X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=globaldata.cpp;h=ce10ee1bca9ea35dca648c97a49e1657a11509ee;hb=dc08123b7f14e2305e5bb2b3a8fcef96fc829b07;hp=67c49bd28c942d5c432538b6f965406c0b592ae6;hpb=2e5ec5cbbd23637ed20da9bdd544d178a3b5d949;p=mothur.git

diff --git a/globaldata.cpp b/globaldata.cpp
index 67c49bd..ce10ee1 100644
--- a/globaldata.cpp
+++ b/globaldata.cpp
@@ -1,9 +1,6 @@
 #include "globaldata.hpp"
-#include "sparsematrix.hpp"
 #include "tree.h"
-#include "rabundvector.hpp"
-#include "sabundvector.hpp"
-#include "listvector.hpp"
+#include "sparsematrix.hpp"
 
 /*******************************************************/
 
@@ -76,6 +73,7 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 				if (key == "step")			{ step = value;			}
 				if (key == "form")			{ form = value;			}
 				if (key == "sorted")		{ sorted = value;		}
+				if (key == "scale")			{ scale = value;		}
 				
 
 				
@@ -131,6 +129,8 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 			if (key == "step")			{ step = value;			}
 			if (key == "form")			{ form = value;			}
 			if (key == "sorted")		{ sorted = value;		}
+			if (key == "scale")			{ scale = value;		}
+			
 
 			if (key == "line") {//stores lines to be used in a vector
 				lines.clear();
@@ -140,6 +140,7 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 				if (line != "all") {  splitAtDash(value, lines);  allLines = 0;  }
 				else { allLines = 1;  }
 			}
+			
 			if (key == "label") {//stores lines to be used in a vector
 				labels.clear();
 				lines.clear();
@@ -162,7 +163,7 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 				
 		//input defaults for calculators
 		if (commandName == "collect.single") {
-			if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson-geom-qstat-logsd-bergerparker-bstick"; }
+			if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
 			Estimators.clear();
 			splitAtDash(calc, Estimators); 
 		}
@@ -172,17 +173,17 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 			splitAtDash(calc, Estimators); 
 		}
 		if (commandName == "collect.shared") {
-			if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-sharedjabund-sharedsorensonabund-sharedjclass-sharedsorclass-sharedjest-sharedsorest-sharedthetayc-sharedthetan-sharedkstest-sharedbdiversity"; }
+			if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan"; }
 			Estimators.clear();
 			splitAtDash(calc, Estimators); 
 		}
 		if (commandName == "summary.single") {
-			if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson-geom-logsd-qstat-bergerparker-bstick"; }
+			if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
 			Estimators.clear();
 			splitAtDash(calc, Estimators); 
 		}
 		if (commandName == "summary.shared") {
-			if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-sharedjabund-sharedsorensonabund-sharedjclass-sharedsorclass-sharedjest-sharedsorest-sharedthetayc-sharedthetan-sharedkstest-sharedbdiversity"; }
+			if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan"; }
 			Estimators.clear();
 			splitAtDash(calc, Estimators); 
 		}
@@ -199,6 +200,13 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 			Estimators.clear();
 			splitAtDash(calc, Estimators); 
 		}
+		if ((commandName == "tree.shared") || (commandName == "bootstrap.shared")) {
+			if (calc != "") { 
+				Estimators.clear();
+				splitAtDash(calc, Estimators);			
+			}else { cout << "You have not specified any calculators." << endl; }
+		}
+
 
 		//if you have done a read.otu with a groupfile but don't want to use it anymore because you want to do single commands
 		if ((commandName == "collect.single") || (commandName == "rarefaction.single") || (commandName == "summary.single")) {
@@ -245,6 +253,7 @@ string GlobalData::getGroups()			{	return groups;		}
 string GlobalData::getStep()			{	return step;		}
 string GlobalData::getForm()			{	return form;		}
 string GlobalData::getSorted()			{	return sorted;		}
+string GlobalData::getScale()			{	return scale;		}
 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;}
@@ -263,6 +272,8 @@ GlobalData::GlobalData() {
 	//option definitions should go here...
 	helpRequest = "";
 	clear();
+	gListVector == NULL;		
+	gSparseMatrix == NULL;	
 }
 /*******************************************************/
 
@@ -295,7 +306,8 @@ void GlobalData::clear() {
 	abund           =   "10";
 	step			=	"0.01";
 	form			=	"integral";
-	sorted			=	"1";  //0 means don't sort, 1 means sort.
+	sorted			=	"T";  //F means don't sort, T means sort.
+	scale			=	"log10";
 }
 
 //*******************************************************/
@@ -307,7 +319,7 @@ void GlobalData::reset() {
 	iters			=	"1000"; 
 	groups			=	"";
 	jumble			=	"1";	//0 means don't jumble, 1 means jumble.
-	sorted			=	"1";  //0 means don't sort, 1 means sort.
+	sorted			=	"T";  //F means don't sort, T means sort.
 	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";
@@ -382,7 +394,7 @@ void GlobalData::parseTreeFile() {
 			
 			//use nexus translation rather than parsing tree to save time
 			if ((holder == "translate") || (holder == "Translate")) {
-cout << "there is a translate " << endl;
+
 				string number, name, h;
 				h = ""; // so it enters the loop the first time
 				while((h != ";") && (number != ";")) {