X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=globaldata.cpp;h=fddb5c9caadb3e2e7fcaf7f940718eacb6c39e30;hb=ec453945974b5c72af0bea042e3517312566d592;hp=ae1b0e2ebbb463fefc32a2f8ad3fd1816b01109d;hpb=3117b1c3109121dff476997d3c5db5b47a77729b;p=mothur.git

diff --git a/globaldata.cpp b/globaldata.cpp
index ae1b0e2..fddb5c9 100644
--- a/globaldata.cpp
+++ b/globaldata.cpp
@@ -43,7 +43,7 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 		}
 		
 		//set default value for cutoff
-		if (commandName == "distance") {	cutoff = "1.0";		}
+		if (commandName == "dist.seq") {	cutoff = "1.0";		}
 
 		string key, value;		
 		//reads in parameters and values
@@ -215,7 +215,7 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 			Estimators.clear();
 			splitAtDash(calc, Estimators); 
 		}
-		if (commandName == "distance") {
+		if (commandName == "dist.seq") {
 			if ((calc == "default") || (calc == "")) {  calc = "onegap";  }
 			Estimators.clear();
 			splitAtDash(calc, Estimators); 
@@ -290,11 +290,13 @@ string GlobalData::getScale()			{	return scale;		}
 string GlobalData::getEnds()			{   return ends;		}
 string GlobalData::getProcessors()		{	return processors;	}
 
-void GlobalData::setListFile(string file)	{	listfile = file;	inputFileName = file;}
-void GlobalData::setRabundFile(string file)	{	rabundfile = file;	inputFileName = file;}
-void GlobalData::setSabundFile(string file)	{	sabundfile = file;	inputFileName = file;}
-void GlobalData::setPhylipFile(string file)	{	phylipfile = file;    inputFileName = file;}
-void GlobalData::setColumnFile(string file)	{	columnfile = file;    inputFileName = file;}
+void GlobalData::setListFile(string file)		{	listfile = file;	inputFileName = file;}
+void GlobalData::setGroupFile(string file)		{	groupfile = file;	}
+void GlobalData::setRabundFile(string file)		{	rabundfile = file;	inputFileName = file;}
+void GlobalData::setSabundFile(string file)		{	sabundfile = file;	inputFileName = file;}
+void GlobalData::setPhylipFile(string file)		{	phylipfile = file;    inputFileName = file;}
+void GlobalData::setColumnFile(string file)		{	columnfile = file;    inputFileName = file;}
+void GlobalData::setSharedFile(string file)		{	sharedfile = file;	inputFileName = file; fileroot = file;}
 void GlobalData::setNameFile(string file)		{	namefile = file;		}
 void GlobalData::setFormat(string Format)		{	format = Format;		}
 void GlobalData::setRandomTree(string Random)	{	randomtree = Random;	}