X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=globaldata.cpp;h=1baf4edf1bf90ef469a9426de2e06f0a3ce137fc;hb=b22853b5cfbf5c47949ad2a084f2fad88b2e4be4;hp=8b8f9e39b083d9d4329ff500f335d9f4f04cb786;hpb=bdb56fb93c1f0acfb8fa6542ebc444a0701c1f5a;p=mothur.git

diff --git a/globaldata.cpp b/globaldata.cpp
index 8b8f9e3..1baf4ed 100644
--- a/globaldata.cpp
+++ b/globaldata.cpp
@@ -86,10 +86,6 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 				if (key == "ends" )			{ ends = value;			}
 				if (key == "processors" )	{ processors = value;	}
 				if (key == "size" )         { size = value;         }
-				
-
-				
-
 				if (key == "template")		{ templatefile = value;	}
 				if (key == "search")		{ search = value;		}
 				if (key == "ksize")			{ ksize = value;		}
@@ -161,7 +157,6 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 			if (key == "ends" )			{ ends = value;			}
 			if (key == "processors" )	{ processors = value;	}
 			if (key == "size" )         { size = value;         }
-
 			if (key == "template")		{ templatefile = value;	}
 			if (key == "search")		{ search = value;		}
 			if (key == "ksize")			{ ksize = value;		}
@@ -308,12 +303,6 @@ string GlobalData::getScale()			{	return scale;		}
 string GlobalData::getEnds()			{   return ends;		}
 string GlobalData::getProcessors()		{	return processors;	}
 string GlobalData::getSize()            {   return size;        }
-
-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;}
 string GlobalData::getTemplateFile()	{	return templatefile;}
 string GlobalData::getSearch()			{	return search;		}
 string GlobalData::getKSize()			{	return ksize;		}
@@ -323,6 +312,12 @@ string GlobalData::getMismatch()		{	return mismatch;	}
 string GlobalData::getGapopen()			{	return gapopen;		}
 string GlobalData::getGapextend()		{	return gapextend;	}
 
+
+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::setGroupFile(string file)		{	groupfile = file;	}
 void GlobalData::setSharedFile(string file)		{	sharedfile = file;	inputFileName = file; fileroot = file;}
 void GlobalData::setNameFile(string file)		{	namefile = file;		}