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

[mothur.git] / aligncommand.cpp

diff --git a/aligncommand.cpp b/aligncommand.cpp
index 87ceb2c41a2f22e8a3b55a672641a06095f7f0f2..05ecd46ac6a3e192d834c6f26cdb5e1aa533cb71 100644 (file)
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -302,7 +302,7 @@ int AlignCommand::execute(){
        try {
                if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 
-               templateDB = new AlignmentDB(templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch);
+               templateDB = new AlignmentDB(templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch, rand());
                
                for (int s = 0; s < candidateFileNames.size(); s++) {
                        if (m->control_pressed) { outputTypes.clear(); return 0; }
@@ -431,14 +431,18 @@ int AlignCommand::execute(){
                        positions = m->divideFile(candidateFileNames[s], processors);
                        for (int i = 0; i < (positions.size()-1); i++) {        lines.push_back(new linePair(positions[i], positions[(i+1)]));  }
                #else
-                       positions = m->setFilePosFasta(candidateFileNames[s], numFastaSeqs); 
-                       
-                       //figure out how many sequences you have to process
-                       int numSeqsPerProcessor = numFastaSeqs / processors;
-                       for (int i = 0; i < processors; i++) {
-                               int startIndex =  i * numSeqsPerProcessor;
-                               if(i == (processors - 1)){      numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;   }
-                               lines.push_back(new linePair(positions[startIndex], numSeqsPerProcessor));
+                       if (processors == 1) {
+                               lines.push_back(new linePair(0, 1000));
+                       }else {
+                               positions = m->setFilePosFasta(candidateFileNames[s], numFastaSeqs); 
+                               
+                               //figure out how many sequences you have to process
+                               int numSeqsPerProcessor = numFastaSeqs / processors;
+                               for (int i = 0; i < processors; i++) {
+                                       int startIndex =  i * numSeqsPerProcessor;
+                                       if(i == (processors - 1)){      numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;   }
+                                       lines.push_back(new linePair(positions[startIndex], numSeqsPerProcessor));
+                               }
                        }
                #endif
                        
@@ -919,7 +923,7 @@ int AlignCommand::createProcesses(string alignFileName, string reportFileName, s
                        string extension = "";
                        if (i != 0) { extension = toString(i) + ".temp"; }
                        
-                       alignData* tempalign = new alignData((alignFileName + extension), (reportFileName + extension), (accnosFName + extension), filename, align, search, kmerSize, m, lines[i]->start, lines[i]->end, flip, match, misMatch, gapOpen, gapExtend, threshold);
+                       alignData* tempalign = new alignData((alignFileName + extension), (reportFileName + extension), (accnosFName + extension), filename, align, search, kmerSize, m, lines[i]->start, lines[i]->end, flip, match, misMatch, gapOpen, gapExtend, threshold, i);
                        pDataArray.push_back(tempalign);
                        processIDS.push_back(i);