X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedrabundvector.cpp;h=9276b7bfdc0ae441a883f42ddd0aabcddf1f04bd;hb=3fd6dd6e4f19a458ac2966ee5458787e998a1bde;hp=d135091c3301ed428a8e8e0391a2120643a21520;hpb=e189982e0a9b7352ad57cc38ccee675f128be22e;p=mothur.git

diff --git a/sharedrabundvector.cpp b/sharedrabundvector.cpp
index d135091..9276b7b 100644
--- a/sharedrabundvector.cpp
+++ b/sharedrabundvector.cpp
@@ -73,8 +73,12 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0),
 		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 +102,12 @@ 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 +115,7 @@ 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 +132,12 @@ 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 +205,16 @@ 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;
@@ -483,15 +496,15 @@ 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) {