parsimony calculator changed order of groups to reflect change in shared Utils made...

[mothur.git] / mothurout.cpp

diff --git a/mothurout.cpp b/mothurout.cpp
index 9ec847c81152b3ee0b33742c0d369acb74a4f98a..bd1a098c8d5662044552071c7c44a273214018ce 100644 (file)
--- a/mothurout.cpp
+++ b/mothurout.cpp
@@ -522,7 +522,7 @@ string MothurOut::getFullPathName(string fileName){
                                newFileName = homeDir + fileName.substr(fileName.find("~")+1);
                                return newFileName;
                        }else { //find path
-                               if (path.rfind("./") == -1) { return fileName; } //already complete name
+                               if (path.rfind("./") == string::npos) { return fileName; } //already complete name
                                else { newFileName = fileName.substr(fileName.rfind("./")+2); } //save the complete part of the name
                                
                                //char* cwdpath = new char[1024];
@@ -542,7 +542,7 @@ string MothurOut::getFullPathName(string fileName){
                                
                                //break apart the current working directory
                                vector<string> dirs;
-                               while (simpleCWD.find_first_of('/') != -1) {
+                               while (simpleCWD.find_first_of('/') != string::npos) {
                                        string dir = simpleCWD.substr(0,simpleCWD.find_first_of('/'));
                                        simpleCWD = simpleCWD.substr(simpleCWD.find_first_of('/')+1, simpleCWD.length());
                                        dirs.push_back(dir);
@@ -553,7 +553,7 @@ string MothurOut::getFullPathName(string fileName){
                        
                                int index = dirs.size()-1;
                
-                               while((pos = path.rfind("./")) != -1) { //while you don't have a complete path
+                               while((pos = path.rfind("./")) != string::npos) { //while you don't have a complete path
                                        if (pos == 0) { break;  //you are at the end
                                        }else if (path[(pos-1)] == '.') { //you want your parent directory ../
                                                path = path.substr(0, pos-1);
@@ -573,12 +573,12 @@ string MothurOut::getFullPathName(string fileName){
                                return newFileName;
                        }       
                #else
-                       if (path.find("~") != -1) { //go to home directory
+                       if (path.find("~") != string::npos) { //go to home directory
                                string homeDir = getenv ("HOMEPATH");
                                newFileName = homeDir + fileName.substr(fileName.find("~")+1);
                                return newFileName;
                        }else { //find path
-                               if (path.rfind(".\\") == -1) { return fileName; } //already complete name
+                               if (path.rfind(".\\") == string::npos) { return fileName; } //already complete name
                                else { newFileName = fileName.substr(fileName.rfind(".\\")+2); } //save the complete part of the name
                                                        
                                char *cwdpath = NULL;
@@ -599,7 +599,7 @@ string MothurOut::getFullPathName(string fileName){
                                        
                                int index = dirs.size()-1;
                                        
-                               while((pos = path.rfind(".\\")) != -1) { //while you don't have a complete path
+                               while((pos = path.rfind(".\\")) != string::npos) { //while you don't have a complete path
                                        if (pos == 0) { break;  //you are at the end
                                        }else if (path[(pos-1)] == '.') { //you want your parent directory ../
                                                path = path.substr(0, pos-1);
@@ -658,7 +658,7 @@ int MothurOut::openInputFile(string fileName, ifstream& fileHandle, string m){
 
                        fileHandle.open(completeFileName.c_str());
                        if(!fileHandle) {
-                               mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine();
+                               //mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine();
                                return 1;
                        }else {
                                //check for blank file