X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedlistvector.cpp;h=6dfcb97f0aff013d15c1c641e93a24b0d7b229a3;hb=49d2b7459c5027557564b21e9487dadafbbbdc96;hp=cc3cd8df4205e2f37182a8a80037bc02bb37ca45;hpb=74844a60d80c6dd06e3fb02ee9b928424f9019b0;p=mothur.git

diff --git a/sharedlistvector.cpp b/sharedlistvector.cpp
index cc3cd8d..6dfcb97 100644
--- a/sharedlistvector.cpp
+++ b/sharedlistvector.cpp
@@ -16,32 +16,30 @@
 
 /***********************************************************************/
 
-SharedListVector::SharedListVector() : DataVector(), maxRank(0), numBins(0), numSeqs(0){globaldata = GlobalData::getInstance(); groupmap = NULL; }
+SharedListVector::SharedListVector() : DataVector(), maxRank(0), numBins(0), numSeqs(0){ groupmap = NULL; }
 
 /***********************************************************************/
 
-SharedListVector::SharedListVector(int n):	DataVector(), data(n, "") , maxRank(0), numBins(0), numSeqs(0){globaldata = GlobalData::getInstance(); groupmap = NULL; }
+SharedListVector::SharedListVector(int n):	DataVector(), data(n, "") , maxRank(0), numBins(0), numSeqs(0){ groupmap = NULL; }
 
 /***********************************************************************/
 SharedListVector::SharedListVector(ifstream& f) : DataVector(), maxRank(0), numBins(0), numSeqs(0) {
 	try {
-		globaldata = GlobalData::getInstance();
-
 		//set up groupmap for later.
-		groupmap = new GroupMap(globaldata->getGroupFile());
-		groupmap->readMap();
+		groupmap = new GroupMap(m->getGroupFile());
+		groupmap->readMap(); 
 
 		int hold;
 		string inputData;
 		f >> label >> hold;
 	
 		data.assign(hold, "");
-	
+		
 		for(int i=0;i<hold;i++){
 			f >> inputData;
 			set(i, inputData);
 		}
-	
+		
 	}
 	catch(exception& e) {
 		m->errorOut(e, "SharedListVector", "SharedListVector");
@@ -52,15 +50,17 @@ SharedListVector::SharedListVector(ifstream& f) : DataVector(), maxRank(0), numB
 /***********************************************************************/
 void SharedListVector::set(int binNumber, string seqNames){
 	try {
-		int nNames_old = getNumNames(data[binNumber]);
+		int nNames_old = m->getNumNames(data[binNumber]);
 		data[binNumber] = seqNames;
-		int nNames_new = getNumNames(seqNames);
+		int nNames_new = m->getNumNames(seqNames);
 	
 		if(nNames_old == 0)			{	numBins++;				}
 		if(nNames_new == 0)			{	numBins--;				}
 		if(nNames_new > maxRank)	{	maxRank = nNames_new;	}
 	
 		numSeqs += (nNames_new - nNames_old);
+		
+			 
 	}
 	catch(exception& e) {
 		m->errorOut(e, "SharedListVector", "set");
@@ -79,7 +79,7 @@ string SharedListVector::get(int index){
 void SharedListVector::push_back(string seqNames){
 	try {
 		data.push_back(seqNames);
-		int nNames = getNumNames(seqNames);
+		int nNames = m->getNumNames(seqNames);
 	
 		numBins++;
 	
@@ -141,7 +141,7 @@ RAbundVector SharedListVector::getRAbundVector(){
 		RAbundVector rav;
 	
 		for(int i=0;i<data.size();i++){
-			int binSize = getNumNames(data[i]);
+			int binSize = m->getNumNames(data[i]);
 			rav.push_back(binSize);
 		}
 	
@@ -171,7 +171,7 @@ SAbundVector SharedListVector::getSAbundVector(){
 		SAbundVector sav(maxRank+1);
 	
 		for(int i=0;i<data.size();i++){
-			int binSize = getNumNames(data[i]);	
+			int binSize = m->getNumNames(data[i]);	
 			sav.set(binSize, sav.get(binSize) + 1);	
 		}
 		sav.set(0, 0);
@@ -194,7 +194,7 @@ SharedOrderVector* SharedListVector::getSharedOrderVector(){
 		order->setLabel(label);
 	
 		for(int i=0;i<numBins;i++){
-			int binSize = getNumNames(get(i));	//find number of individual in given bin	
+			int binSize = m->getNumNames(get(i));	//find number of individual in given bin	
 			names = get(i);
 			while (names.find_first_of(',') != -1) { 
 				name = names.substr(0,names.find_first_of(','));
@@ -266,38 +266,62 @@ vector<SharedRAbundVector*> SharedListVector::getSharedRAbundVector() {
 		vector<SharedRAbundVector*> lookup;  //contains just the groups the user selected
 		map<string, SharedRAbundVector*> finder;  //contains all groups in groupmap
 		string group, names, name;
-	
-		util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups);
+		
+		vector<string> Groups = m->getGroups();
+		vector<string> allGroups = groupmap->getNamesOfGroups();
+		util->setGroups(Groups, allGroups);
+		m->setGroups(Groups);
 		delete util;
 
-		for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
+		for (int i = 0; i < allGroups.size(); i++) {
 			SharedRAbundVector* temp = new SharedRAbundVector(data.size());
-			finder[globaldata->gGroupmap->namesOfGroups[i]] = temp;
-			finder[globaldata->gGroupmap->namesOfGroups[i]]->setLabel(label);
-			finder[globaldata->gGroupmap->namesOfGroups[i]]->setGroup(globaldata->gGroupmap->namesOfGroups[i]);
-			if (inVector(globaldata->gGroupmap->namesOfGroups[i], globaldata->Groups)) {  //if this group is in user groups
-				lookup.push_back(finder[globaldata->gGroupmap->namesOfGroups[i]]);
+			finder[allGroups[i]] = temp;
+			finder[allGroups[i]]->setLabel(label);
+			finder[allGroups[i]]->setGroup(allGroups[i]);
+			if (m->inUsersGroups(allGroups[i], m->getGroups())) {  //if this group is in user groups
+				lookup.push_back(finder[allGroups[i]]);
 			}
 		}
 	
 		//fill vectors
 		for(int i=0;i<numBins;i++){
 			names = get(i);  
-			while (names.find_first_of(',') != -1) { 
-				name = names.substr(0,names.find_first_of(','));
-				names = names.substr(names.find_first_of(',')+1, names.length());
-				group = groupmap->getGroup(name);
-				if(group == "not found") {	m->mothurOut("Error: Sequence '" + name + "' was not found in the group file, please correct."); m->mothurOutEndLine();  exit(1); }
-				finder[group]->set(i, finder[group]->getAbundance(i) + 1, group);  //i represents what bin you are in
+			int nameLength = names.size();
+			string seqName = "";
+			
+			for(int j=0;j<nameLength;j++){
+				if(names[j] == ','){
+					group = groupmap->getGroup(seqName);
+					if(group == "not found") {	m->mothurOut("Error: Sequence '" + seqName + "' was not found in the group file, please correct."); m->mothurOutEndLine();  exit(1); }
+					finder[group]->set(i, finder[group]->getAbundance(i) + 1, group);  //i represents what bin you are in
+					
+					seqName = "";
+				}
+				else{
+					seqName += names[j];
+				}
 			}
+			group = groupmap->getGroup(seqName);
+			if(group == "not found") {	m->mothurOut("Error: Sequence '" + seqName + "' was not found in the group file, please correct."); m->mothurOutEndLine();  exit(1); }
+			finder[group]->set(i, finder[group]->getAbundance(i) + 1, group);  //i represents what bin you are in
+			
+			
+			
+//			while (names.find_first_of(',') != -1) { 
+//				name = names.substr(0,names.find_first_of(','));
+//				names = names.substr(names.find_first_of(',')+1, names.length());
+//				group = groupmap->getGroup(name);
+//				if(group == "not found") {	m->mothurOut("Error: Sequence '" + name + "' was not found in the group file, please correct."); m->mothurOutEndLine();  exit(1); }
+//				finder[group]->set(i, finder[group]->getAbundance(i) + 1, group);  //i represents what bin you are in
+//			}
 			
 			//get last name
-			group = groupmap->getGroup(names);
-			if(group == "not found") {	m->mothurOut("Error: Sequence '" + names + "' was not found in the group file, please correct."); m->mothurOutEndLine();  exit(1); }
-			finder[group]->set(i, finder[group]->getAbundance(i) + 1, group);  //i represents what bin you are in
+//			group = groupmap->getGroup(names);
+//			if(group == "not found") {	m->mothurOut("Error: Sequence '" + names + "' was not found in the group file, please correct."); m->mothurOutEndLine();  exit(1); }
+//			finder[group]->set(i, finder[group]->getAbundance(i) + 1, group);  //i represents what bin you are in
 			
 		}
-		
+
 		return lookup;
 	}
 	catch(exception& e) {
@@ -331,7 +355,7 @@ OrderVector SharedListVector::getOrderVector(map<string,int>* orderMap = NULL){
 			OrderVector ov;
 		
 			for(int i=0;i<data.size();i++){
-				int binSize = getNumNames(data[i]);		
+				int binSize = m->getNumNames(data[i]);		
 				for(int j=0;j<binSize;j++){
 					ov.push_back(i);
 				}