added indicator command

[mothur.git] / mothurout.cpp

diff --git a/mothurout.cpp b/mothurout.cpp
index b1d818850bd974ff482bc8c88ffc4bdc0a3dc7bd..b30ee3ca630c91fea01343c9d873e709e027a4fb 100644 (file)
--- a/mothurout.cpp
+++ b/mothurout.cpp
@@ -9,6 +9,7 @@
 
 #include "mothurout.h"
 
+
 /******************************************************/
 MothurOut* MothurOut::getInstance() {
        if( _uniqueInstance == 0) {
@@ -359,18 +360,21 @@ string MothurOut::getline(ifstream& fileHandle) {
 }
 /***********************************************************************/
 
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 #ifdef USE_COMPRESSION
 inline bool endsWith(string s, const char * suffix){
   size_t suffixLength = strlen(suffix);
   return s.size() >= suffixLength && s.substr(s.size() - suffixLength, suffixLength).compare(suffix) == 0;
 }
 #endif
+#endif
 
 string MothurOut::getRootName(string longName){
        try {
        
                string rootName = longName;
 
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 #ifdef USE_COMPRESSION
     if (endsWith(rootName, ".gz") || endsWith(rootName, ".bz2")) {
       int pos = rootName.find_last_of('.');
@@ -378,7 +382,7 @@ string MothurOut::getRootName(string longName){
       cerr << "shortening " << longName << " to " << rootName << "\n";
     }
 #endif
-
+#endif
                if(rootName.find_last_of(".") != rootName.npos){
                        int pos = rootName.find_last_of('.')+1;
                        rootName = rootName.substr(0, pos);
@@ -632,7 +636,7 @@ int MothurOut::openInputFile(string fileName, ifstream& fileHandle, string m){
        try {
                        //get full path name
                        string completeFileName = getFullPathName(fileName);
-
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 #ifdef USE_COMPRESSION
       // check for gzipped or bzipped file
       if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
@@ -655,7 +659,7 @@ int MothurOut::openInputFile(string fileName, ifstream& fileHandle, string m){
         }
       }
 #endif
-
+#endif
                        fileHandle.open(completeFileName.c_str());
                        if(!fileHandle) {
                                //mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine();
@@ -678,7 +682,7 @@ int MothurOut::openInputFile(string fileName, ifstream& fileHandle){
 
                //get full path name
                string completeFileName = getFullPathName(fileName);
-
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 #ifdef USE_COMPRESSION
   // check for gzipped or bzipped file
   if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
@@ -701,7 +705,7 @@ int MothurOut::openInputFile(string fileName, ifstream& fileHandle){
     }
   }
 #endif
-
+#endif
 
                fileHandle.open(completeFileName.c_str());
                if(!fileHandle) {
@@ -756,7 +760,7 @@ int MothurOut::openOutputFile(string fileName, ofstream& fileHandle){
        try { 
        
                string completeFileName = getFullPathName(fileName);
-
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 #ifdef USE_COMPRESSION
     // check for gzipped file
     if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
@@ -776,7 +780,7 @@ int MothurOut::openOutputFile(string fileName, ofstream& fileHandle){
       }
     }
 #endif
-
+#endif
                fileHandle.open(completeFileName.c_str(), ios::trunc);
                if(!fileHandle) {
                        mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine();