X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=screenseqscommand.cpp;h=7ac910d4a74b9fc1bffeacb32f5893941f3eb60f;hb=ee8403d4eb5760187d62b42a9cf4272de8fc0ec4;hp=9494865c4f66e302182b8fd221e0b44951cb2518;hpb=5d00ef3e809832f08efdd691a9eace8ac20feb07;p=mothur.git

diff --git a/screenseqscommand.cpp b/screenseqscommand.cpp
index 9494865..7ac910d 100644
--- a/screenseqscommand.cpp
+++ b/screenseqscommand.cpp
@@ -288,7 +288,7 @@ int ScreenSeqsCommand::execute(){
 			getSummary(positions); 
 		} 
 		else { 
-			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                 positions = m->divideFile(fastafile, processors);
                 for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(linePair(positions[i], positions[(i+1)])); }
 			#else 
@@ -296,6 +296,7 @@ int ScreenSeqsCommand::execute(){
                 else {
                     int numFastaSeqs = 0;
                     positions = m->setFilePosFasta(fastafile, numFastaSeqs); 
+                    if (positions.size() < processors) { processors = positions.size(); }
                 
                     //figure out how many sequences you have to process
                     int numSeqsPerProcessor = numFastaSeqs / processors;
@@ -398,17 +399,10 @@ int ScreenSeqsCommand::execute(){
 			MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 					
 #else
-						
-	//#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-			if(processors == 1){
-				numFastaSeqs = driver(lines[0], goodSeqFile, badAccnosFile, fastafile, badSeqNames);		
-			}else{
-				numFastaSeqs = createProcesses(goodSeqFile, badAccnosFile, fastafile, badSeqNames); 
-            }
-	//#else
-	//		numFastaSeqs = driver(lines[0], goodSeqFile, badAccnosFile, fastafile, badSeqNames);		
-	//#endif
-            if (m->control_pressed) { m->mothurRemove(goodSeqFile); return 0; }
+        if(processors == 1){ numFastaSeqs = driver(lines[0], goodSeqFile, badAccnosFile, fastafile, badSeqNames);	}	
+        else{ numFastaSeqs = createProcesses(goodSeqFile, badAccnosFile, fastafile, badSeqNames); }
+        
+        if (m->control_pressed) { m->mothurRemove(goodSeqFile); return 0; }
 #endif		
 
 		#ifdef USE_MPI
@@ -618,7 +612,7 @@ int ScreenSeqsCommand::getSummary(vector<unsigned long long>& positions){
 		vector<int> longHomoPolymer;
 		
         vector<unsigned long long> positions;
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 		positions = m->divideFile(fastafile, processors);
 		for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(linePair(positions[i], positions[(i+1)])); }	
 #else
@@ -626,6 +620,7 @@ int ScreenSeqsCommand::getSummary(vector<unsigned long long>& positions){
         else {
             int numFastaSeqs = 0;
             positions = m->setFilePosFasta(fastafile, numFastaSeqs); 
+            if (positions.size() < processors) { processors = positions.size(); }
             
             //figure out how many sequences you have to process
             int numSeqsPerProcessor = numFastaSeqs / processors;
@@ -645,7 +640,7 @@ int ScreenSeqsCommand::getSummary(vector<unsigned long long>& positions){
 			driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[0]);
 #else
 		int numSeqs = 0;
-		//#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+		//#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 			if(processors == 1){
 				numSeqs = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[0]);
 			}else{
@@ -750,7 +745,7 @@ int ScreenSeqsCommand::driverCreateSummary(vector<int>& startPosition, vector<in
 				count++;
 			}
 			//if((count) % 100 == 0){	m->mothurOut("Optimizing sequence: " + toString(count)); m->mothurOutEndLine();		}
-			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 				unsigned long long pos = in.tellg();
 				if ((pos == -1) || (pos >= filePos.end)) { break; }
 			#else
@@ -776,7 +771,7 @@ int ScreenSeqsCommand::createProcessesCreateSummary(vector<int>& startPosition,
 		int num = 0;
 		vector<int> processIDS;
 
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 				
 		//loop through and create all the processes you want
 		while (process != processors) {
@@ -1170,7 +1165,7 @@ int ScreenSeqsCommand::driver(linePair filePos, string goodFName, string badAccn
 			count++;
 			}
 			
-			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 				unsigned long long pos = inFASTA.tellg();
 				if ((pos == -1) || (pos >= filePos.end)) { break; }
 			#else
@@ -1282,7 +1277,7 @@ int ScreenSeqsCommand::createProcesses(string goodFileName, string badAccnos, st
         int process = 1;
 		int num = 0;
 
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 				
 		//loop through and create all the processes you want
 		while (process != processors) {
@@ -1363,7 +1358,7 @@ int ScreenSeqsCommand::createProcesses(string goodFileName, string badAccnos, st
             if (i!=0) {extension += toString(i) + ".temp"; processIDS.push_back(i); }
             
 			// Allocate memory for thread data.
-			sumScreenData* tempSum = new sumScreenData(startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength, filename, m, lines[i].start, lines[i].end,goodFileName+extension, badAccnos+extension, &badSeqNames);
+			sumScreenData* tempSum = new sumScreenData(startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength, filename, m, lines[i].start, lines[i].end,goodFileName+extension, badAccnos+extension);
 			pDataArray.push_back(tempSum);
 			
 			//default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
@@ -1380,6 +1375,7 @@ int ScreenSeqsCommand::createProcesses(string goodFileName, string badAccnos, st
 		//Close all thread handles and free memory allocations.
 		for(int i=0; i < pDataArray.size(); i++){
 			num += pDataArray[i]->count;
+            for (set<string>::iterator it = pDataArray[i]->badSeqNames.begin(); it != pDataArray[i]->badSeqNames.end(); it++) {	badSeqNames.insert(*it);       }
 			CloseHandle(hThreadArray[i]);
 			delete pDataArray[i];
 		}