X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedrabundvector.cpp;h=a050ab3fe71998b5a8a6abf2b34b0e67f0083808;hb=37eac2026d91179acda0494c4dcca22f176551b9;hp=d135091c3301ed428a8e8e0391a2120643a21520;hpb=e189982e0a9b7352ad57cc38ccee675f128be22e;p=mothur.git

diff --git a/sharedrabundvector.cpp b/sharedrabundvector.cpp
index d135091..a050ab3 100644
--- a/sharedrabundvector.cpp
+++ b/sharedrabundvector.cpp
@@ -70,11 +70,14 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0),
 		string holdLabel, nextLabel, groupN;
 		individual newguy;
 		
-		for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; }
-		lookup.clear();
+		for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; }  lookup.clear();
+		
+		if (globaldata->saveNextLabel == "") {  f >> label;  }
+		else { label = globaldata->saveNextLabel; }
 		
 		//read in first row since you know there is at least 1 group.
-		f >> label >> groupN >> num;
+		f >> groupN >> num;
+
 		holdLabel = label;
 		
 		//add new vector to lookup
@@ -98,13 +101,12 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0),
 			//numSeqs += inputData;
 			//numBins++;
 			if (inputData > maxRank) { maxRank = inputData; }
-			
 		}
 		
-		gobble(f);
-		
-		if (f.eof() != true) { f >> nextLabel; }
+		m->gobble(f);
 		
+		if (!(f.eof())) { f >> nextLabel; }
+	
 		//read the rest of the groups info in
 		while ((nextLabel == holdLabel) && (f.eof() != true)) {
 			f >> groupN >> num;
@@ -112,6 +114,7 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0),
 			
 			if (globaldata->gGroupmap == NULL) { 
 				//save group in groupmap
+	
 				groupmap->namesOfGroups.push_back(groupN);
 				groupmap->groupIndex[groupN] = count;
 			}
@@ -128,13 +131,12 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0),
 				lookup[count]->push_back(inputData, groupN); //abundance, bin, group
 			}
 			
-			gobble(f);
+			m->gobble(f);
 				
 			if (f.eof() != true) { f >> nextLabel; }
 		}
-		
-		//put file pointer back since you are now at a new distance label
-		for (int i = 0; i < nextLabel.length(); i++) { f.unget();  }
+	
+		globaldata->saveNextLabel = nextLabel;
 	
 		if (globaldata->gGroupmap == NULL) { globaldata->gGroupmap = groupmap;  }
 		
@@ -202,6 +204,16 @@ vector <individual> SharedRAbundVector::getData(){
 }
 /***********************************************************************/
 
+void SharedRAbundVector::clear(){
+	numBins = 0;
+	maxRank = 0;
+	numSeqs = 0;
+	data.clear();
+	for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; }
+	lookup.clear();
+}
+/***********************************************************************/
+
 void SharedRAbundVector::push_back(int binSize, string groupName){
 	try {
 		individual newGuy;
@@ -359,10 +371,12 @@ vector<SharedRAbundVector*> SharedRAbundVector::getSharedRAbundVectors(){
 		util = new SharedUtil();
 		
 		util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups);
-
+		
+		bool remove = false;
 		for (int i = 0; i < lookup.size(); i++) {
 			//if this sharedrabund is not from a group the user wants then delete it.
 			if (util->isValidGroup(lookup[i]->getGroup(), globaldata->Groups) == false) { 
+				remove = true;
 				delete lookup[i]; lookup[i] = NULL;
 				lookup.erase(lookup.begin()+i); 
 				i--; 
@@ -370,6 +384,8 @@ vector<SharedRAbundVector*> SharedRAbundVector::getSharedRAbundVectors(){
 		}
 		
 		delete util;
+		
+		if (remove) { eliminateZeroOTUS(lookup); }
 	
 		return lookup;
 	}
@@ -378,6 +394,81 @@ vector<SharedRAbundVector*> SharedRAbundVector::getSharedRAbundVectors(){
 		exit(1);
 	}
 }
+//**********************************************************************************************************************
+int SharedRAbundVector::eliminateZeroOTUS(vector<SharedRAbundVector*>& thislookup) {
+		try {
+			
+			vector<SharedRAbundVector*> newLookup;
+			for (int i = 0; i < thislookup.size(); i++) {
+				SharedRAbundVector* temp = new SharedRAbundVector();
+				temp->setLabel(thislookup[i]->getLabel());
+				temp->setGroup(thislookup[i]->getGroup());
+				newLookup.push_back(temp);
+			}
+			
+			//for each bin
+			for (int i = 0; i < thislookup[0]->getNumBins(); i++) {
+				if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) {  delete newLookup[j];  } return 0; }
+				
+				//look at each sharedRabund and make sure they are not all zero
+				bool allZero = true;
+				for (int j = 0; j < thislookup.size(); j++) {
+					if (thislookup[j]->getAbundance(i) != 0) { allZero = false;  break;  }
+				}
+				
+				//if they are not all zero add this bin
+				if (!allZero) {
+					for (int j = 0; j < thislookup.size(); j++) {
+						newLookup[j]->push_back(thislookup[j]->getAbundance(i), thislookup[j]->getGroup());
+					}
+				}
+			}
+			
+			for (int j = 0; j < thislookup.size(); j++) {  delete thislookup[j];  }
+			
+			thislookup = newLookup;
+			
+			return 0;
+			
+		}
+		catch(exception& e) {
+			m->errorOut(e, "SharedRAbundVector", "eliminateZeroOTUS");
+			exit(1);
+		}
+	}
+	
+/***********************************************************************/
+vector<SharedRAbundFloatVector*> SharedRAbundVector::getSharedRAbundFloatVectors(vector<SharedRAbundVector*> thislookup){
+	try {
+		vector<SharedRAbundFloatVector*> newLookupFloat;	
+		for (int i = 0; i < lookup.size(); i++) {
+			SharedRAbundFloatVector* temp = new SharedRAbundFloatVector();
+			temp->setLabel(thislookup[i]->getLabel());
+			temp->setGroup(thislookup[i]->getGroup());
+			newLookupFloat.push_back(temp);
+		}
+		
+		for (int i = 0; i < thislookup.size(); i++) {
+			
+			for (int j = 0; j < thislookup[i]->getNumBins(); j++) {
+				
+				if (m->control_pressed) { return newLookupFloat; }
+				
+				int abund = thislookup[i]->getAbundance(j);
+				
+				float relabund = abund / (float) thislookup[i]->getNumSeqs();
+				
+				newLookupFloat[i]->push_back(relabund, thislookup[i]->getGroup());
+			}
+		}
+		
+		return newLookupFloat;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SharedRAbundVector", "getSharedRAbundVectors");
+		exit(1);
+	}
+}
 /***********************************************************************/
 
 RAbundVector SharedRAbundVector::getRAbundVector() {
@@ -483,15 +574,15 @@ SharedOrderVector SharedRAbundVector::getSharedOrderVector() {
 OrderVector SharedRAbundVector::getOrderVector(map<string,int>* nameMap = NULL) {
 	try {
 		OrderVector ov;
-	
-		for(int i=0;i<data.size();i++){
+		for(int i=0;i<numBins;i++){
 			for(int j=0;j<data[i].abundance;j++){
 				ov.push_back(i);
 			}
 		}
 		random_shuffle(ov.begin(), ov.end());
-
+		
 		ov.setLabel(label);	
+
 		return ov;
 	}
 	catch(exception& e) {