X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedrabundvector.cpp;h=7bc333bc02e737f7caab1f4b4d34ec0c131dc2dd;hb=1a968f34ae2d2680eaf189a197d1a21b8dfd6c03;hp=4a0e5e8f09c59c18c419353cbecbdfecae2c1ba9;hpb=e0dc0bcef2a0f7e1f63abb531dbb1ad533da98ca;p=mothur.git

diff --git a/sharedrabundvector.cpp b/sharedrabundvector.cpp
index 4a0e5e8..7bc333b 100644
--- a/sharedrabundvector.cpp
+++ b/sharedrabundvector.cpp
@@ -55,7 +55,7 @@ SharedRAbundVector::SharedRAbundVector(string id, vector<individual> rav) : Data
 }
 
 
-/***********************************************************************/
+***********************************************************************/
 //reads a shared file
 SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0), numBins(0), numSeqs(0) {
 	try {
@@ -95,15 +95,36 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0),
 					m->binLabelsInFile.push_back(temp);
 				}
 				
-				f >> label;
-			}
-		}else { label = m->saveNextLabel; }
+				f >> label >> groupN >> num;
+			}else {
+                //read in first row since you know there is at least 1 group.
+                f >> groupN >> num;
+                
+                //make binlabels because we don't have any
+                string snumBins = toString(num);
+                m->binLabelsInFile.clear();
+                for (int i = 0; i < num; i++) {  
+                    //if there is a bin label use it otherwise make one
+                    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;
+                    m->binLabelsInFile.push_back(binLabel);
+                }
+            }
+		}else { 
+            label = m->saveNextLabel; 
+            
+            //read in first row since you know there is at least 1 group.
+            f >> groupN >> num;
+        }
 		
 		//reset labels, currentLabels may have gotten changed as otus were eliminated because of group choices or sampling
 		m->currentBinLabels = m->binLabelsInFile;
 		
-		//read in first row since you know there is at least 1 group.
-		f >> groupN >> num;
 		holdLabel = label;
 		
 		//add new vector to lookup
@@ -190,6 +211,18 @@ int SharedRAbundVector::getAbundance(int index){
 	return data[index].abundance;
 	
 }
+/***********************************************************************/
+//returns vector of abundances 
+vector<int> SharedRAbundVector::getAbundances(){
+    vector<int> abunds;
+    for (int i = 0; i < data.size(); i++) {
+        abunds.push_back(data[i].abundance);
+    }
+    
+	return abunds;
+}
+
+
 /***********************************************************************/
 
 int SharedRAbundVector::numNZ(){