Default clustering method=opti

mothur · eba2e8bc76583423e73d40965efe137b395c5d1b · mothur-westcott committed Jan 9, 2017 · Jan 9, 2017 · eba2e8b
1 parent df42fe0
commit eba2e8bc76583423e73d40965efe137b395c5d1b
Unified Split

Showing with 9 additions and 5 deletions.

+4 −1 source/commands/clustercommand.cpp

+1 −1 source/commands/clustersplitcommand.cpp

+4 −3 source/mothur.cpp
diff --git a/source/commands/clustercommand.cpp b/source/commands/clustercommand.cpp
@@ -296,7 +296,10 @@ ClusterCommand::ClusterCommand(string option)  {
             m->mothurConvert(temp, processors);
             
 			method = validParameter.validFile(parameters, "method", false);
-			if (method == "not found") { method = "opti"; }
+			if (method == "not found") {
+                method = "opti";
+                m->mothurOut("[NOTE]: Default clustering method has changed to opti. To use average neighbor, set method=average."); m->mothurOutEndLine();
+            }
 			
             if ((method == "furthest") || (method == "nearest") || (method == "average") || (method == "weighted") || (method == "agc") || (method == "dgc") || (method == "opti")) { }
             else { m->mothurOut("[ERROR]: Not a valid clustering method.  Valid clustering algorithms are furthest, nearest, average, weighted, agc, dgc and opti."); m->mothurOutEndLine(); abort = true; }
diff --git a/source/commands/clustersplitcommand.cpp b/source/commands/clustersplitcommand.cpp
@@ -381,7 +381,7 @@ ClusterSplitCommand::ClusterSplitCommand(string option)  {
             else { m->mothurOut("[ERROR]: Not a valid initialization.  Valid initializations are singleton and oneotu."); m->mothurOutEndLine(); abort = true; }
 
             
-			method = validParameter.validFile(parameters, "method", false);		if (method == "not found") { method = "opti"; }
+			method = validParameter.validFile(parameters, "method", false);		if (method == "not found") { method = "opti"; m->mothurOut("[NOTE]: Default clustering method has changed to opti. To use average neighbor, set method=average."); m->mothurOutEndLine(); }
 			
             if ((method == "furthest") || (method == "nearest") || (method == "average") || (method == "weighted") || (method == "agc") || (method == "dgc") || (method == "opti")) { }
             else { m->mothurOut("[ERROR]: Not a valid clustering method.  Valid clustering algorithms are furthest, nearest, average, weighted, agc, dgc and opti."); m->mothurOutEndLine(); abort = true; }
diff --git a/source/mothur.cpp b/source/mothur.cpp
@@ -145,8 +145,6 @@ int main(int argc, char *argv[]){
 			m->mothurOut("Department of Microbiology & Immunology");
 			m->mothurOutEndLine();	
 			m->mothurOut("University of Michigan");
-			m->mothurOutEndLine();			
-			m->mothurOut("pschloss@umich.edu");
 			m->mothurOutEndLine();		
 			m->mothurOut("http://www.mothur.org");
 			m->mothurOutEndLine();
@@ -161,7 +159,10 @@ int main(int argc, char *argv[]){
 			m->mothurOutEndLine();			
 			m->mothurOut("Type 'help()' for information on the commands that are available");
 			m->mothurOutEndLine();
-			m->mothurOutEndLine();			
+            m->mothurOutEndLine();
+            m->mothurOut("For questions and analysis support, please visit our forum at https://www.mothur.org/forum");
+			m->mothurOutEndLine();
+            m->mothurOutEndLine();
 			m->mothurOut("Type 'quit()' to exit program");
 			m->mothurOutEndLine();
 		}