X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothurout.cpp;h=9704464bf80326c87d4afa556e3353b95fcbf37e;hb=5a4ac4f954c4b4445bcee272f1f8220ddcc9c1e4;hp=14840c16e162bc599c242e289e3c5899fb396de4;hpb=f06b339c5fc4b6d1b9d2a08fe16bf7670bf7aeb4;p=mothur.git

diff --git a/mothurout.cpp b/mothurout.cpp
index 14840c1..9704464 100644
--- a/mothurout.cpp
+++ b/mothurout.cpp
@@ -43,7 +43,7 @@ set<string> MothurOut::getCurrentTypes()  {
         types.insert("tree");
         types.insert("flow");
         types.insert("biom");
-        types.insert("counttable");
+        types.insert("count");
         types.insert("processors");
 
 		return types;
@@ -79,7 +79,7 @@ void MothurOut::printCurrentFiles()  {
 		if (treefile != "")			{  mothurOut("tree=" + treefile); mothurOutEndLine();				}
 		if (flowfile != "")			{  mothurOut("flow=" + flowfile); mothurOutEndLine();				}
         if (biomfile != "")			{  mothurOut("biom=" + biomfile); mothurOutEndLine();				}
-        if (counttablefile != "")	{  mothurOut("counttable=" + counttablefile); mothurOutEndLine();	}
+        if (counttablefile != "")	{  mothurOut("count=" + counttablefile); mothurOutEndLine();	}
 		if (processors != "1")		{  mothurOut("processors=" + processors); mothurOutEndLine();		}
 		
 	}
@@ -1052,6 +1052,9 @@ int MothurOut::openInputFile(string fileName, ifstream& fileHandle){
 
 int MothurOut::renameFile(string oldName, string newName){
 	try {
+        
+        if (oldName == newName) { return 0; }
+        
 		ifstream inTest;
 		int exist = openInputFile(newName, inTest, "");
 		inTest.close();
@@ -2017,6 +2020,28 @@ bool MothurOut::mothurConvert(string item, int& num){
 		exit(1);
 	}
 }
+/***********************************************************************/
+bool MothurOut::mothurConvert(string item, intDist& num){
+	try {
+		bool error = false;
+		
+		if (isNumeric1(item)) {
+			convert(item, num);
+		}else {
+			num = 0;
+			error = true;
+			mothurOut("[ERROR]: cannot convert " + item + " to an integer."); mothurOutEndLine();
+			commandInputsConvertError = true;
+		}
+		
+		return error;
+	}
+	catch(exception& e) {
+		errorOut(e, "MothurOut", "mothurConvert");
+		exit(1);
+	}
+}
+
 /***********************************************************************/
 bool MothurOut::isNumeric1(string stringToCheck){
 	try {