added modify names parameter to set.dir

[mothur.git] / mothurout.cpp

diff --git a/mothurout.cpp b/mothurout.cpp
index 0efa551565c6e18001cd6ed53e0643a50f525f37..2900c7ec4fc8e0df952163554f6fefb7e622cd64 100644 (file)
--- a/mothurout.cpp
+++ b/mothurout.cpp
@@ -348,6 +348,27 @@ void MothurOut::mothurOut(string output) {
        }
 }
 /*********************************************************************************************/
+void MothurOut::mothurOutJustToScreen(string output) {
+       try {
+               
+#ifdef USE_MPI
+        int pid;
+        MPI_Comm_rank(MPI_COMM_WORLD, &pid);
+        
+        if (pid == 0) { //only one process should output to screen
+#endif
+            logger() << output;
+            
+#ifdef USE_MPI
+        }
+#endif
+       }
+       catch(exception& e) {
+               errorOut(e, "MothurOut", "MothurOut");
+               exit(1);
+       }
+}
+/*********************************************************************************************/
 void MothurOut::mothurOutEndLine() {
        try {
                #ifdef USE_MPI
@@ -2221,9 +2242,11 @@ map<string, int> MothurOut::readNames(string namefile, unsigned long int& numSeq
 /************************************************************/
 int MothurOut::checkName(string& name) {
     try {
-        for (int i = 0; i < name.length(); i++) {
-            if (name[i] == ':') { name[i] = '_'; changedSeqNames = true; }
-        }        
+        if (modifyNames) {
+            for (int i = 0; i < name.length(); i++) {
+                if (name[i] == ':') { name[i] = '_'; changedSeqNames = true; }
+            }
+        }
         return 0;
     }
        catch(exception& e) {