added clearcut source to mothur, fixed mislabeled sharedcalcs

[mothur.git] / clearcutcommand.cpp

diff --git a/clearcutcommand.cpp b/clearcutcommand.cpp
index d6c284d68159b66255d3cdb29d57217e9dd73af6..7d0d539eddeeae6e3ee6bfbe3e114c6b90e1bb7a 100644 (file)
--- a/clearcutcommand.cpp
+++ b/clearcutcommand.cpp
@@ -8,6 +8,8 @@
  */
 
 #include "clearcutcommand.h"
+#include "clearcut.h"
+
 
 /**************************************************************************************/
 ClearcutCommand::ClearcutCommand(string option)  {     
@@ -177,52 +179,81 @@ int ClearcutCommand::execute() {
                //prepare filename
                string outputName = outputDir + m->getRootName(m->getSimpleName(inputFile)) + "tre";
                
-               //get location of clearcut
-               GlobalData* globaldata = GlobalData::getInstance();
-               string path = globaldata->argv;
-               path = path.substr(0, (path.find_last_of('m')));
+               vector<char*> cPara;
                
-               string clearcutCommand = path + "clearcut ";
+               char* tempClearcut = new char[8];  strcpy(tempClearcut, "clearcut");  cPara.push_back(tempClearcut);
                                
                //you gave us a distance matrix
-               if (phylipfile != "") { clearcutCommand += "--distance ";       }
+               if (phylipfile != "") {  char* temp = new char[10];  strcpy(temp, "--distance");  cPara.push_back(temp);        }
                
                //you gave us a fastafile
-               if (fastafile != "") { clearcutCommand += "--alignment ";       }
+               if (fastafile != "") { char* temp = new char[11];  strcpy(temp, "--alignment");  cPara.push_back(temp);         }
                
-               if (version)                    {  clearcutCommand += "--version ";             }
-               if (verbose)                    {  clearcutCommand += "--verbose ";             }
-               if (quiet)                              {  clearcutCommand += "--quiet ";               }
-               if (seed != "*")                {  clearcutCommand += "--seed=" + seed + " "; }
-               if (norandom)                   {  clearcutCommand += "--norandom ";    }
-               if (shuffle)                    {  clearcutCommand += "--shuffle ";             }
-               if (neighbor)                   {  clearcutCommand += "--neighbor ";    }
+               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 (seed != "*")                {  
+                       string tempSeed = "--seed=" + seed;
+                       char* temp = new char[tempSeed.length()];
+                       strcpy(temp, tempSeed.c_str());
+                       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);      }
                
+               string tempIn = "";
                #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-                       clearcutCommand += "--in=" + inputFile + " "; 
+                       tempIn += "--in=" + inputFile; 
                #else
-                       clearcutCommand += "--in=\"" + inputFile + "\" "; 
+                       tempIn += "--in=\"" + inputFile + "\"";  
                #endif
                
-               if (stdoutWanted)               {  clearcutCommand += "--stdout ";              }
+               char* tempI = new char[tempIn.length()];
+               strcpy(tempI, tempIn.c_str());
+               cPara.push_back(tempI);
+               
+               if (stdoutWanted)               {  char* temp = new char[8];  strcpy(temp, "--stdout");  cPara.push_back(temp); }
                else{  
+                       string tempOut = "";
                        #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-                               clearcutCommand += "--out=" + outputName + " "; }
+                               tempOut += "--out=" + outputName;  
                        #else
-                               clearcutCommand += "--out=\"" + outputName + "\" "; }
+                               tempOut += "--out=\"" + outputName + "\""; 
                        #endif
+                       
+                       char* temp = new char[tempOut.length()];
+                       strcpy(temp, tempOut.c_str());
+                       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 (matrixout != "")    {  
+                       string tempMatrix =  "--matrixout=" + matrixout; 
+                       char* temp = new char[tempMatrix.length()];
+                       strcpy(temp, tempMatrix.c_str());
+                       cPara.push_back(temp);
+               }
+
+               if (ntrees != "1")              {  
+                       string tempNtrees = "--ntrees=" + ntrees; 
+                       char* temp = new char[tempNtrees.length()];
+                       strcpy(temp, tempNtrees.c_str());
+                       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); }
+               
+               char** clearcutParameters;
+               clearcutParameters = new char*[cPara.size()];
+               for (int i = 0; i < cPara.size(); i++) {  clearcutParameters[i] = cPara[i];  }
+               int numArgs = cPara.size();
                
-               if (DNA)                                {  clearcutCommand += "--DNA ";                 }
-               if (protein)                    {  clearcutCommand += "--protein ";             }
-               if (jukes)                              {  clearcutCommand += "--jukes ";               }
-               if (kimura)                             {  clearcutCommand += "--kimura ";              }
-               if (matrixout != "")    {  clearcutCommand += "--matrixout=" + matrixout + " ";  }
-               if (ntrees != "1")              {  clearcutCommand += "--ntrees=" + ntrees + " "; }
-               if (expblen)                    {  clearcutCommand += "--expblen ";             }
-               if (expdist)                    {  clearcutCommand += "--expdist ";             }
-       
-               //run clearcut
-               system(clearcutCommand.c_str());
+               clearcut_main(numArgs, clearcutParameters); 
                
                if (!stdoutWanted) {    
                        m->mothurOutEndLine();