added mothur executable to cvs

[mothur.git] / clearcutcommand.cpp

diff --git a/clearcutcommand.cpp b/clearcutcommand.cpp
index 7d0d539eddeeae6e3ee6bfbe3e114c6b90e1bb7a..c76de383fce839d31dd95e56bb7288a6df617d3c 100644 (file)
--- a/clearcutcommand.cpp
+++ b/clearcutcommand.cpp
@@ -137,7 +137,6 @@ void ClearcutCommand::help(){
        try {
                m->mothurOut("The clearcut command interfaces mothur with the clearcut program written by Initiative for Bioinformatics and Evolutionary Studies (IBEST) at the University of Idaho.\n");
                m->mothurOut("For more information about clearcut refer to http://bioinformatics.hungry.com/clearcut/ \n");
-               m->mothurOut("The clearcut executable must be in a folder called clearcut in the same folder as your mothur executable, similar to mothur's requirements for using blast. \n");
                m->mothurOut("The clearcut command parameters are phylip, fasta, version, verbose, quiet, seed, norandom, shuffle, neighbor, expblen, expdist, ntrees, matrixout, stdout, kimura, jukes, protein, DNA. \n");
                m->mothurOut("The phylip parameter allows you to enter your phylip formatted distance matrix. \n");
                m->mothurOut("The fasta parameter allows you to enter your aligned fasta file, if you enter a fastafile you specify if the sequences are DNA or protein using the DNA or protein parameters. \n");
@@ -175,13 +174,15 @@ int ClearcutCommand::execute() {
        try {
                
                if (abort == true) { return 0; }
-                               
+               
                //prepare filename
                string outputName = outputDir + m->getRootName(m->getSimpleName(inputFile)) + "tre";
                
                vector<char*> cPara;
                
-               char* tempClearcut = new char[8];  strcpy(tempClearcut, "clearcut");  cPara.push_back(tempClearcut);
+               char* tempClearcut = new char[8];  
+               strcpy(tempClearcut, "clearcut"); 
+               cPara.push_back(tempClearcut);
                                
                //you gave us a distance matrix
                if (phylipfile != "") {  char* temp = new char[10];  strcpy(temp, "--distance");  cPara.push_back(temp);        }
@@ -202,25 +203,14 @@ int ClearcutCommand::execute() {
                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)
-                       tempIn += "--in=" + inputFile; 
-               #else
-                       tempIn += "--in=\"" + inputFile + "\"";  
-               #endif
-               
+               string tempIn = "--in=" + inputFile;  
                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)
-                               tempOut += "--out=" + outputName;  
-                       #else
-                               tempOut += "--out=\"" + outputName + "\""; 
-                       #endif
+                       string tempOut = "--out=" + outputName;  
                        
                        char* temp = new char[tempOut.length()];
                        strcpy(temp, tempOut.c_str());
@@ -232,7 +222,7 @@ int ClearcutCommand::execute() {
                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; 
+                       string tempMatrix =  "--matrixout=" + outputDir + matrixout; 
                        char* temp = new char[tempMatrix.length()];
                        strcpy(temp, tempMatrix.c_str());
                        cPara.push_back(temp);
@@ -255,11 +245,15 @@ int ClearcutCommand::execute() {
                
                clearcut_main(numArgs, clearcutParameters); 
                
+               //free memory
+               for(int i = 0; i < cPara.size(); i++)  {  delete[] cPara[i];  }
+               delete[] clearcutParameters; 
+               
                if (!stdoutWanted) {    
                        m->mothurOutEndLine();
                        m->mothurOut("Output File Names: "); m->mothurOutEndLine();
                        m->mothurOut(outputName); m->mothurOutEndLine();
-                       if (matrixout != "")    {  m->mothurOut(matrixout); m->mothurOutEndLine();  }
+                       if (matrixout != "")    {  m->mothurOut(outputDir+matrixout); m->mothurOutEndLine();  }
                        m->mothurOutEndLine();
                }