X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=filterseqscommand.cpp;h=a6290a6afe55a28001e5e229e518a7c03c6a1c28;hb=cd985cf388dcc4c7de8251339206aec5f7e12f1e;hp=b64e2f530ff91af78cc69dea71b9d2f53f3f981b;hpb=a61980e36d61937acccadc41be260165a1e389f4;p=mothur.git

diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp
index b64e2f5..a6290a6 100644
--- a/filterseqscommand.cpp
+++ b/filterseqscommand.cpp
@@ -282,13 +282,16 @@ int FilterSeqsCommand::filterSequences() {
 					numSeqs += num;
 					
 					//send file positions to all processes
-					MPI_Bcast(&num, 1, MPI_INT, 0, MPI_COMM_WORLD);  //send numSeqs
-					MPI_Bcast(&MPIPos[0], (num+1), MPI_LONG, 0, MPI_COMM_WORLD); //send file pos	
+					for(int i = 1; i < processors; i++) { 
+						MPI_Send(&num, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
+						MPI_Send(&MPIPos[0], (num+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
+					}
 					
 					//figure out how many sequences you have to do
 					numSeqsPerProcessor = num / processors;
-					if(pid == (processors - 1)){	numSeqsPerProcessor = num - pid * numSeqsPerProcessor; 	}
 					int startIndex =  pid * numSeqsPerProcessor;
+					if(pid == (processors - 1)){	numSeqsPerProcessor = num - pid * numSeqsPerProcessor; 	}
+					
 				
 					//do your part
 					driverMPIRun(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
@@ -302,15 +305,16 @@ int FilterSeqsCommand::filterSequences() {
 					}
 					
 				}else { //you are a child process
-					MPI_Bcast(&num, 1, MPI_INT, 0, MPI_COMM_WORLD); //get numSeqs
-					numSeqs += num;
+					MPI_Recv(&num, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 					MPIPos.resize(num+1);
-					MPI_Bcast(&MPIPos[0], (num+1), MPI_LONG, 0, MPI_COMM_WORLD); //get file positions
+					numSeqs += num;
+					MPI_Recv(&MPIPos[0], (num+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 					
 					//figure out how many sequences you have to align
 					numSeqsPerProcessor = num / processors;
-					if(pid == (processors - 1)){	numSeqsPerProcessor = num - pid * numSeqsPerProcessor; 	}
 					int startIndex =  pid * numSeqsPerProcessor;
+					if(pid == (processors - 1)){	numSeqsPerProcessor = num - pid * numSeqsPerProcessor; 	}
+					
 					
 					//align your part
 					driverMPIRun(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);		
@@ -326,17 +330,21 @@ int FilterSeqsCommand::filterSequences() {
 				
 				MPI_File_close(&outMPI);
 				MPI_File_close(&inMPI);
+				MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 				
 #else
 		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 				if(processors == 1){
 					ifstream inFASTA;
+					int numFastaSeqs;
 					openInputFile(fastafileNames[s], inFASTA);
-					int numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+					getNumSeqs(inFASTA, numFastaSeqs);
 					inFASTA.close();
 					
 					lines.push_back(new linePair(0, numFastaSeqs));
 					
+					numSeqs += numFastaSeqs;
+					
 					driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]);
 				}else{
 					setLines(fastafileNames[s]);
@@ -354,12 +362,15 @@ int FilterSeqsCommand::filterSequences() {
 				if (m->control_pressed) {  return 1; }
 		#else
 				ifstream inFASTA;
+				int numFastaSeqs;
 				openInputFile(fastafileNames[s], inFASTA);
-				int numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+				getNumSeqs(inFASTA, numFastaSeqs);
 				inFASTA.close();
 					
 				lines.push_back(new linePair(0, numFastaSeqs));
 				
+				numSeqs += numFastaSeqs;
+				
 				driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]);
 
 				if (m->control_pressed) {  return 1; }
@@ -537,7 +548,7 @@ string FilterSeqsCommand::createFilter() {
 		
 		F.setLength(alignmentLength);
 		
-		if(soft != 0 || isTrue(vertical)){
+		if(trump != '*' || isTrue(vertical) || soft != 0){
 			F.initialize();
 		}
 		
@@ -575,13 +586,16 @@ string FilterSeqsCommand::createFilter() {
 						numSeqs += num;
 						
 						//send file positions to all processes
-						MPI_Bcast(&num, 1, MPI_INT, 0, MPI_COMM_WORLD);  //send numSeqs
-						MPI_Bcast(&MPIPos[0], (num+1), MPI_LONG, 0, MPI_COMM_WORLD); //send file pos	
+						for(int i = 1; i < processors; i++) { 
+							MPI_Send(&num, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
+							MPI_Send(&MPIPos[0], (num+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
+						}
 								
 						//figure out how many sequences you have to do
 						numSeqsPerProcessor = num / processors;
-						if(pid == (processors - 1)){	numSeqsPerProcessor = num - pid * numSeqsPerProcessor; 	}
 						int startIndex =  pid * numSeqsPerProcessor;
+						if(pid == (processors - 1)){	numSeqsPerProcessor = num - pid * numSeqsPerProcessor; 	}
+						
 				
 						//do your part
 						MPICreateFilter(startIndex, numSeqsPerProcessor, F, inMPI, MPIPos);
@@ -589,16 +603,16 @@ string FilterSeqsCommand::createFilter() {
 						if (m->control_pressed) {  MPI_File_close(&inMPI);  return 0;  }
 												
 				}else { //i am the child process
-			
-					MPI_Bcast(&num, 1, MPI_INT, 0, MPI_COMM_WORLD); //get numSeqs
+					MPI_Recv(&num, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 					MPIPos.resize(num+1);
 					numSeqs += num;
-					MPI_Bcast(&MPIPos[0], (num+1), MPI_LONG, 0, MPI_COMM_WORLD); //get file positions
+					MPI_Recv(&MPIPos[0], (num+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 					
 					//figure out how many sequences you have to align
 					numSeqsPerProcessor = num / processors;
-					if(pid == (processors - 1)){	numSeqsPerProcessor = num - pid * numSeqsPerProcessor; 	}
 					int startIndex =  pid * numSeqsPerProcessor;
+					if(pid == (processors - 1)){	numSeqsPerProcessor = num - pid * numSeqsPerProcessor; 	}
+					
 					
 					//do your part
 					MPICreateFilter(startIndex, numSeqsPerProcessor, F, inMPI,  MPIPos);
@@ -607,13 +621,15 @@ string FilterSeqsCommand::createFilter() {
 				}
 				
 				MPI_File_close(&inMPI);
+				MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 				
 #else
 		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 				if(processors == 1){
 					ifstream inFASTA;
+					int numFastaSeqs;
 					openInputFile(fastafileNames[s], inFASTA);
-					int numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+					getNumSeqs(inFASTA, numFastaSeqs);
 					inFASTA.close();
 					
 					numSeqs += numFastaSeqs;
@@ -629,8 +645,9 @@ string FilterSeqsCommand::createFilter() {
 				if (m->control_pressed) {  return filterString; }
 		#else
 				ifstream inFASTA;
+				int numFastaSeqs;
 				openInputFile(fastafileNames[s], inFASTA);
-				int numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+				getNumSeqs(inFASTA, numFastaSeqs);
 				inFASTA.close();
 				
 				numSeqs += numFastaSeqs;
@@ -660,20 +677,24 @@ string FilterSeqsCommand::createFilter() {
 				vector<int> temp; temp.resize(alignmentLength+1);
 								
 				//get the frequencies from the child processes
-				for(int i = 0; i < ((processors-1)*5); i++) { 
-					MPI_Recv(&temp[0], (alignmentLength+1), MPI_INT, MPI_ANY_SOURCE, 2001, MPI_COMM_WORLD, &status); 
-					int receiveTag = temp[temp.size()-1];  //child process added a int to the end to indicate what letter count this is for
-					
-					if (receiveTag == Atag) { //you are recieveing the A frequencies
-						for (int k = 0; k < alignmentLength; k++) {		F.a[k] += temp[k];	}
-					}else if (receiveTag == Ttag) { //you are recieveing the T frequencies
-						for (int k = 0; k < alignmentLength; k++) {		F.t[k] += temp[k];	}
-					}else if (receiveTag == Ctag) { //you are recieveing the C frequencies
-						for (int k = 0; k < alignmentLength; k++) {		F.c[k] += temp[k];	}
-					}else if (receiveTag == Gtag) { //you are recieveing the G frequencies
-						for (int k = 0; k < alignmentLength; k++) {		F.g[k] += temp[k];	}
-					}else if (receiveTag == Gaptag) { //you are recieveing the gap frequencies
-						for (int k = 0; k < alignmentLength; k++) {		F.gap[k] += temp[k];	}
+				for(int i = 1; i < processors; i++) { 
+				
+					for (int j = 0; j < 5; j++) {
+					
+						MPI_Recv(&temp[0], (alignmentLength+1), MPI_INT, i, 2001, MPI_COMM_WORLD, &status); 
+						int receiveTag = temp[temp.size()-1];  //child process added a int to the end to indicate what letter count this is for
+						
+						if (receiveTag == Atag) { //you are recieveing the A frequencies
+							for (int k = 0; k < alignmentLength; k++) {		F.a[k] += temp[k];	}
+						}else if (receiveTag == Ttag) { //you are recieveing the T frequencies
+							for (int k = 0; k < alignmentLength; k++) {		F.t[k] += temp[k];	}
+						}else if (receiveTag == Ctag) { //you are recieveing the C frequencies
+							for (int k = 0; k < alignmentLength; k++) {		F.c[k] += temp[k];	}
+						}else if (receiveTag == Gtag) { //you are recieveing the G frequencies
+							for (int k = 0; k < alignmentLength; k++) {		F.g[k] += temp[k];	}
+						}else if (receiveTag == Gaptag) { //you are recieveing the gap frequencies
+							for (int k = 0; k < alignmentLength; k++) {		F.gap[k] += temp[k];	}
+						}
 					}
 				} 
 			}else{
@@ -693,6 +714,8 @@ string FilterSeqsCommand::createFilter() {
 			
 		}
 		
+		MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
+		
 		if (pid == 0) { //only one process should output the filter
 #endif
 		F.setNumSeqs(numSeqs);
@@ -704,10 +727,14 @@ string FilterSeqsCommand::createFilter() {
 		
 #ifdef USE_MPI
 		//send filter string to kids
-		MPI_Bcast(&filterString[0], alignmentLength, MPI_CHAR, 0, MPI_COMM_WORLD); 
+		//for(int i = 1; i < processors; i++) { 
+		//	MPI_Send(&filterString[0], alignmentLength, MPI_CHAR, i, 2001, MPI_COMM_WORLD);
+		//}
+		MPI_Bcast(&filterString[0], alignmentLength, MPI_CHAR, 0, MPI_COMM_WORLD);
 	}else{
 		//recieve filterString
 		char* tempBuf = new char[alignmentLength];
+		//MPI_Recv(&tempBuf[0], alignmentLength, MPI_CHAR, 0, 2001, MPI_COMM_WORLD, &status);
 		MPI_Bcast(tempBuf, alignmentLength, MPI_CHAR, 0, MPI_COMM_WORLD);
 		
 		filterString = tempBuf;
@@ -717,8 +744,7 @@ string FilterSeqsCommand::createFilter() {
 	
 	MPI_Barrier(MPI_COMM_WORLD);
 #endif
-		
-		
+				
 		return filterString;
 	}
 	catch(exception& e) {