X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=globaldata.cpp;h=6138e2cc1b8f4fc70b8febc1105fcecca0448306;hb=4f4070ac3fbb5da75f834b48062e9123364b006e;hp=a8e88c52ffbd9d9fe9bb711d4be2cf0c361c9212;hpb=a8f5a612bba54ceb74e17efc027d3a7f5aa93c9a;p=mothur.git

diff --git a/globaldata.cpp b/globaldata.cpp
index a8e88c5..6138e2c 100644
--- a/globaldata.cpp
+++ b/globaldata.cpp
@@ -60,8 +60,6 @@ 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;		}
@@ -96,6 +94,12 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 				if (key == "mismatch")		{ mismatch = value;	    }
 				if (key == "gapopen")		{ gapopen = value;		}
 				if (key == "gapextend" )	{ gapextend = value;	}
+				if (key == "start" )		{ startPos = value;	}
+				if (key == "end" )			{ endPos = value;	}
+				if (key == "maxambig" )		{ maxAmbig = value;	}
+				if (key == "maxhomop" )		{ maxHomoPolymer = value;	}
+				if (key == "minlength" )	{ minLength = value;	}
+				if (key == "maxlength" )	{ maxLength = value;	}
 				
 				if (key == "line") {//stores lines to be used in a vector
 					lines.clear();
@@ -132,10 +136,8 @@ 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 == "shared" )	{ sharedfile = value; inputFileName = value; fileroot = value; format = "sharedfile";	}
 			if (key == "name" )		{ namefile = value;		}
 			if (key == "order" )	{ orderfile = value;	}
 			if (key == "group" )	{ groupfile = value;	}
@@ -168,6 +170,13 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 			if (key == "mismatch")		{ mismatch = value;	    }
 			if (key == "gapopen")		{ gapopen = value;		}
 			if (key == "gapextend" )	{ gapextend = value;	}
+			if (key == "start" )		{ startPos = value;	}
+			if (key == "end" )			{ endPos = value;	}
+			if (key == "maxambig" )		{ maxAmbig = value;	}
+			if (key == "maxhomop" )		{ maxHomoPolymer = value;	}
+			if (key == "minlength" )	{ minLength = value;	}
+			if (key == "maxlength" )	{ maxLength = value;	}
+
 
 			if (key == "line") {//stores lines to be used in a vector
 				lines.clear();
@@ -211,7 +220,6 @@ 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); 
@@ -291,8 +299,6 @@ 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;	}
@@ -323,6 +329,12 @@ string GlobalData::getMatch()			{	return match;		}
 string GlobalData::getMismatch()		{	return mismatch;	}
 string GlobalData::getGapopen()			{	return gapopen;		}
 string GlobalData::getGapextend()		{	return gapextend;	}
+string GlobalData::getStartPos()		{	return startPos;	}
+string GlobalData::getEndPos()			{	return endPos;		}
+string GlobalData::getMaxAmbig()		{	return maxAmbig;	}
+string GlobalData::getMaxHomoPolymer()	{	return maxHomoPolymer;	}
+string GlobalData::getMinLength()		{	return minLength;	}
+string GlobalData::getMaxLength()		{	return maxLength;	}
 
 
 void GlobalData::setListFile(string file)		{	listfile = file;	inputFileName = file;					}
@@ -348,8 +360,8 @@ GlobalData::GlobalData() {
 	//option definitions should go here...
 	helpRequest = "";
 	clear();
-	gListVector == NULL;		
-	gSparseMatrix == NULL;	
+	gListVector = NULL;		
+	gSparseMatrix = NULL;	
 }
 /*******************************************************/
 
@@ -365,8 +377,6 @@ void GlobalData::clear() {
 	groupfile		=	""; 
 	orderfile		=	"";
 	fastafile		=   "";
-	nexusfile		=   "";
-	clustalfile		=   "";
 	treefile		=	"";
 	sharedfile		=	"";
 	candidatefile	=	"";
@@ -386,7 +396,7 @@ void GlobalData::clear() {
 	step			=	"0.01";
 	form			=	"integral";
 	sorted			=	"T";  //F means don't sort, T means sort.
-	vertical        =   "";		
+	vertical        =   "F";		
 	trump           =	"";		
 	hard			=   "";		
 	soft            =   "";	
@@ -395,18 +405,27 @@ void GlobalData::clear() {
 	processors		=	"1";
 	size            =   "0";
 	search			=	"kmer";
-	ksize			=	"7";
+	ksize			=	"8";
 	align			=	"needleman";
 	match			=	"1.0";
 	mismatch		=	"-1.0";
 	gapopen			=	"-1.0";
 	gapextend		=	"-2.0";
+	startPos		=	"-1";
+	endPos			=	"-1";
+	maxAmbig		=	"-1";
+	maxHomoPolymer	=	"-1";
+	minLength		=	"-1";
+	maxLength		=	"-1";
+	
 }
 
 //*******************************************************/
 
 /******************************************************/
 void GlobalData::reset() {
+	label			=	"";
+	line			=   "";
 	cutoff			=	"10.00";
 	precision		=	"100";
 	iters			=	"1000"; 
@@ -424,7 +443,7 @@ void GlobalData::reset() {
 	processors		=	"1";
 	size            =   "0";
 	search			=	"kmer";
-	ksize			=	"7";
+	ksize			=	"8";
 	align			=	"needleman";
 	match			=	"1.0";
 	mismatch		=	"-1.0";
@@ -434,7 +453,13 @@ void GlobalData::reset() {
 	trump           =   "";		
 	hard			=   "";		
 	soft            =   "";	
-
+	startPos		=	"-1";
+	endPos			=	"-1";
+	maxAmbig		=	"-1";
+	maxHomoPolymer	=	"-1";
+	minLength		=	"-1";
+	maxLength		=	"-1";
+	
 }
 /*******************************************************/
 
@@ -449,6 +474,8 @@ GlobalData::~GlobalData() {
 
 /*******************************************************/
 void GlobalData::parseTreeFile() {
+	//Why is THIS in GlobalData??? - PDS
+	
 	//only takes names from the first tree and assumes that all trees use the same names.
 	try {
 		string filename = treefile;