removing chime source files from mother project.

[mothur.git] / distancecommand.cpp

diff --git a/distancecommand.cpp b/distancecommand.cpp
index 65edcf75366d4096b1256266b05296146c30167b..79b8fe7c10544dafd2675a963a2229eb2e3e7046 100644 (file)
--- a/distancecommand.cpp
+++ b/distancecommand.cpp
@@ -380,7 +380,7 @@ 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 +507,7 @@ 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 +1014,7 @@ 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 +1094,7 @@ int DistanceCommand::convertMatrix(string outputFile) {
                exit(1);
        }
 }
-/**************************************************************************************************
+**************************************************************************************************
 int DistanceCommand::convertToLowerTriangle(string outputFile) {
        try{
 
@@ -1102,7 +1102,7 @@ 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 +1188,7 @@ 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.