X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clearcutcommand.cpp;h=c76de383fce839d31dd95e56bb7288a6df617d3c;hb=1d7a10dc3dafd1606d6255bdb54e02429cbee47c;hp=7d0d539eddeeae6e3ee6bfbe3e114c6b90e1bb7a;hpb=1b4aa03040e61f4c2d47ce32cb12726dcdadb917;p=mothur.git

diff --git a/clearcutcommand.cpp b/clearcutcommand.cpp
index 7d0d539..c76de38 100644
--- 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();
 		}