X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=globaldata.cpp;h=a0ccdcb690eda34efb4fe9964b375b47b0e71d2f;hb=2d2fbc80f9359b19873ba3e63970b58f4f8f49f3;hp=3ddd02e5c24dc03cd8ff7549b6b03a32982562e9;hpb=39ef0543b73cb12dfc64529522b66ad3df7527d0;p=mothur.git

diff --git a/globaldata.cpp b/globaldata.cpp
index 3ddd02e..a0ccdcb 100644
--- a/globaldata.cpp
+++ b/globaldata.cpp
@@ -20,7 +20,6 @@ GlobalData* GlobalData::getInstance() {
 //This function parses through the option string of the command to remove its parameters
 void GlobalData::parseGlobalData(string commandString, string optionText){
 	try {
-		allLines = 1;
 		commandName = commandString; //save command name to be used by other classes
 		
 		//set all non filename paramters to default
@@ -32,6 +31,7 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 			gGroupmap = NULL;
 			gTree.clear();
 			labels.clear(); lines.clear(); groups.clear();
+			allLines = 1;
 		}
 		
 		//saves help request
@@ -39,6 +39,11 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 			helpRequest = optionText;
 		}
 		
+		if (commandName == "libshuff") {
+			iters = "10000";
+			cutoff = "1.0";
+		}
+		
 		string key, value;		
 		//reads in parameters and values
 		if((optionText != "") && (commandName != "help")){
@@ -66,7 +71,10 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 				if (key == "fileroot" )		{ fileroot = value;		}
 				if (key == "abund" )        { abund = value;        }
 				if (key == "random" )		{ randomtree = value;	}
-				if (key == "calc")			{ calc = value;		}
+				if (key == "calc")			{ calc = value;			}
+				if (key == "step")			{ step = value;			}
+				if (key == "form")			{ form = value;			}
+				
 
 				
 				if (key == "line") {//stores lines to be used in a set
@@ -116,22 +124,24 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 			if (key == "abund" )        { abund = value;        }
 			if (key == "random" )		{ randomtree = value;	}
 			if (key == "calc")			{ calc = value;		}
-
+			if (key == "step")			{ step = value;			}
+			if (key == "form")			{ form = value;			}
 
 			if (key == "line") {//stores lines to be used in a vector
 				lines.clear();
 				line = value;
 				label = "";
-				splitAtDash(value, lines);
-				allLines = 0;
+				if (line != "all") {  splitAtDash(value, lines);  allLines = 0;  }
+				else { allLines = 1;  }
 			}
 			if (key == "label") {//stores lines to be used in a vector
 				labels.clear();
 				label = value;
 				line = "";
-				splitAtDash(value, labels);
-				allLines = 0;
+				if (label != "all") {  splitAtDash(value, labels);  allLines = 0;  }
+				else { allLines = 1;  }
 			}
+			
 			if (key == "groups") {//stores groups to be used in a vector
 					Groups.clear();
 					groups = value;
@@ -217,6 +227,8 @@ string GlobalData::getFreq()			{	return freq;		}
 string GlobalData::getAbund()           {   return abund;       }
 string GlobalData::getRandomTree()		{	return randomtree;	}
 string GlobalData::getGroups()			{	return groups;		}
+string GlobalData::getStep()			{	return step;		}
+string GlobalData::getForm()			{	return form;		}
 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;}
@@ -265,6 +277,8 @@ void GlobalData::clear() {
 	method			=	"furthest";
 	fileroot		=	"";
 	abund           =   "10";
+	step			=	"0.01";
+	form			=	"integral";
 }
 
 //*******************************************************/
@@ -274,15 +288,15 @@ void GlobalData::reset() {
 	cutoff			=	"10.00";
 	precision		=	"100";
 	iters			=	"1000"; 
-	line			=   "";
-	label			=	"";
 	groups			=	"";
 	jumble			=	"1";	//0 means don't jumble, 1 means jumble.
 	randomtree		=	"";  //"" means user will enter some user trees, "outputfile" means they just want the random tree distribution to be outputted to outputfile.
 	freq			=	"100";
 	method			=	"furthest";
 	calc			=	"";
-	abund = "10";
+	abund			=   "10";
+	step			=	"0.01";
+	form			=	"integral";
 }
 /*******************************************************/