classify.seqs allows sequences to be in taxonomy file that are not in template. ...

[mothur.git] / clearcutcommand.cpp

diff --git a/clearcutcommand.cpp b/clearcutcommand.cpp
index 6a0eb259379df8480341a5542a7456fc674aea74..55fbe0a1dceb9a2d2c16e2f6936646d3e851ee19 100644 (file)
--- a/clearcutcommand.cpp
+++ b/clearcutcommand.cpp
@@ -269,51 +269,50 @@ int ClearcutCommand::execute() {
                
                vector<char*> cPara;
                
-               char* tempClearcut = new char[8];  
-               strcpy(tempClearcut, "clearcut"); 
+               char* tempClearcut = new char[9];  
+               *tempClearcut = '\0'; strncat(tempClearcut, "clearcut", 8); 
                cPara.push_back(tempClearcut);
                                
                //you gave us a distance matrix
-               if (phylipfile != "") {  char* temp = new char[10];  strcpy(temp, "--distance");  cPara.push_back(temp);        }
+               if (phylipfile != "") {  char* temp = new char[11];  *temp = '\0'; strncat(temp, "--distance", 10);  cPara.push_back(temp);     }
                
                //you gave us a fastafile
-               if (fastafile != "") { char* temp = new char[11];  strcpy(temp, "--alignment");  cPara.push_back(temp);         }
+               if (fastafile != "") { char* temp = new char[12];  *temp = '\0'; strncat(temp, "--alignment", 11);  cPara.push_back(temp);      }
                
-               if (version)                    {  char* temp = new char[9];  strcpy(temp, "--version");  cPara.push_back(temp);        }
-               if (verbose)                    {  char* temp = new char[9];  strcpy(temp, "--verbose");  cPara.push_back(temp);        }
-               if (quiet)                              {  char* temp = new char[7];  strcpy(temp, "--quiet");  cPara.push_back(temp);  }
+               if (version)                    {  char* temp = new char[10];  *temp = '\0'; strncat(temp, "--version", 9);  cPara.push_back(temp);     }
+               if (verbose)                    {  char* temp = new char[10];  *temp = '\0'; strncat(temp, "--verbose", 9);  cPara.push_back(temp);     }
+               if (quiet)                              {  char* temp = new char[8];  *temp = '\0'; strncat(temp, "--quiet", 7);  cPara.push_back(temp);        }
                if (seed != "*")                {  
                        string tempSeed = "--seed=" + seed;
-                       char* temp = new char[tempSeed.length()];
-                       strcpy(temp, tempSeed.c_str());
+                       char* temp = new char[tempSeed.length()+1];
+                       *temp = '\0'; strncat(temp, tempSeed.c_str(), tempSeed.length());
                        cPara.push_back(temp);
                }
-               if (norandom)                   {  char* temp = new char[10];  strcpy(temp, "--norandom");  cPara.push_back(temp);      }
-               if (shuffle)                    {  char* temp = new char[9];  strcpy(temp, "--shuffle");  cPara.push_back(temp);        }
-               if (neighbor)                   {  char* temp = new char[10];  strcpy(temp, "--neighbor");  cPara.push_back(temp);      }
+               if (norandom)                   {  char* temp = new char[11];  *temp = '\0'; strncat(temp, "--norandom", 10);  cPara.push_back(temp);   }
+               if (shuffle)                    {  char* temp = new char[10];  *temp = '\0'; strncat(temp, "--shuffle", 9);  cPara.push_back(temp);     }
+               if (neighbor)                   {  char* temp = new char[11];  *temp = '\0'; strncat(temp, "--neighbor", 10);  cPara.push_back(temp);   }
                
                string tempIn = "--in=" + inputFile;  
-               char* tempI = new char[tempIn.length()];
-               strcpy(tempI, tempIn.c_str());
+               char* tempI = new char[tempIn.length()+1];
+               *tempI = '\0'; strncat(tempI, tempIn.c_str(), tempIn.length());
                cPara.push_back(tempI);
                
-               if (stdoutWanted)               {  char* temp = new char[8];  strcpy(temp, "--stdout");  cPara.push_back(temp); }
+               if (stdoutWanted)               {  char* temp = new char[9];  *temp = '\0'; strncat(temp, "--stdout", 8);  cPara.push_back(temp);       }
                else{  
                        string tempOut = "--out=" + outputName;  
-                       
-                       char* temp = new char[tempOut.length()];
-                       strcpy(temp, tempOut.c_str());
+                       char* temp = new char[tempOut.length()+1];
+                       *temp = '\0'; strncat(temp, tempOut.c_str(), tempOut.length());
                        cPara.push_back(temp);
                }
                        
-               if (DNA)                                {  char* temp = new char[5];  strcpy(temp, "--DNA");  cPara.push_back(temp);            }
-               if (protein)                    {  char* temp = new char[9];  strcpy(temp, "--protein");  cPara.push_back(temp);        }
-               if (jukes)                              {  char* temp = new char[7];  strcpy(temp, "--jukes");  cPara.push_back(temp);          }
-               if (kimura)                             { char* temp = new char[8];  strcpy(temp, "--kimura");  cPara.push_back(temp);          }
+               if (DNA)                                {  char* temp = new char[6];  *temp = '\0'; strncat(temp, "--DNA", 5);  cPara.push_back(temp);          }
+               if (protein)                    {  char* temp = new char[10];  *temp = '\0'; strncat(temp, "--protein", 9);  cPara.push_back(temp);     }
+               if (jukes)                              {  char* temp = new char[8];  *temp = '\0'; strncat(temp, "--jukes", 7);  cPara.push_back(temp);                }
+               if (kimura)                             { char* temp = new char[9];  *temp = '\0'; strncat(temp, "--kimura", 8);  cPara.push_back(temp);                }
                if (matrixout != "")    {  
                        string tempMatrix =  "--matrixout=" + outputDir + matrixout; 
-                       char* temp = new char[tempMatrix.length()];
-                       strcpy(temp, tempMatrix.c_str());
+                       char* temp = new char[tempMatrix.length()+1];
+                       *temp = '\0'; strncat(temp, tempMatrix.c_str(), tempMatrix.length());
                        cPara.push_back(temp);
                        outputNames.push_back((outputDir + matrixout));
                        outputTypes["matrixout"].push_back((outputDir + matrixout));
@@ -321,13 +320,13 @@ int ClearcutCommand::execute() {
 
                if (ntrees != "1")              {  
                        string tempNtrees = "--ntrees=" + ntrees; 
-                       char* temp = new char[tempNtrees.length()];
-                       strcpy(temp, tempNtrees.c_str());
+                       char* temp = new char[tempNtrees.length()+1];
+                       *temp = '\0'; strncat(temp, tempNtrees.c_str(), tempNtrees.length());
                        cPara.push_back(temp);
                }
 
-               if (expblen)                    { char* temp = new char[9];  strcpy(temp, "--expblen");  cPara.push_back(temp);         }
-               if (expdist)                    { char* temp = new char[9];  strcpy(temp, "--expdist");  cPara.push_back(temp); }
+               if (expblen)                    { char* temp = new char[10];  *temp = '\0'; strncat(temp, "--expblen", 9);  cPara.push_back(temp);      }
+               if (expdist)                    { char* temp = new char[10];  *temp = '\0'; strncat(temp, "--expdist", 9);  cPara.push_back(temp);      }
                
                char** clearcutParameters;
                clearcutParameters = new char*[cPara.size()];