X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedrabundvector.cpp;h=f42d24ba4081cd95c1aa2f89367054755f136807;hb=ba2b95b22ab8947d5583ca2c2da74557870b6861;hp=74fb1c51ebb37d10185dced775be0af3829a7c41;hpb=1bf53bca7e26bf091588bc8ca6e68cbfae1df6fe;p=mothur.git

diff --git a/sharedrabundvector.cpp b/sharedrabundvector.cpp
index 74fb1c5..f42d24b 100644
--- a/sharedrabundvector.cpp
+++ b/sharedrabundvector.cpp
@@ -59,8 +59,9 @@ SharedRAbundVector::SharedRAbundVector(string id, vector<individual> rav) : Data
 //reads a shared file
 SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0), numBins(0), numSeqs(0) {
 	try {
-		m->namesOfGroups.clear();
-				
+		m->clearAllGroups();
+		vector<string> allGroups;
+		
 		int num, inputData, count;
 		count = 0;  
 		string holdLabel, nextLabel, groupN;
@@ -112,7 +113,7 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0),
 		lookup[0]->setLabel(label);
 		lookup[0]->setGroup(groupN);
 		
-		m->namesOfGroups.push_back(groupN);
+		allGroups.push_back(groupN);
 		
 		//fill vector.  data = first sharedrabund in file
 		for(int i=0;i<num;i++){
@@ -133,7 +134,7 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0),
 			f >> groupN >> num;
 			count++;
 			
-			m->namesOfGroups.push_back(groupN);
+			allGroups.push_back(groupN);
 			
 			//add new vector to lookup
 			temp = new SharedRAbundVector();
@@ -152,7 +153,8 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0),
 				
 			if (f.eof() != true) { f >> nextLabel; }
 		}
-			m->saveNextLabel = nextLabel;
+		m->saveNextLabel = nextLabel;
+		m->setAllGroups(allGroups);
 		
 	}
 	catch(exception& e) {
@@ -334,13 +336,19 @@ int SharedRAbundVector::size(){
 /***********************************************************************/
 void SharedRAbundVector::printHeaders(ostream& output){
 	try {
-		
+		string snumBins = toString(numBins);
 		output << "label\tGroup\tnumOtus\t";
 		if (m->sharedHeaderMode == "tax") {
 			for (int i = 0; i < numBins; i++) {  
 				
 				//if there is a bin label use it otherwise make one
-				string binLabel = "PhyloType" + toString(i+1);
+				string binLabel = "PhyloType";
+				string sbinNumber = toString(i+1);
+				if (sbinNumber.length() < snumBins.length()) { 
+					int diff = snumBins.length() - sbinNumber.length();
+					for (int h = 0; h < diff; h++) { binLabel += "0"; }
+				}
+				binLabel += sbinNumber;
 				if (i < m->currentBinLabels.size()) {  binLabel = m->currentBinLabels[i]; }
 				
 				output << binLabel << '\t'; 
@@ -349,10 +357,16 @@ void SharedRAbundVector::printHeaders(ostream& output){
 		}else {
 			for (int i = 0; i < numBins; i++) {  
 				//if there is a bin label use it otherwise make one
-				string mybinLabel = "Otu" + toString(i+1);
-				if (i < m->currentBinLabels.size()) {  mybinLabel = m->currentBinLabels[i]; }
+				string binLabel = "Otu";
+				string sbinNumber = toString(i+1);
+				if (sbinNumber.length() < snumBins.length()) { 
+					int diff = snumBins.length() - sbinNumber.length();
+					for (int h = 0; h < diff; h++) { binLabel += "0"; }
+				}
+				binLabel += sbinNumber;
+				if (i < m->currentBinLabels.size()) {  binLabel = m->currentBinLabels[i]; }
 				
-				output << mybinLabel << '\t'; 
+				output << binLabel << '\t'; 
 			}
 			
 			output << endl;
@@ -393,7 +407,7 @@ int SharedRAbundVector::getGroupIndex()  { return index; }
 void SharedRAbundVector::setGroupIndex(int vIndex)	{ index = vIndex; }
 /***********************************************************************/
 int SharedRAbundVector::getNumBins(){
-	return numBins;
+		return numBins;
 }
 
 /***********************************************************************/
@@ -418,12 +432,15 @@ vector<SharedRAbundVector*> SharedRAbundVector::getSharedRAbundVectors(){
 		SharedUtil* util;
 		util = new SharedUtil();
 		
-		util->setGroups(m->Groups, m->namesOfGroups);
+		vector<string> Groups = m->getGroups();
+		vector<string> allGroups = m->getAllGroups();
+		util->setGroups(Groups, allGroups);
+		m->setGroups(Groups);
 		
 		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(), m->Groups) == false) { 
+			if (util->isValidGroup(lookup[i]->getGroup(), m->getGroups()) == false) { 
 				remove = true;
 				delete lookup[i]; lookup[i] = NULL;
 				lookup.erase(lookup.begin()+i); 
@@ -456,6 +473,7 @@ int SharedRAbundVector::eliminateZeroOTUS(vector<SharedRAbundVector*>& thislooku
 			
 			//for each bin
 			vector<string> newBinLabels;
+			string snumBins = toString(thislookup[0]->getNumBins());
 			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; }
 				
@@ -472,7 +490,13 @@ int SharedRAbundVector::eliminateZeroOTUS(vector<SharedRAbundVector*>& thislooku
 					}
 					
 					//if there is a bin label use it otherwise make one
-					string binLabel = "Otu" + (i+1);
+					string binLabel = "Otu";
+					string sbinNumber = toString(i+1);
+					if (sbinNumber.length() < snumBins.length()) { 
+						int diff = snumBins.length() - sbinNumber.length();
+						for (int h = 0; h < diff; h++) { binLabel += "0"; }
+					}
+					binLabel += sbinNumber; 
 					if (i < m->currentBinLabels.size()) {  binLabel = m->currentBinLabels[i]; }
 					
 					newBinLabels.push_back(binLabel);