X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=globaldata.cpp;h=16d434bcb47dbd18e91914214cd8fda032e9f47b;hb=0e14094b51dd81c07c6a56b7b51533eff2332339;hp=494b664fb841389aff6dca6305963d68a1a5a8cf;hpb=ee27b6e01a979fdf832668eb87412b029f77e4d7;p=mothur.git

diff --git a/globaldata.cpp b/globaldata.cpp
index 494b664..16d434b 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.seqs") {	cutoff = "1.0";		}
 
 		string key, value;		
 		//reads in parameters and values
@@ -85,10 +85,15 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 				if (key == "scale")			{ scale = value;		}
 				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;		}
+				if (key == "align")		    { align = value;		}
+				if (key == "match")			{ match = value;		}
+				if (key == "mismatch")		{ mismatch = value;	    }
+				if (key == "gapopen")		{ gapopen = value;		}
+				if (key == "gapextend" )	{ gapextend = value;	}
 				
 				if (key == "line") {//stores lines to be used in a set
 					lines.clear();
@@ -151,7 +156,15 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 			if (key == "scale")			{ scale = value;		}
 			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;		}
+			if (key == "align")		    { align = value;		}
+			if (key == "match")			{ match = value;		}
+			if (key == "mismatch")		{ mismatch = value;	    }
+			if (key == "gapopen")		{ gapopen = value;		}
+			if (key == "gapextend" )	{ gapextend = value;	}
 
 			if (key == "line") {//stores lines to be used in a vector
 				lines.clear();
@@ -185,7 +198,7 @@ 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"; }
+			if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson-efron-boneh-solow-shen"; }
 			Estimators.clear();
 			splitAtDash(calc, Estimators); 
 		}
@@ -201,7 +214,7 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 			splitAtDash(calc, Estimators); 
 		}
 		if (commandName == "summary.single") {
-			if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
+			if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson-efron-boneh-solow-shen"; }
 			Estimators.clear();
 			splitAtDash(calc, Estimators); 
 		}
@@ -215,7 +228,7 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 			Estimators.clear();
 			splitAtDash(calc, Estimators); 
 		}
-		if (commandName == "distance") {
+		if (commandName == "dist.seqs") {
 			if ((calc == "default") || (calc == "")) {  calc = "onegap";  }
 			Estimators.clear();
 			splitAtDash(calc, Estimators); 
@@ -228,7 +241,7 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 			Estimators.clear();
 			splitAtDash(calc, Estimators); 
 		}
-		if ((commandName == "tree.shared") || (commandName == "bootstrap.shared")) {
+		if ((commandName == "tree.shared") || (commandName == "bootstrap.shared") || (commandName == "dist.shared")) {
 			if (calc != "") { 
 				Estimators.clear();
 				splitAtDash(calc, Estimators);			
@@ -289,13 +302,23 @@ 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;}
+string GlobalData::getSize()            {   return size;        }
+string GlobalData::getTemplateFile()	{	return templatefile;}
+string GlobalData::getSearch()			{	return search;		}
+string GlobalData::getKSize()			{	return ksize;		}
+string GlobalData::getAlign()			{	return align;		}
+string GlobalData::getMatch()			{	return match;		}
+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::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;		}
@@ -334,6 +357,7 @@ void GlobalData::clear() {
 	clustalfile		=   "";
 	treefile		=	"";
 	sharedfile		=	"";
+	templatefile	=	"";
 	cutoff			=	"10.00";
 	format			=	"";
 	precision		=	"100";
@@ -357,7 +381,14 @@ void GlobalData::clear() {
 	scale			=	"log10";
 	ends			=   "T";  //yes
 	processors		=	"1";
-
+	size            =   "1000";
+	search			=	"suffix";
+	ksize			=	"7";
+	align			=	"blast";
+	match			=	"1.0";
+	mismatch		=	"-1.0";
+	gapopen			=	"-5.0";
+	gapextend		=	"-2.0";
 }
 
 //*******************************************************/
@@ -379,6 +410,14 @@ void GlobalData::reset() {
 	form			=	"integral";
 	ends			=   "T";
 	processors		=	"1";
+	size            =   "1000";
+	search			=	"suffix";
+	ksize			=	"7";
+	align			=	"blast";
+	match			=	"1.0";
+	mismatch		=	"-1.0";
+	gapopen			=	"-5.0";
+	gapextend		=	"-2.0";
 }
 /*******************************************************/