X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothurout.cpp;h=b30ee3ca630c91fea01343c9d873e709e027a4fb;hb=d9b668f68b99f92ecdc71dd8cd363cb4e27107f9;hp=bd1a098c8d5662044552071c7c44a273214018ce;hpb=4ad32478c7b1bbb464c839a6e133f5b517a3efec;p=mothur.git

diff --git a/mothurout.cpp b/mothurout.cpp
index bd1a098..b30ee3c 100644
--- 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();
@@ -1462,20 +1466,21 @@ bool MothurOut::anyLabelsToProcess(string label, set<string>& userLabels, string
 		}
 		
 		//go through users set and make them floats
-		for(it = userLabels.begin(); it != userLabels.end(); ++it) {
+		for(it = userLabels.begin(); it != userLabels.end();) {
 			
 			float temp;
 			if ((*it != "unique") && (convertTestFloat(*it, temp) == true)){
 				convert(*it, temp);
 				orderFloat.push_back(temp);
 				userMap[*it] = temp;
+				it++;
 			}else if (*it == "unique") { 
 				orderFloat.push_back(-1.0);
 				userMap["unique"] = -1.0;
+				it++;
 			}else {
-				if (errorOff == "") {  cout << *it << " is not a valid label." << endl;  }
-				userLabels.erase(*it); 
-				it--;
+				if (errorOff == "") {  mothurOut(*it + " is not a valid label."); mothurOutEndLine();  }
+				userLabels.erase(it++); 
 			}
 		}
 		
@@ -1491,11 +1496,11 @@ bool MothurOut::anyLabelsToProcess(string label, set<string>& userLabels, string
 			if (orderFloat[i] < labelFloat) {
 				smaller = true;
 				if (orderFloat[i] == -1) { 
-					if (errorOff == "") { cout << "Your file does not include the label unique." << endl; }
+					if (errorOff == "") { mothurOut("Your file does not include the label unique."); mothurOutEndLine(); }
 					userLabels.erase("unique");
 				}
 				else {  
-					if (errorOff == "") { cout << "Your file does not include the label " << endl; }
+					if (errorOff == "") { mothurOut("Your file does not include the label "); mothurOutEndLine(); }
 					string s = "";
 					for (it2 = userMap.begin(); it2!= userMap.end(); it2++) {  
 						if (it2->second == orderFloat[i]) {  
@@ -1505,7 +1510,7 @@ bool MothurOut::anyLabelsToProcess(string label, set<string>& userLabels, string
 							break;
 						}
 					}
-					if (errorOff == "") {cout << s <<  ". I will use the next smallest distance. " << endl; }
+					if (errorOff == "") {mothurOut( s +  ". I will use the next smallest distance. "); mothurOutEndLine(); }
 				}
 			//since they are sorted once you find a bigger one stop looking
 			}else { break; }