X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clearcutcommand.cpp;h=55fbe0a1dceb9a2d2c16e2f6936646d3e851ee19;hb=006601d68abe8d0061f77e8d28323b160750e343;hp=04dbc79aa15d3c4b6913a2e8131283b849dd90b9;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77;p=mothur.git

diff --git a/clearcutcommand.cpp b/clearcutcommand.cpp
index 04dbc79..55fbe0a 100644
--- a/clearcutcommand.cpp
+++ b/clearcutcommand.cpp
@@ -86,7 +86,27 @@ string ClearcutCommand::getHelpString(){
 		exit(1);
 	}
 }
-
+//**********************************************************************************************************************
+string ClearcutCommand::getOutputFileNameTag(string type, string inputName=""){	
+	try {
+        string outputFileName = "";
+		map<string, vector<string> >::iterator it;
+        
+        //is this a type this command creates
+        it = outputTypes.find(type);
+        if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+        else {
+            if (type == "tree") {  outputFileName =  "tre"; }
+            else if (type == "matrixout") {  outputFileName =  ""; }
+            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
+        }
+        return outputFileName;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ClearcutCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
 //**********************************************************************************************************************
 ClearcutCommand::ClearcutCommand(){	
 	try {
@@ -155,21 +175,21 @@ ClearcutCommand::ClearcutCommand(string option)  {
 			fastafile = validParameter.validFile(parameters, "fasta", true);
 			if (fastafile == "not open") { fastafile = ""; abort = true; }
 			else if (fastafile == "not found") { fastafile = ""; }	
-			else { inputFile = fastafile;  }
+			else { inputFile = fastafile;  m->setFastaFile(fastafile); }
 			
 			phylipfile = validParameter.validFile(parameters, "phylip", true);
 			if (phylipfile == "not open") { phylipfile = ""; abort = true; }
 			else if (phylipfile == "not found") { phylipfile = ""; }
-			else { inputFile = phylipfile;  }
+			else { inputFile = phylipfile;  m->setPhylipFile(phylipfile); }
 				
 			if ((phylipfile == "") && (fastafile == "")) {  
 				//is there are current file available for either of these?
 				//give priority to phylip, then fasta
 				phylipfile = m->getPhylipFile(); 
-				if (phylipfile != "") {  m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
+				if (phylipfile != "") {  inputFile = phylipfile; m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
 				else { 
 					fastafile = m->getFastaFile(); 
-					if (fastafile != "") {  m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
+					if (fastafile != "") { inputFile = fastafile;  m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 					else { 
 						m->mothurOut("No valid current files. You must provide a phylip or fasta file before you can use the clearcut command."); m->mothurOutEndLine(); 
 						abort = true;
@@ -244,56 +264,55 @@ int ClearcutCommand::execute() {
 		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		//prepare filename
-		string outputName = outputDir + m->getRootName(m->getSimpleName(inputFile)) + "tre";
+		string outputName = outputDir + m->getRootName(m->getSimpleName(inputFile)) + getOutputFileNameTag("tree");
 		outputNames.push_back(outputName); outputTypes["tree"].push_back(outputName);
 		
 		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));
@@ -301,13 +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()];