sped up align.seqs appending of files

diff --git a/aligncommand.cpp b/aligncommand.cpp
index 304848179331ab980730713c5a35998bb54a80bc..7bed27f7725f78425a3c2e8f61f528b24b00c830 100644 (file)
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -422,62 +422,12 @@ int AlignCommand::execute(){
        #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
                        if(processors == 1){
                                numFastaSeqs = driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
-                               
-                               if (m->control_pressed) { remove(accnosFileName.c_str()); remove(alignFileName.c_str()); remove(reportFileName.c_str()); outputTypes.clear(); return 0; }
-                               
-                               //delete accnos file if its blank else report to user
-                               if (m->isBlank(accnosFileName)) {  remove(accnosFileName.c_str());  hasAccnos = false; }
-                               else { 
-                                       m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
-                                       if (!flip) {
-                                               m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well."); 
-                                       }else{  m->mothurOut(" If the reverse compliment proved to be better it was reported.");  }
-                                       m->mothurOutEndLine();
-                               }
                        }else{
-                               processIDS.resize(0);
-                               
                                numFastaSeqs = createProcesses(alignFileName, reportFileName, accnosFileName, candidateFileNames[s]); 
-                               
-                               rename((alignFileName + toString(processIDS[0]) + ".temp").c_str(), alignFileName.c_str());
-                               rename((reportFileName + toString(processIDS[0]) + ".temp").c_str(), reportFileName.c_str());
-                               
-                               //append alignment and report files
-                               for(int i=1;i<processors;i++){
-                                       appendAlignFiles((alignFileName + toString(processIDS[i]) + ".temp"), alignFileName);
-                                       remove((alignFileName + toString(processIDS[i]) + ".temp").c_str());
-                                       
-                                       appendReportFiles((reportFileName + toString(processIDS[i]) + ".temp"), reportFileName);
-                                       remove((reportFileName + toString(processIDS[i]) + ".temp").c_str());
-                               }
-                               
-                               vector<string> nonBlankAccnosFiles;
-                               //delete blank accnos files generated with multiple processes
-                               for(int i=0;i<processors;i++){  
-                                       if (!(m->isBlank(accnosFileName + toString(processIDS[i]) + ".temp"))) {
-                                               nonBlankAccnosFiles.push_back(accnosFileName + toString(processIDS[i]) + ".temp");
-                                       }else { remove((accnosFileName + toString(processIDS[i]) + ".temp").c_str());  }
-                               }
-                               
-                               //append accnos files
-                               if (nonBlankAccnosFiles.size() != 0) { 
-                                       rename(nonBlankAccnosFiles[0].c_str(), accnosFileName.c_str());
-                                       
-                                       for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
-                                               appendAlignFiles(nonBlankAccnosFiles[h], accnosFileName);
-                                               remove(nonBlankAccnosFiles[h].c_str());
-                                       }
-                                       m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
-                                       if (!flip) {
-                                               m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well."); 
-                                       }else{  m->mothurOut(" If the reverse compliment proved to be better it was reported.");  }
-                                       m->mothurOutEndLine();
-                               }else{ hasAccnos = false;  }
-                               
-                               if (m->control_pressed) { remove(accnosFileName.c_str()); remove(alignFileName.c_str()); remove(reportFileName.c_str()); outputTypes.clear(); return 0; }
                        }
        #else
                        numFastaSeqs = driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
+       #endif
                        
                        if (m->control_pressed) { remove(accnosFileName.c_str()); remove(alignFileName.c_str()); remove(reportFileName.c_str()); outputTypes.clear();  return 0; }
                        
@@ -490,8 +440,6 @@ int AlignCommand::execute(){
                                }else{  m->mothurOut(" If the reverse compliment proved to be better it was reported.");  }
                                m->mothurOutEndLine();
                        }
-                       
-       #endif
 
 #endif         
 
@@ -827,7 +775,8 @@ int AlignCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& align
 int AlignCommand::createProcesses(string alignFileName, string reportFileName, string accnosFName, string filename) {
        try {
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-               int process = 0;
+               processIDS.resize(0);
+               int process = 1;
                int num = 0;
                //              processIDS.resize(0);
                
@@ -856,18 +805,50 @@ int AlignCommand::createProcesses(string alignFileName, string reportFileName, s
                        }
                }
                
+               //do my part
+               num = driver(lines[0], alignFileName, reportFileName, accnosFName, filename);
+               
                //force parent to wait until all the processes are done
                for (int i=0;i<processors;i++) { 
                        int temp = processIDS[i];
                        wait(&temp);
                }
                
+               vector<string> nonBlankAccnosFiles;
+               if (!(m->isBlank(accnosFName))) { nonBlankAccnosFiles.push_back(accnosFName); }
+               else { remove(accnosFName.c_str()); } //remove so other files can be renamed to it
+                       
                for (int i = 0; i < processIDS.size(); i++) {
                        ifstream in;
                        string tempFile =  alignFileName + toString(processIDS[i]) + ".num.temp";
                        m->openInputFile(tempFile, in);
                        if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
                        in.close(); remove(tempFile.c_str());
+                       
+                       appendAlignFiles((alignFileName + toString(processIDS[i]) + ".temp"), alignFileName);
+                       remove((alignFileName + toString(processIDS[i]) + ".temp").c_str());
+                       
+                       appendReportFiles((reportFileName + toString(processIDS[i]) + ".temp"), reportFileName);
+                       remove((reportFileName + toString(processIDS[i]) + ".temp").c_str());
+                       
+                       if (!(m->isBlank(accnosFName + toString(processIDS[i]) + ".temp"))) {
+                               nonBlankAccnosFiles.push_back(accnosFName + toString(processIDS[i]) + ".temp");
+                       }else { remove((accnosFName + toString(processIDS[i]) + ".temp").c_str());  }
+                       
+               }
+               
+               //append accnos files
+               if (nonBlankAccnosFiles.size() != 0) { 
+                       rename(nonBlankAccnosFiles[0].c_str(), accnosFName.c_str());
+                       
+                       for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
+                               appendAlignFiles(nonBlankAccnosFiles[h], accnosFName);
+                               remove(nonBlankAccnosFiles[h].c_str());
+                       }
+               }else { //recreate the accnosfile if needed
+                       ofstream out;
+                       m->openOutputFile(accnosFName, out);
+                       out.close();
                }
                
                return num;