X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedrabundfloatvector.cpp;h=9f6c15687edc77d0fbd77df7de286cbe98b6339e;hb=bb8d942036365d2a66330944269f17841ed2388a;hp=8d91d7ede187510f66b63b25c7488ce822aba966;hpb=1bf53bca7e26bf091588bc8ca6e68cbfae1df6fe;p=mothur.git

diff --git a/sharedrabundfloatvector.cpp b/sharedrabundfloatvector.cpp
index 8d91d7e..9f6c156 100644
--- a/sharedrabundfloatvector.cpp
+++ b/sharedrabundfloatvector.cpp
@@ -33,7 +33,8 @@ SharedRAbundFloatVector::SharedRAbundFloatVector(int n) : DataVector(), maxRank(
 SharedRAbundFloatVector::SharedRAbundFloatVector(ifstream& f) : DataVector(), maxRank(0.0), numBins(0), numSeqs(0.0) {
 	try {
 		
-		m->namesOfGroups.clear();
+		m->clearAllGroups();
+		vector<string> allGroups;
 		
 		int num, count;
 		float inputData;
@@ -75,7 +76,7 @@ SharedRAbundFloatVector::SharedRAbundFloatVector(ifstream& f) : DataVector(), ma
 		}else { label = m->saveNextLabel; }
 		
 		//reset labels, currentLabels may have gotten changed as otus were eliminated because of group choices or sampling
-		m->currentBinLabels = m-> binLabelsInFile;
+		m->currentBinLabels = m->binLabelsInFile;
 		
 		//read in first row since you know there is at least 1 group.
 		f >> groupN >> num;
@@ -88,7 +89,7 @@ SharedRAbundFloatVector::SharedRAbundFloatVector(ifstream& f) : DataVector(), ma
 		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++){
@@ -107,9 +108,11 @@ SharedRAbundFloatVector::SharedRAbundFloatVector(ifstream& f) : DataVector(), ma
 		//read the rest of the groups info in
 		while ((nextLabel == holdLabel) && (f.eof() != true)) {
 			f >> groupN >> num;
+            
+            if (num != 1000) { break; }
 			count++;
 			
-			m->namesOfGroups.push_back(groupN);
+			allGroups.push_back(groupN);
 			
 			//add new vector to lookup
 			temp = new SharedRAbundFloatVector();
@@ -129,6 +132,7 @@ SharedRAbundFloatVector::SharedRAbundFloatVector(ifstream& f) : DataVector(), ma
 		}
 		
 		m->saveNextLabel = nextLabel;
+		m->setAllGroups(allGroups);
 	
 	}
 	catch(exception& e) {
@@ -250,12 +254,19 @@ int SharedRAbundFloatVector::size(){
 /***********************************************************************/
 void SharedRAbundFloatVector::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'; 
@@ -264,7 +275,13 @@ void SharedRAbundFloatVector::printHeaders(ostream& output){
 		}else {
 			for (int i = 0; i < numBins; i++) {  
 				//if there is a bin label use it otherwise make one
-				string binLabel = "Otu" + toString(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]; }
 				
 				output << binLabel << '\t'; 
@@ -333,18 +350,21 @@ SharedRAbundVector SharedRAbundFloatVector::getSharedRAbundVector(){
 		exit(1);
 	}		
 }
-/***********************************************************************/
+***********************************************************************/
 vector<SharedRAbundFloatVector*> SharedRAbundFloatVector::getSharedRAbundFloatVectors(){
 	try {
 		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) { 
 				delete lookup[i]; lookup[i] = NULL;
 				lookup.erase(lookup.begin()+i); 
 				i--; 
@@ -401,7 +421,7 @@ SharedSAbundVector SharedRAbundVector::getSharedSAbundVector(){
 		exit(1);
 	}
 }
-/***********************************************************************/
+***********************************************************************/
 
 SAbundVector SharedRAbundFloatVector::getSAbundVector() {
 	try {
@@ -443,7 +463,7 @@ SharedOrderVector SharedRAbundFloatVector::getSharedOrderVector() {
 		exit(1);
 	}
 }
-/***********************************************************************/
+***********************************************************************/
 //this is not functional, not sure how to handle it yet, but I need the stub because it is a pure function
 OrderVector SharedRAbundFloatVector::getOrderVector(map<string,int>* nameMap = NULL) {
 	try {
@@ -479,6 +499,7 @@ int SharedRAbundFloatVector::eliminateZeroOTUS(vector<SharedRAbundFloatVector*>&
 		
 		//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; }
 			
@@ -494,7 +515,13 @@ int SharedRAbundFloatVector::eliminateZeroOTUS(vector<SharedRAbundFloatVector*>&
 					newLookup[j]->push_back(thislookup[j]->getAbundance(i), thislookup[j]->getGroup());
 				}
 				//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);