1.9

[mothur.git] / chimeracheckrdp.cpp

diff --git a/chimeracheckrdp.cpp b/chimeracheckrdp.cpp
index 51a3d9bbac0eaea545e1626682049db382a973ac..cb101b6af9dd8d0c412a69067597d9a022f2e623 100644 (file)
--- a/chimeracheckrdp.cpp
+++ b/chimeracheckrdp.cpp
@@ -97,11 +97,12 @@ int ChimeraCheckRDP::print(MPI_File& out, MPI_File& outAcc) {
                
                MPI_Status status;
                int length = outString.length();
-               char buf[length];
-               strcpy(buf, outString.c_str()); 
+               char* buf = new char[length];\r
+               memcpy(buf, outString.c_str(), length);
                                
                MPI_File_write_shared(out, buf, length, MPI_CHAR, &status);
-               
+               delete buf;
+
                if (svg) {
                        if (name != "") { //if user has specific names
                                map<string, string>::iterator it = names.find(querySeq->getName());
@@ -261,19 +262,22 @@ void ChimeraCheckRDP::readName(string namefile) {
                MPI_File inMPI;
                MPI_Offset size;
                MPI_Status status;
-               
-               char inFileName[namefile.length()];
-               strcpy(inFileName, namefile.c_str());
+
+               char* inFileName = new char[namefile.length()];\r
+               memcpy(inFileName, namefile.c_str(), namefile.length());
 
                MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);  
                MPI_File_get_size(inMPI, &size);
 
-               char buffer[size];
+               delete inFileName;
+
+               char* buffer = new char[size];
                MPI_File_read(inMPI, buffer, size, MPI_CHAR, &status);
 
                string tempBuf = buffer;
                if (tempBuf.length() > size) { tempBuf = tempBuf.substr(0, size);  }
                istringstream iss (tempBuf,istringstream::in);
+               delete buffer;
                
                while(!iss.eof()) {
                        iss >> name; gobble(iss);
@@ -347,12 +351,14 @@ void ChimeraCheckRDP::makeSVGpic(vector<sim> info) {
                
                MPI_File outSVG;
                int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
-               
-               char FileName[file.length()];
-               strcpy(FileName, file.c_str());
+
+               char* FileName = new char[file.length()];\r
+               memcpy(FileName, file.c_str(), file.length());
                
                MPI_File_open(MPI_COMM_SELF, FileName, outMode, MPI_INFO_NULL, &outSVG);  //comm, filename, mode, info, filepointer
                
+               delete FileName;
+
                int width = (info.size()*5) + 150;
                
                string outString = "";
@@ -398,10 +404,11 @@ void ChimeraCheckRDP::makeSVGpic(vector<sim> info) {
                
                MPI_Status status;
                int length = outString.length();
-               char buf2[length];
-               strcpy(buf2, outString.c_str()); 
+               char* buf2 = new char[length];\r
+               memcpy(buf2, outString.c_str(), length);
                                
                MPI_File_write(outSVG, buf2, length, MPI_CHAR, &status);
+               delete buf2;
                
                MPI_File_close(&outSVG);