X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sharedrabundfloatvector.cpp;h=9eeb0f21bf3626620806c49372ab36efd0ff0831;hp=b8b91028625cec0cfd1ef59d7dc82ab67b40cde5;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=ce8794490ab1d83adcdb2b92e0302a1e43e17adf

diff --git a/sharedrabundfloatvector.cpp b/sharedrabundfloatvector.cpp
index b8b9102..9eeb0f2 100644
--- a/sharedrabundfloatvector.cpp
+++ b/sharedrabundfloatvector.cpp
@@ -62,13 +62,13 @@ SharedRAbundFloatVector::SharedRAbundFloatVector(ifstream& f) : DataVector(), ma
 				
 				//parse labels to save
 				istringstream iStringStream(label);
-				m->binLabelsInFile.clear();
+				m->sharedBinLabelsInFile.clear();
 				while(!iStringStream.eof()){
 					if (m->control_pressed) { break; }
 					string temp;
 					iStringStream >> temp;  m->gobble(iStringStream);
                     
-					m->binLabelsInFile.push_back(temp);
+					m->sharedBinLabelsInFile.push_back(temp);
 				}
 				
 				f >> label >> groupN >> num;
@@ -78,7 +78,7 @@ SharedRAbundFloatVector::SharedRAbundFloatVector(ifstream& f) : DataVector(), ma
                 
                 //make binlabels because we don't have any
                 string snumBins = toString(num);
-                m->binLabelsInFile.clear();
+                m->sharedBinLabelsInFile.clear();
                 for (int i = 0; i < num; i++) {  
                     //if there is a bin label use it otherwise make one
                     string binLabel = "Otu";
@@ -88,7 +88,7 @@ SharedRAbundFloatVector::SharedRAbundFloatVector(ifstream& f) : DataVector(), ma
                         for (int h = 0; h < diff; h++) { binLabel += "0"; }
                     }
                     binLabel += sbinNumber;
-                    m->binLabelsInFile.push_back(binLabel);
+                    m->sharedBinLabelsInFile.push_back(binLabel);
                 }
             }
 		}else { 
@@ -99,7 +99,7 @@ SharedRAbundFloatVector::SharedRAbundFloatVector(ifstream& f) : DataVector(), ma
         }
 		
 		//reset labels, currentLabels may have gotten changed as otus were eliminated because of group choices or sampling
-		m->currentBinLabels = m->binLabelsInFile;
+		m->currentSharedBinLabels = m->sharedBinLabelsInFile;
 		
 		holdLabel = label;
 		
@@ -152,8 +152,6 @@ SharedRAbundFloatVector::SharedRAbundFloatVector(ifstream& f) : DataVector(), ma
 		
 		m->saveNextLabel = nextLabel;
 		m->setAllGroups(allGroups);
-        for (int i = 0; i < allGroups.size(); i++) { cout << allGroups[i] << endl; }
-	
 	}
 	catch(exception& e) {
 		m->errorOut(e, "SharedRAbundFloatVector", "SharedRAbundFloatVector");
@@ -193,6 +191,16 @@ float SharedRAbundFloatVector::getAbundance(int index){
 	return data[index].abundance;	
 }
 /***********************************************************************/
+//returns vector of abundances
+vector<float> SharedRAbundFloatVector::getAbundances(){
+    vector<float> abunds;
+    for (int i = 0; i < data.size(); i++) {
+        abunds.push_back(data[i].abundance);
+    }
+    
+	return abunds;
+}
+/***********************************************************************/
 individualFloat SharedRAbundFloatVector::get(int index){
 	return data[index];	
 }
@@ -287,7 +295,7 @@ void SharedRAbundFloatVector::printHeaders(ostream& output){
 					for (int h = 0; h < diff; h++) { binLabel += "0"; }
 				}
 				binLabel += sbinNumber;
-				if (i < m->currentBinLabels.size()) {  binLabel = m->currentBinLabels[i]; }
+				if (i < m->currentSharedBinLabels.size()) {  binLabel = m->currentSharedBinLabels[i]; }
 				
 				output << binLabel << '\t'; 
 			}
@@ -302,7 +310,7 @@ void SharedRAbundFloatVector::printHeaders(ostream& output){
 					for (int h = 0; h < diff; h++) { binLabel += "0"; }
 				}
 				binLabel += sbinNumber;
-				if (i < m->currentBinLabels.size()) {  binLabel = m->currentBinLabels[i]; }
+				if (i < m->currentSharedBinLabels.size()) {  binLabel = m->currentSharedBinLabels[i]; }
 				
 				output << binLabel << '\t'; 
 			}
@@ -310,7 +318,7 @@ void SharedRAbundFloatVector::printHeaders(ostream& output){
 			output << endl;
 		}
 		
-		m->printedHeaders = true;
+		m->printedSharedHeaders = true;
 	}
 	catch(exception& e) {
 		m->errorOut(e, "SharedRAbundVector", "printHeaders");
@@ -542,7 +550,7 @@ int SharedRAbundFloatVector::eliminateZeroOTUS(vector<SharedRAbundFloatVector*>&
 					for (int h = 0; h < diff; h++) { binLabel += "0"; }
 				}
 				binLabel += sbinNumber; 
-				if (i < m->currentBinLabels.size()) {  binLabel = m->currentBinLabels[i]; }
+				if (i < m->currentSharedBinLabels.size()) {  binLabel = m->currentSharedBinLabels[i]; }
 				
 				newBinLabels.push_back(binLabel);
 			}
@@ -551,7 +559,7 @@ int SharedRAbundFloatVector::eliminateZeroOTUS(vector<SharedRAbundFloatVector*>&
 		for (int j = 0; j < thislookup.size(); j++) {  delete thislookup[j];  }
 		
 		thislookup = newLookup;
-		m->currentBinLabels = newBinLabels;
+		m->currentSharedBinLabels = newBinLabels;
 		
 		return 0;