X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=globaldata.cpp;h=ae1b0e2ebbb463fefc32a2f8ad3fd1816b01109d;hb=3117b1c3109121dff476997d3c5db5b47a77729b;hp=312b314120adf6eef3beb5d09bf21517e103c5cc;hpb=477e76a8a79b60f6cd4253324dd830bdea25e3e9;p=mothur.git

diff --git a/globaldata.cpp b/globaldata.cpp
index 312b314..ae1b0e2 100644
--- a/globaldata.cpp
+++ b/globaldata.cpp
@@ -42,6 +42,9 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 			cutoff = "1.0";
 		}
 		
+		//set default value for cutoff
+		if (commandName == "distance") {	cutoff = "1.0";		}
+
 		string key, value;		
 		//reads in parameters and values
 		if((optionText != "") && (commandName != "help")){
@@ -54,7 +57,9 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 				if (key == "list" )		{ listfile = value; inputFileName = value; fileroot = value; format = "list";		}
 				if (key == "rabund" )	{ rabundfile = value; inputFileName = value; fileroot = value; format = "rabund";	}
 				if (key == "sabund" )	{ sabundfile = value; inputFileName = value; fileroot = value; format = "sabund";	} 
-				if (key == "fasta" )	{ fastafile = value; inputFileName = value; fileroot = value; format = "fasta";		} 
+				if (key == "fasta" )	{ fastafile = value; inputFileName = value; fileroot = value; format = "fasta";		}
+				if (key == "nexus" )	{ nexusfile = value; inputFileName = value; fileroot = value; format = "nexus";		} 
+				if (key == "clustal" )	{ clustalfile = value; inputFileName = value; fileroot = value; format = "clustal"; }
 				if (key == "tree" )		{ treefile = value; inputFileName = value; fileroot = value; format = "tree";		}
 				if (key == "shared" )	{ sharedfile = value; inputFileName = value; fileroot = value; format = "sharedfile";	}
 				if (key == "name" )		{ namefile = value;		}
@@ -73,7 +78,15 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 				if (key == "step")			{ step = value;			}
 				if (key == "form")			{ form = value;			}
 				if (key == "sorted")		{ sorted = value;		}
+				if (key == "vertical")		{ vertical = value;		}
+				if (key == "trump")		    { trump = value;		}
+				if (key == "filter")		{ filter = value;		}
+				if (key == "soft")		    { soft = value;		    }
 				if (key == "scale")			{ scale = value;		}
+				if (key == "ends" )			{ ends = value;			}
+				if (key == "processors" )	{ processors = value;	}
+				
+
 				
 
 				
@@ -111,6 +124,8 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 			if (key == "rabund" )	{ rabundfile = value; inputFileName = value; fileroot = value; format = "rabund";	}
 			if (key == "sabund" )	{ sabundfile = value; inputFileName = value; fileroot = value; format = "sabund";	}
 			if (key == "fasta" )	{ fastafile = value; inputFileName = value; fileroot = value; format = "fasta";		}
+			if (key == "nexus" )	{ nexusfile = value; inputFileName = value; fileroot = value; format = "nexus";		}
+			if (key == "clustal" )	{ clustalfile = value; inputFileName = value; fileroot = value; format = "clustal"; } 
 			if (key == "tree" )		{ treefile = value; inputFileName = value; fileroot = value; format = "tree";		} 
 			if (key == "shared" )	{ sharedfile = value; inputFileName = value; fileroot = value; format = "sharedfile";	} 
 			if (key == "name" )		{ namefile = value;		}
@@ -129,8 +144,14 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 			if (key == "step")			{ step = value;			}
 			if (key == "form")			{ form = value;			}
 			if (key == "sorted")		{ sorted = value;		}
+			if (key == "vertical")		{ vertical = value;		}
+			if (key == "trump")		    { trump = value;		}
+			if (key == "filter")		{ filter = value;		}
+			if (key == "soft")		    { soft = value;		    }
 			if (key == "scale")			{ scale = value;		}
-			
+			if (key == "ends" )			{ ends = value;			}
+			if (key == "processors" )	{ processors = value;	}
+
 
 			if (key == "line") {//stores lines to be used in a vector
 				lines.clear();
@@ -163,6 +184,7 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 				
 		//input defaults for calculators
 		if (commandName == "collect.single") {
+
 			if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
 			Estimators.clear();
 			splitAtDash(calc, Estimators); 
@@ -173,6 +195,7 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 			splitAtDash(calc, Estimators); 
 		}
 		if (commandName == "collect.shared") {
+
 			if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan"; }
 			Estimators.clear();
 			splitAtDash(calc, Estimators); 
@@ -192,6 +215,11 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 			Estimators.clear();
 			splitAtDash(calc, Estimators); 
 		}
+		if (commandName == "distance") {
+			if ((calc == "default") || (calc == "")) {  calc = "onegap";  }
+			Estimators.clear();
+			splitAtDash(calc, Estimators); 
+		}
 		if (commandName == "venn") {
 			if ((calc == "default") || (calc == "")) { 
 				if (format == "list") { calc = "sobs"; }
@@ -239,6 +267,8 @@ string GlobalData::getOrderFile()		{	return orderfile;	}
 string GlobalData::getTreeFile()		{	return treefile;	}
 string GlobalData::getSharedFile()		{	return sharedfile;	}
 string GlobalData::getFastaFile()		{	return fastafile;	}
+string GlobalData::getNexusFile()		{	return nexusfile;	}
+string GlobalData::getClustalFile()     {   return clustalfile; }
 string GlobalData::getCutOff()			{	return cutoff;		}
 string GlobalData::getFormat()			{	return format;		}
 string GlobalData::getPrecision()		{	return precision;	}
@@ -253,7 +283,13 @@ string GlobalData::getGroups()			{	return groups;		}
 string GlobalData::getStep()			{	return step;		}
 string GlobalData::getForm()			{	return form;		}
 string GlobalData::getSorted()			{	return sorted;		}
+string GlobalData::getTrump()			{   return trump;       }
+string GlobalData::getSoft()			{   return soft;		}
+string GlobalData::getFilter()			{   return filter;		}
 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;}
@@ -264,6 +300,9 @@ void GlobalData::setFormat(string Format)		{	format = Format;		}
 void GlobalData::setRandomTree(string Random)	{	randomtree = Random;	}
 void GlobalData::setGroups(string g)			{	groups = g;				}
 void GlobalData::setCalc(string Calc)			{	calc = Calc;			}
+void GlobalData::setEnds(string e)				{   ends = e;				}
+void GlobalData::setProcessors(string p)		{	processors = p;			}
+
 
 /*******************************************************/
 
@@ -272,6 +311,8 @@ GlobalData::GlobalData() {
 	//option definitions should go here...
 	helpRequest = "";
 	clear();
+	gListVector == NULL;		
+	gSparseMatrix == NULL;	
 }
 /*******************************************************/
 
@@ -287,6 +328,8 @@ void GlobalData::clear() {
 	groupfile		=	""; 
 	orderfile		=	"";
 	fastafile		=   "";
+	nexusfile		=   "";
+	clustalfile		=   "";
 	treefile		=	"";
 	sharedfile		=	"";
 	cutoff			=	"10.00";
@@ -305,7 +348,14 @@ void GlobalData::clear() {
 	step			=	"0.01";
 	form			=	"integral";
 	sorted			=	"T";  //F means don't sort, T means sort.
+	vertical        =   "";		
+	trump           =   "";		
+	filter          =   "";		
+	soft            =   "";	
 	scale			=	"log10";
+	ends			=   "T";  //yes
+	processors		=	"1";
+
 }
 
 //*******************************************************/
@@ -325,6 +375,8 @@ void GlobalData::reset() {
 	abund			=   "10";
 	step			=	"0.01";
 	form			=	"integral";
+	ends			=   "T";
+	processors		=	"1";
 }
 /*******************************************************/