a few modifications for 1.9

[mothur.git] / classifyseqscommand.cpp

diff --git a/classifyseqscommand.cpp b/classifyseqscommand.cpp
index e4fcb2b9b61c926dfe996d5c643934cc9a926739..bed65806ca72aecc1c26536e1dcbbe6d74b8b67b 100644 (file)
--- a/classifyseqscommand.cpp
+++ b/classifyseqscommand.cpp
@@ -328,22 +328,31 @@ int ClassifySeqsCommand::execute(){
                                int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY; 
                                int inMode=MPI_MODE_RDONLY; 
                                
-                               char* outNewTax = new char[newTaxonomyFile.length()];\r
-                               memcpy(outNewTax, newTaxonomyFile.c_str(), newTaxonomyFile.length());
-                       
-                               char* outTempTax = new char[tempTaxonomyFile.length()];\r
-                               memcpy(outTempTax, tempTaxonomyFile.c_str(), tempTaxonomyFile.length());
+                               //char* outNewTax = new char[newTaxonomyFile.length()];
+                               //memcpy(outNewTax, newTaxonomyFile.c_str(), newTaxonomyFile.length());
+                               
+                               char outNewTax[1024];
+                               strcpy(outNewTax, newTaxonomyFile.c_str());
+
+                               //char* outTempTax = new char[tempTaxonomyFile.length()];
+                               //memcpy(outTempTax, tempTaxonomyFile.c_str(), tempTaxonomyFile.length());
+                               
+                               char outTempTax[1024];
+                               strcpy(outTempTax, tempTaxonomyFile.c_str());
 
-                               char* inFileName = new char[fastaFileNames[s].length()];\r
-                               memcpy(inFileName, fastaFileNames[s].c_str(), fastaFileNames[s].length());
+                               //char* inFileName = new char[fastaFileNames[s].length()];
+                               //memcpy(inFileName, fastaFileNames[s].c_str(), fastaFileNames[s].length());
+                               
+                               char inFileName[1024];
+                               strcpy(inFileName, fastaFileNames[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, outNewTax, outMode, MPI_INFO_NULL, &outMPINewTax);
                                MPI_File_open(MPI_COMM_WORLD, outTempTax, outMode, MPI_INFO_NULL, &outMPITempTax);
                                
-                               delete outNewTax;
-                               delete outTempTax;
-                               delete inFileName;
+                               //delete outNewTax;
+                               //delete outTempTax;
+                               //delete inFileName;
 
                                if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPINewTax);   MPI_File_close(&outMPITempTax);  delete classify; return 0;  }
 
@@ -758,7 +767,7 @@ int ClassifySeqsCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File
                                        }
                                        
                                        int length = outputString.length();
-                                       char* buf2 = new char[length];\r
+                                       char* buf2 = new char[length];
                                        memcpy(buf2, outputString.c_str(), length);
                                
                                        MPI_File_write_shared(newFile, buf2, length, MPI_CHAR, &statusNew);
@@ -766,7 +775,7 @@ int ClassifySeqsCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File
 
                                        outputString =  candidateSeq->getName() + "\t" + classify->getSimpleTax() + "\n";
                                        length = outputString.length();
-                                       char* buf = new char[length];\r
+                                       char* buf = new char[length];
                                        memcpy(buf, outputString.c_str(), length);
                                
                                        MPI_File_write_shared(tempFile, buf, length, MPI_CHAR, &statusTemp);
@@ -799,12 +808,15 @@ int ClassifySeqsCommand::MPIReadNamesFile(string nameFilename){
                MPI_Offset size;
                MPI_Status status;
 
-               char* inFileName = new char[nameFilename.length()];\r
-               memcpy(inFileName, nameFilename.c_str(), nameFilename.length());
+               //char* inFileName = new char[nameFilename.length()];
+               //memcpy(inFileName, nameFilename.c_str(), nameFilename.length());
+               
+               char inFileName[1024];
+               strcpy(inFileName, nameFilename.c_str());
 
                MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);  
                MPI_File_get_size(inMPI, &size);
-               delete inFileName;
+               //delete inFileName;
 
                char* buffer = new char[size];
                MPI_File_read(inMPI, buffer, size, MPI_CHAR, &status);