X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=seqsummarycommand.cpp;h=ee8835386e1937bd8bc6d51ab2b0779f05f6a679;hb=fc1ed1ae1b022719176910ab71993bd6535810ad;hp=2fbf6d1ca616033f4fd52993412f0e720f8187af;hpb=c651c46022761aef61644f78462365d8f767ff0b;p=mothur.git

diff --git a/seqsummarycommand.cpp b/seqsummarycommand.cpp
index 2fbf6d1..ee88353 100644
--- a/seqsummarycommand.cpp
+++ b/seqsummarycommand.cpp
@@ -8,7 +8,7 @@
  */
 
 #include "seqsummarycommand.h"
-#include "sequence.hpp"
+
 
 //**********************************************************************************************************************
 vector<string> SeqSummaryCommand::setParameters(){	
@@ -281,31 +281,30 @@ int SeqSummaryCommand::execute(){
 				
 				MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 #else
-			vector<unsigned long int> positions = m->divideFile(fastafile, processors);
-				
-			for (int i = 0; i < (positions.size()-1); i++) {
-				lines.push_back(new linePair(positions[i], positions[(i+1)]));
-			}	
-
-		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-				if(processors == 1){
-					numSeqs = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, summaryFile, lines[0]);
-				}else{
-					numSeqs = createProcessesCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, summaryFile); 
-					
-					rename((summaryFile + toString(processIDS[0]) + ".temp").c_str(), summaryFile.c_str());
-					//append files
-					for(int i=1;i<processors;i++){
-						m->appendFiles((summaryFile + toString(processIDS[i]) + ".temp"), summaryFile);
-						m->mothurRemove((summaryFile + toString(processIDS[i]) + ".temp"));
-					}
+			vector<unsigned long int> positions; 
+			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+				positions = m->divideFile(fastafile, processors);
+				for (int i = 0; i < (positions.size()-1); i++) {	lines.push_back(new linePair(positions[i], positions[(i+1)]));	}
+			#else
+				positions = m->setFilePosFasta(fastafile, numSeqs); 
+		
+				//figure out how many sequences you have to process
+				int numSeqsPerProcessor = numSeqs / processors;
+				for (int i = 0; i < processors; i++) {
+					int startIndex =  i * numSeqsPerProcessor;
+					if(i == (processors - 1)){	numSeqsPerProcessor = numSeqs - i * numSeqsPerProcessor; 	}
+					lines.push_back(new linePair(positions[startIndex], numSeqsPerProcessor));
 				}
-				
-				if (m->control_pressed) {  return 0; }
-		#else
+			#endif
+			
+
+			if(processors == 1){
 				numSeqs = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, summaryFile, lines[0]);
-				if (m->control_pressed) {  return 0; }
-		#endif
+			}else{
+				numSeqs = createProcessesCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, summaryFile); 
+			}
+			
+			if (m->control_pressed) {  return 0; }
 #endif
 			
 		#ifdef USE_MPI
@@ -507,11 +506,12 @@ int SeqSummaryCommand::MPICreateSummary(int start, int num, vector<int>& startPo
 /**************************************************************************************************/
 int SeqSummaryCommand::createProcessesCreateSummary(vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, string filename, string sumFile) {
 	try {
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-		int process = 0;
+		int process = 1;
 		int num = 0;
 		processIDS.clear();
 		
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+		
 		//loop through and create all the processes you want
 		while (process != processors) {
 			int pid = fork();
@@ -545,8 +545,11 @@ int SeqSummaryCommand::createProcessesCreateSummary(vector<int>& startPosition,
 			}
 		}
 		
+		//do your part
+		num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, sumFile, lines[0]);
+
 		//force parent to wait until all the processes are done
-		for (int i=0;i<processors;i++) { 
+		for (int i=0;i<processIDS.size();i++) { 
 			int temp = processIDS[i];
 			wait(&temp);
 		}
@@ -568,10 +571,54 @@ int SeqSummaryCommand::createProcessesCreateSummary(vector<int>& startPosition,
 				
 			in.close();
 			m->mothurRemove(tempFilename);
+			
+			m->appendFiles((sumFile + toString(processIDS[i]) + ".temp"), sumFile);
+			m->mothurRemove((sumFile + toString(processIDS[i]) + ".temp"));
 		}
 		
-		return num;
+#else
+		//////////////////////////////////////////////////////////////////////////////////////////////////////
+		//Windows version shared memory, so be careful when passing variables through the seqSumData struct. 
+		//Above fork() will clone, so memory is separate, but that's not the case with windows, 
+		//Taking advantage of shared memory to allow both threads to add info to vectors.
+		//////////////////////////////////////////////////////////////////////////////////////////////////////
+		
+		vector<seqSumData*> pDataArray; 
+		DWORD   dwThreadIdArray[processors];
+		HANDLE  hThreadArray[processors]; 
+		
+		//Create processor worker threads.
+		for( int i=0; i<processors; i++ ){
+			
+			//cout << i << '\t' << lines[i]->start << '\t' << lines[i]->end << endl;
+			// 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);
+			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]);   
+		}
+			
+		//Wait until all threads have terminated.
+		WaitForMultipleObjects(processors, hThreadArray, TRUE, INFINITE);
+		
+		//Close all thread handles and free memory allocations.
+		for(int i=0; i < pDataArray.size(); i++){
+			num += pDataArray[i]->count;
+			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);
+			m->mothurRemove((sumFile + toString(processIDS[i]) + ".temp"));
+		}
 #endif		
+		return num;
 	}
 	catch(exception& e) {
 		m->errorOut(e, "SeqSummaryCommand", "createProcessesCreateSummary");