changes while testing

[mothur.git] / mothurout.cpp

diff --git a/mothurout.cpp b/mothurout.cpp
index 0efa551565c6e18001cd6ed53e0643a50f525f37..8a3b6313072a158f611e1a69a84d0a9713add18c 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) {
@@ -3249,6 +3272,26 @@ vector<double> MothurOut::getAverages(vector< vector<double> >& dists) {
                exit(1);
        }
 }
+/**************************************************************************************************/
+double MothurOut::getAverage(vector<double> dists) {
+       try{
+        double average = 0;
+        
+        for (int i = 0; i < dists.size(); i++) {
+            average += dists[i];
+        }
+       
+        //finds average.
+        average /= (double) dists.size(); 
+        
+        return average;
+    }
+       catch(exception& e) {
+               errorOut(e, "MothurOut", "getAverage");
+               exit(1);
+       }
+}
+
 /**************************************************************************************************/
 vector<double> MothurOut::getStandardDeviation(vector< vector<double> >& dists) {
        try{