X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=distancecommand.cpp;h=99e89bafecdf8c2d5740aeb12446d04b8d9e4fdd;hb=49d2b7459c5027557564b21e9487dadafbbbdc96;hp=0f067aeab3b6ce1a50ba5e60870b410bbf72ba67;hpb=ba2b95b22ab8947d5583ca2c2da74557870b6861;p=mothur.git

diff --git a/distancecommand.cpp b/distancecommand.cpp
index 0f067ae..99e89ba 100644
--- a/distancecommand.cpp
+++ b/distancecommand.cpp
@@ -59,6 +59,27 @@ string DistanceCommand::getHelpString(){
 	}
 }
 //**********************************************************************************************************************
+string DistanceCommand::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 == "phylip") {  outputFileName =  "dist"; }
+            else if (type == "column") {  outputFileName =  "dist"; }
+            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, "DistanceCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
 DistanceCommand::DistanceCommand(){	
 	try {
 		abort = true; calledHelp = true; 
@@ -179,11 +200,11 @@ DistanceCommand::DistanceCommand(string option) {
 			convert(temp, countends); 
 			
 			temp = validParameter.validFile(parameters, "cutoff", false);		if(temp == "not found"){	temp = "1.0"; }
-			convert(temp, cutoff); 
+			m->mothurConvert(temp, cutoff); 
 			
 			temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = m->getProcessors();	}
 			m->setProcessors(temp);
-			convert(temp, processors);
+			m->mothurConvert(temp, processors);
 			
 			temp = validParameter.validFile(parameters, "compress", false);		if(temp == "not found"){  temp = "F"; }
 			convert(temp, compress);
@@ -229,12 +250,12 @@ int DistanceCommand::execute(){
 		string outputFile;
 				
 		if (output == "lt") { //does the user want lower triangle phylip formatted file 
-			outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "phylip.dist";
+			outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "phylip." + getOutputFileNameTag("phylip");
 			m->mothurRemove(outputFile); outputTypes["phylip"].push_back(outputFile);
 			
 			//output numSeqs to phylip formatted dist file
 		}else if (output == "column") { //user wants column format
-			outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "dist";
+			outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("column");
 			outputTypes["column"].push_back(outputFile);
 			
 			//so we don't accidentally overwrite
@@ -245,7 +266,7 @@ int DistanceCommand::execute(){
 			
 			m->mothurRemove(outputFile);
 		}else { //assume square
-			outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "square.dist";
+			outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "square." + getOutputFileNameTag("phylip");
 			m->mothurRemove(outputFile);
 			outputTypes["phylip"].push_back(outputFile);
 		}
@@ -380,7 +401,7 @@ int DistanceCommand::execute(){
 		MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 #else		
 				
-	//#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+	//#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 		//if you don't need to fork anything
 		if(processors == 1){
 			if (output != "square") {  driver(0, numSeqs, outputFile, cutoff); }
@@ -507,7 +528,7 @@ int DistanceCommand::execute(){
 /**************************************************************************************************/
 void DistanceCommand::createProcesses(string filename) {
 	try {
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 		int process = 1;
 		processIDS.clear();
 		
@@ -1014,7 +1035,7 @@ int DistanceCommand::convertMatrix(string outputFile) {
 		string outfile = m->getRootName(outputFile) + "sorted.dist.temp";
 		
 		//use the unix sort 
-		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 			string command = "sort -n " + outputFile + " -o " + outfile;
 			system(command.c_str());
 		#else //sort using windows sort
@@ -1094,7 +1115,7 @@ int DistanceCommand::convertMatrix(string outputFile) {
 		exit(1);
 	}
 }
-/**************************************************************************************************
+**************************************************************************************************
 int DistanceCommand::convertToLowerTriangle(string outputFile) {
 	try{
 
@@ -1102,7 +1123,7 @@ int DistanceCommand::convertToLowerTriangle(string outputFile) {
 		string outfile = m->getRootName(outputFile) + "sorted.dist.temp";
 		
 		//use the unix sort 
-		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 			string command = "sort -n " + outputFile + " -o " + outfile;
 			system(command.c_str());
 		#else //sort using windows sort
@@ -1188,7 +1209,7 @@ int DistanceCommand::convertToLowerTriangle(string outputFile) {
 		exit(1);
 	}
 }
-/**************************************************************************************************/
+**************************************************************************************************/
 //its okay if the column file does not contain all the names in the fasta file, since some distance may have been above a cutoff,
 //but no sequences can be in the column file that are not in oldfasta. also, if a distance is above the cutoff given then remove it.
 //also check to make sure the 2 files have the same alignment length.