cleaned up code2

[mothur.git] / distancecommand.cpp

diff --git a/distancecommand.cpp b/distancecommand.cpp
index 65edcf75366d4096b1256266b05296146c30167b..99e89bafecdf8c2d5740aeb12446d04b8d9e4fdd 100644 (file)
--- 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; 
@@ -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.