector<ofstream*> qualFileNames;
+               //vector<ofstream*> fastaFileNames;
+               //vector<ofstream*> qualFileNames;
                
                if (oligoFile != "") {          
                        m->openOutputFile(groupFile, outGroups);   
                        for (int i = 0; i < fastaNames.size(); i++) {
 
                        #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-                               fastaFileNames.push_back(new ofstream((fastaNames[i] + toString(getpid()) + ".temp").c_str(), ios::ate)); 
+                               fastaNames[i] = (fastaNames[i] + toString(getpid()) + ".temp");
+                               //fastaFileNames.push_back(new ofstream((fastaNames[i] + toString(getpid()) + ".temp").c_str(), ios::ate)); 
+                               //clear old file if it exists
+                               ofstream temp;
+                               m->openOutputFile(fastaNames[i], temp);
+                               temp.close();
                                if(qFileName != ""){
-                                       qualFileNames.push_back(new ofstream((qualNames[i] + toString(getpid()) + ".temp").c_str(), ios::ate)); 
+                                       qualNames[i] = (qualNames[i] + toString(getpid()) + ".temp");
+                                       //qualFileNames.push_back(new ofstream((qualNames[i] + toString(getpid()) + ".temp").c_str(), ios::ate)); 
+                                       //clear old file if it exists
+                                       ofstream temp2;
+                                       m->openOutputFile(qualNames[i], temp2);
+                                       temp2.close();
                                }
                        #else
-                               fastaFileNames.push_back(new ofstream((fastaNames[i] + toString(i) + ".temp").c_str(), ios::ate));                      
+                               //fastaFileNames.push_back(new ofstream((fastaNames[i] + toString(i) + ".temp").c_str(), ios::ate)); 
+                               fastaNames[i] = (fastaNames[i] + toString(i) + ".temp");
+                               ofstream temp;
+                               m->openOutputFile(fastaNames[i], temp);
+                               temp.close();                   
                                if(qFileName != ""){
-                                       qualFileNames.push_back(new ofstream((qualNames[i] + toString(i) + ".temp").c_str(), ios::ate));                        
+                                       //qualFileNames.push_back(new ofstream((qualNames[i] + toString(i) + ".temp").c_str(), ios::ate));      
+                                       qualNames[i] = (qualNames[i] + toString(i) + ".temp");
+                                       ofstream temp2;
+                                       m->openOutputFile(qualNames[i], temp2);
+                                       temp2.close();          
                                }
                        #endif
                        }
@@ -518,11 +536,11 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                                inFASTA.close(); outFASTA.close(); scrapFASTA.close();
                                if (oligoFile != "") {   outGroups.close();   }
                                
-                               for(int i=0;i<fastaFileNames.size();i++){  fastaFileNames[i]->close(); delete fastaFileNames[i];  }     
+                               //for(int i=0;i<fastaFileNames.size();i++){  fastaFileNames[i]->close(); delete fastaFileNames[i];  }   
 
                                if(qFileName != ""){
                                        qFile.close();
-                                       for(int i=0;i<qualFileNames.size();i++){  qualFileNames[i]->close(); delete qualFileNames[i];  }        
+                                       //for(int i=0;i<qualFileNames.size();i++){  qualFileNames[i]->close(); delete qualFileNames[i];  }      
                                }
                                for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); }
 
@@ -609,10 +627,18 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                                                }
                                                outGroups << currSeq.getName() << '\t' << thisGroup << endl;
                                                if(allFiles){
-                                                       currSeq.printSequence(*fastaFileNames[indexToFastaFile]);
+                                                       ofstream outTemp;
+                                                       m->openOutputFileAppend(fastaNames[indexToFastaFile], outTemp);
+                                                       //currSeq.printSequence(*fastaFileNames[indexToFastaFile]);
+                                                       currSeq.printSequence(outTemp);
+                                                       outTemp.close();
                                                        
                                                        if(qFileName != ""){
-                                                               currQual.printQScores(*qualFileNames[indexToFastaFile]);                                                        
+                                                               //currQual.printQScores(*qualFileNames[indexToFastaFile]);
+                                                               ofstream outTemp2;
+                                                               m->openOutputFileAppend(qualNames[indexToFastaFile], outTemp2);
+                                                               currQual.printQScores(outTemp2);
+                                                               outTemp2.close();                                                       
                                                        }
                                                }
                                        }
@@ -648,17 +674,17 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                if (oligoFile != "") {   outGroups.close();   }
                if(qFileName != "")     {       qFile.close();  scrapQual.close(); outQual.close();     }
                
-               for(int i=0;i<fastaFileNames.size();i++){
-                       fastaFileNames[i]->close();
-                       delete fastaFileNames[i];
-               }               
-               
-               if(qFileName != ""){
-                       for(int i=0;i<qualFileNames.size();i++){
-                               qualFileNames[i]->close();
-                               delete qualFileNames[i];
-                       }               
-               }                       
+               //for(int i=0;i<fastaFileNames.size();i++){
+               //      fastaFileNames[i]->close();
+               //      delete fastaFileNames[i];
+               //}             
+               
+               //if(qFileName != ""){
+                       //for(int i=0;i<qualFileNames.size();i++){
+                               //qualFileNames[i]->close();
+                               //delete qualFileNames[i];
+                       //}             
+               //}                     
                
                return count;
        }