sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / sharedrabundvector.cpp

diff --git a/sharedrabundvector.cpp b/sharedrabundvector.cpp
index 4a0e5e8f09c59c18c419353cbecbdfecae2c1ba9..3901650cef965dc7a3c0126ecb54a8fb425e434d 100644 (file)
--- 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