fixed bug in windows summary.seqs and summary.qual paralellization. paralellized...

[mothur.git] / seqsummarycommand.cpp

diff --git a/seqsummarycommand.cpp b/seqsummarycommand.cpp
index be75e4fac4ab60697b0dd84de6eeb275d231a5b3..647334af7f8d66711c8db37b8d6fd00f9a9e38bb 100644 (file)
--- a/seqsummarycommand.cpp
+++ b/seqsummarycommand.cpp
@@ -131,9 +131,13 @@ SeqSummaryCommand::SeqSummaryCommand(string option)  {
                        
                        string temp = validParameter.validFile(parameters, "processors", false);        if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors);
-
-
+                       m->mothurConvert(temp, processors);
+                       
+                       if (namefile == "") {
+                               vector<string> files; files.push_back(fastafile);
+                               parser.getNameFile(files);
+                       }
+                       
                }
        }
        catch(exception& e) {
@@ -317,6 +321,19 @@ int SeqSummaryCommand::execute(){
                sort(ambigBases.begin(), ambigBases.end());
                sort(longHomoPolymer.begin(), longHomoPolymer.end());
                int size = startPosition.size();
+               
+               //find means
+               float meanStartPosition, meanEndPosition, meanSeqLength, meanAmbigBases, meanLongHomoPolymer;
+               meanStartPosition = 0; meanEndPosition = 0; meanSeqLength = 0; meanAmbigBases = 0; meanLongHomoPolymer = 0;
+               for (int i = 0; i < size; i++) {
+                       meanStartPosition += startPosition[i];
+                       meanEndPosition += endPosition[i];
+                       meanSeqLength += seqLength[i];
+                       meanAmbigBases += ambigBases[i];
+                       meanLongHomoPolymer += longHomoPolymer[i];
+               }
+               //this is an int divide so the remainder is lost
+               meanStartPosition /= (float) size; meanEndPosition /= (float) size; meanLongHomoPolymer /= (float) size; meanSeqLength /= (float) size; meanAmbigBases /= (float) size;
                                
                int ptile0_25   = int(size * 0.025);
                int ptile25             = int(size * 0.250);
@@ -340,6 +357,8 @@ int SeqSummaryCommand::execute(){
                m->mothurOut("75%-tile:\t" + toString(startPosition[ptile75]) + "\t" + toString(endPosition[ptile75]) + "\t" + toString(seqLength[ptile75]) + "\t" + toString(ambigBases[ptile75]) + "\t" + toString(longHomoPolymer[ptile75]) + "\t" + toString(ptile75+1)); m->mothurOutEndLine();
                m->mothurOut("97.5%-tile:\t" + toString(startPosition[ptile97_5]) + "\t" + toString(endPosition[ptile97_5]) + "\t" + toString(seqLength[ptile97_5]) + "\t" + toString(ambigBases[ptile97_5]) + "\t" + toString(longHomoPolymer[ptile97_5]) + "\t" + toString(ptile97_5+1)); m->mothurOutEndLine();
                m->mothurOut("Maximum:\t" + toString(startPosition[ptile100]) + "\t" + toString(endPosition[ptile100]) + "\t" + toString(seqLength[ptile100]) + "\t" + toString(ambigBases[ptile100]) + "\t" + toString(longHomoPolymer[ptile100]) + "\t" + toString(ptile100+1)); m->mothurOutEndLine();
+               m->mothurOut("Mean:\t" + toString(meanStartPosition) + "\t" + toString(meanEndPosition) + "\t" + toString(meanSeqLength) + "\t" + toString(meanAmbigBases) + "\t" + toString(meanLongHomoPolymer)); m->mothurOutEndLine();
+
                if (namefile == "") {  m->mothurOut("# of Seqs:\t" + toString(numSeqs)); m->mothurOutEndLine(); }
                else { m->mothurOut("# of unique seqs:\t" + toString(numSeqs)); m->mothurOutEndLine(); m->mothurOut("total # of seqs:\t" + toString(startPosition.size())); m->mothurOutEndLine(); }
                
@@ -584,34 +603,42 @@ int SeqSummaryCommand::createProcessesCreateSummary(vector<int>& startPosition,
                //////////////////////////////////////////////////////////////////////////////////////////////////////
                
                vector<seqSumData*> pDataArray; 
-               DWORD   dwThreadIdArray[processors];
-               HANDLE  hThreadArray[processors]; 
+               DWORD   dwThreadIdArray[processors-1];
+               HANDLE  hThreadArray[processors-1]; 
                
                //Create processor worker threads.
-               for( int i=0; i<processors; i++ ){
-                       
-                       //cout << i << '\t' << lines[i]->start << '\t' << lines[i]->end << endl;
+               for( int i=0; i<processors-1; i++ ){
+            
+            string extension = "";
+            if (i != 0) { extension = toString(i) + ".temp"; processIDS.push_back(i); }
                        // Allocate memory for thread data.
-                       seqSumData* tempSum = new seqSumData(&startPosition, &endPosition, &seqLength, &ambigBases, &longHomoPolymer, filename, (sumFile + toString(i) + ".temp"), m, lines[i]->start, lines[i]->end, namefile, nameMap);
+                       seqSumData* tempSum = new seqSumData(filename, (sumFile+extension), m, lines[i]->start, lines[i]->end, namefile, nameMap);
                        pDataArray.push_back(tempSum);
-                       processIDS.push_back(i);
-                               
+                       
                        //MySeqSumThreadFunction is in header. It must be global or static to work with the threads.
                        //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
                        hThreadArray[i] = CreateThread(NULL, 0, MySeqSumThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);   
                }
-                       
+               
+        //do your part
+               num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, (sumFile+toString(processors-1)+".temp"), lines[processors-1]);
+        processIDS.push_back(processors-1);
+
                //Wait until all threads have terminated.
-               WaitForMultipleObjects(processors, hThreadArray, TRUE, INFINITE);
+               WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
                
                //Close all thread handles and free memory allocations.
                for(int i=0; i < pDataArray.size(); i++){
                        num += pDataArray[i]->count;
+            for (int k = 0; k < pDataArray[i]->startPosition.size(); k++) {    startPosition.push_back(pDataArray[i]->startPosition[k]);       }
+                       for (int k = 0; k < pDataArray[i]->endPosition.size(); k++) {   endPosition.push_back(pDataArray[i]->endPosition[k]);       }
+            for (int k = 0; k < pDataArray[i]->seqLength.size(); k++) {        seqLength.push_back(pDataArray[i]->seqLength[k]);       }
+            for (int k = 0; k < pDataArray[i]->ambigBases.size(); k++) {       ambigBases.push_back(pDataArray[i]->ambigBases[k]);       }
+            for (int k = 0; k < pDataArray[i]->longHomoPolymer.size(); k++) {  longHomoPolymer.push_back(pDataArray[i]->longHomoPolymer[k]);       }
                        CloseHandle(hThreadArray[i]);
                        delete pDataArray[i];
                }
-               
-               //rename((sumFile + toString(processIDS[0]) + ".temp").c_str(), sumFile.c_str());
+    
                //append files
                for(int i=0;i<processIDS.size();i++){
                        m->appendFiles((sumFile + toString(processIDS[i]) + ".temp"), sumFile);