X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothur.h;h=fdaa06362db6ecda7054fe4ff9b21442487c19d4;hb=6777912b79eb6d011163da47f3ada09d1a9293c1;hp=6381e51d626246244b5ce077b9b077337cfc42d8;hpb=315e38cf393c82be238da5b32574f225a020d25c;p=mothur.git

diff --git a/mothur.h b/mothur.h
index 6381e51..fdaa063 100644
--- a/mothur.h
+++ b/mothur.h
@@ -433,8 +433,8 @@ inline string getPathName(string longName){
  
 	string rootPathName = longName;
 	
-	if(longName.find_last_of('/') != longName.npos){
-		int pos = longName.find_last_of('/')+1;
+	if(longName.find_last_of("/\\") != longName.npos){
+		int pos = longName.find_last_of("/\\")+1;
 		rootPathName = longName.substr(0, pos);
 	}
 	
@@ -489,7 +489,7 @@ inline bool isBlank(string fileName){
 inline string getFullPathName(string fileName){
 	
 	string path = hasPath(fileName);
-	string newFileName = getSimpleName(fileName);
+	string newFileName;
 	int pos;
 	
 	if (path == "") { return fileName; } //its a simple name
@@ -501,6 +501,7 @@ inline string getFullPathName(string fileName){
 		//get current working directory 
 		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)	
 			if (path.rfind("./") == -1) { return fileName; } //already complete name
+			else { newFileName = fileName.substr(fileName.rfind("./")+2); } //save the complete part of the name
 			
 			char* cwdpath;
 			size_t size;
@@ -543,6 +544,7 @@ inline string getFullPathName(string fileName){
 				
 		#else
 			if (path.rfind(".\\") == -1) { return fileName; } //already complete name
+			else { newFileName = fileName.substr(fileName.rfind(".\\")+2); } //save the complete part of the name
 						
 			char *cwdpath = NULL;
 			cwdpath = getcwd(NULL, 0); // or _getcwd
@@ -589,19 +591,15 @@ inline int openInputFile(string fileName, ifstream& fileHandle, string m){
 	
 	//get full path name
 	string completeFileName = getFullPathName(fileName);
-	//string completeFileName = fileName;
 
 	fileHandle.open(completeFileName.c_str());
 	if(!fileHandle) {
-		mothurOut("Error: Could not open " + completeFileName);  mothurOutEndLine();
 		return 1;
-	}
-	else {
+	}else {
 		//check for blank file
 		gobble(fileHandle);
 		return 0;
-	}
-	
+	}	
 }
 /***********************************************************************/
 
@@ -623,6 +621,28 @@ inline int openInputFile(string fileName, ifstream& fileHandle){
 	}
 	
 }
+/***********************************************************************/
+
+inline int renameFile(string oldName, string newName){
+	
+	ifstream inTest;
+	int exist = openInputFile(newName, inTest, "");
+	
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)		
+	if (exist == 0) { //you could open it so you want to delete it
+		inTest.close();
+		string command = "rm " + newName;
+		system(command.c_str());
+	}
+			
+	string command = "mv " + oldName + " " + newName;
+	system(command.c_str());
+#else
+	remove(newName.c_str());
+	renameOk = rename(oldName.c_str(), newName.c_str());
+#endif
+	return 0;
+}
 
 /***********************************************************************/