added unix to ifdefs. minor changes while testing 1.24.0.

[mothur.git] / mothurout.cpp

diff --git a/mothurout.cpp b/mothurout.cpp
index 25e534e43880497955512ce7dc2240adf99157e9..c89d580d64f6c69a6afedada448143ae114453a3 100644 (file)
--- a/mothurout.cpp
+++ b/mothurout.cpp
@@ -143,7 +143,7 @@ void MothurOut::setDefaultPath(string pathname)  {
        
                //add / to name if needed
                string lastChar = pathname.substr(pathname.length()-1);
-               #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+               #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                        if (lastChar != "/") { pathname += "/"; }
                #else
                        if (lastChar != "\\") { pathname += "\\"; }     
@@ -334,7 +334,7 @@ void MothurOut::errorOut(exception& e, string object, string function) {
 //
 // On failure, returns 0.0, 0.0
 int MothurOut::mem_usage(double& vm_usage, double& resident_set) {
-  #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+  #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
   
           vm_usage     = 0.0;
           resident_set = 0.0;
@@ -506,7 +506,7 @@ string MothurOut::getline(ifstream& fileHandle) {
 }
 /***********************************************************************/
 
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 #ifdef USE_COMPRESSION
 inline bool endsWith(string s, const char * suffix){
   size_t suffixLength = strlen(suffix);
@@ -520,7 +520,7 @@ string MothurOut::getRootName(string longName){
        
                string rootName = longName;
 
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 #ifdef USE_COMPRESSION
     if (endsWith(rootName, ".gz") || endsWith(rootName, ".bz2")) {
       int pos = rootName.find_last_of('.');
@@ -675,7 +675,7 @@ string MothurOut::getFullPathName(string fileName){
                                
                string cwd;
                //get current working directory 
-               #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)   
+               #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)  
                        
                        if (path.find("~") != -1) { //go to home directory
                                string homeDir;
@@ -798,7 +798,7 @@ int MothurOut::openInputFile(string fileName, ifstream& fileHandle, string m){
        try {
                        //get full path name
                        string completeFileName = getFullPathName(fileName);
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 #ifdef USE_COMPRESSION
       // check for gzipped or bzipped file
       if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
@@ -844,7 +844,7 @@ int MothurOut::openInputFile(string fileName, ifstream& fileHandle){
 
                //get full path name
                string completeFileName = getFullPathName(fileName);
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 #ifdef USE_COMPRESSION
   // check for gzipped or bzipped file
   if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
@@ -895,7 +895,7 @@ int MothurOut::renameFile(string oldName, string newName){
                int exist = openInputFile(newName, inTest, "");
                inTest.close();
                
-       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)           
+       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)          
                if (exist == 0) { //you could open it so you want to delete it
                        string command = "rm " + newName;
                        system(command.c_str());
@@ -922,7 +922,7 @@ int MothurOut::openOutputFile(string fileName, ofstream& fileHandle){
        try { 
        
                string completeFileName = getFullPathName(fileName);
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 #ifdef USE_COMPRESSION
     // check for gzipped file
     if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
@@ -998,7 +998,7 @@ string MothurOut::sortFile(string distFile, string outputDir){
 
                
                //if you can, use the unix sort since its been optimized for years
-               #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+               #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                        string command = "sort -n -k +3 " + distFile + " -o " + outfile;
                        system(command.c_str());
                #else //you are stuck with my best attempt...
@@ -1201,7 +1201,7 @@ vector<unsigned long long> MothurOut::divideFile(string filename, int& proc) {
                        fclose (pFile);
                }
                
-       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                                
                //estimate file breaks
                unsigned long long chunkSize = 0;