X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=aligncommand.cpp;h=a246ecc5806320efeadda6fa82f67fd2f2d99e21;hb=13193e6688c91b6a25e39d357caa7f4b4bf5de5f;hp=38afa3543a0218bcef7602d61a71d9d8e8332f36;hpb=2bbb7273d4bf5209f098c764551c6e072d60df36;p=mothur.git

diff --git a/aligncommand.cpp b/aligncommand.cpp
index 38afa35..a246ecc 100644
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -267,28 +267,35 @@ int AlignCommand::execute(){
 				int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY; 
 				int inMode=MPI_MODE_RDONLY; 
 				
-				char* outAlignFilename = new char[alignFileName.length()];
-				memcpy(outAlignFilename, alignFileName.c_str(), alignFileName.length());
-
-				char* outReportFilename = new char[reportFileName.length()];
-				memcpy(outReportFilename, reportFileName.c_str(), reportFileName.length());
+				//char* outAlignFilename = new char[alignFileName.length()];
+				//memcpy(outAlignFilename, alignFileName.c_str(), alignFileName.length());
+				
+				char outAlignFilename[1024];
+				strcpy(outAlignFilename, alignFileName.c_str());
 
-				char* outAccnosFilename = new char[accnosFileName.length()];
-				memcpy(outAccnosFilename, accnosFileName.c_str(), accnosFileName.length());
+				//char* outReportFilename = new char[reportFileName.length()];
+				//memcpy(outReportFilename, reportFileName.c_str(), reportFileName.length());
+				
+				char outReportFilename[1024];
+				strcpy(outReportFilename, reportFileName.c_str());
 
-				char* inFileName = new char[candidateFileNames[s].length()];
-				memcpy(inFileName, candidateFileNames[s].c_str(), candidateFileNames[s].length());
+				//char* outAccnosFilename = new char[accnosFileName.length()];
+				//memcpy(outAccnosFilename, accnosFileName.c_str(), accnosFileName.length());
+				
+				char outAccnosFilename[1024];
+				strcpy(outAccnosFilename, accnosFileName.c_str());
 
+				//char* inFileName = new char[candidateFileNames[s].length()];
+				//memcpy(inFileName, candidateFileNames[s].c_str(), candidateFileNames[s].length());
+				
+				char inFileName[1024];
+				strcpy(inFileName, candidateFileNames[s].c_str());
+				
 				MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 				MPI_File_open(MPI_COMM_WORLD, outAlignFilename, outMode, MPI_INFO_NULL, &outMPIAlign);
 				MPI_File_open(MPI_COMM_WORLD, outReportFilename, outMode, MPI_INFO_NULL, &outMPIReport);
 				MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
 				
-				delete outAlignFilename;
-				delete inFileName;
-				delete outReportFilename;
-				delete outAccnosFilename;
-
 				if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIAlign);  MPI_File_close(&outMPIReport);  MPI_File_close(&outMPIAccnos); return 0; }
 				
 				if (pid == 0) { //you are the root process 
@@ -301,8 +308,9 @@ int AlignCommand::execute(){
 					
 					//figure out how many sequences you have to align
 					numSeqsPerProcessor = numFastaSeqs / processors;
-					if(pid == (processors - 1)){	numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor; 	}
 					int startIndex =  pid * numSeqsPerProcessor;
+					if(pid == (processors - 1)){	numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor; 	}
+					
 				
 					//align your part
 					driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIAlign, outMPIReport, outMPIAccnos, MPIPos);
@@ -321,8 +329,9 @@ int AlignCommand::execute(){
 					
 					//figure out how many sequences you have to align
 					numSeqsPerProcessor = numFastaSeqs / processors;
-					if(pid == (processors - 1)){	numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor; 	}
 					int startIndex =  pid * numSeqsPerProcessor;
+					if(pid == (processors - 1)){	numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor; 	}
+					
 					
 					//align your part
 					driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIAlign, outMPIReport, outMPIAccnos, MPIPos);