changes while testing

[mothur.git] / sharedrabundvector.cpp

diff --git a/sharedrabundvector.cpp b/sharedrabundvector.cpp
index 3901650cef965dc7a3c0126ecb54a8fb425e434d..9b2bb678ca7688777aa87a9f60015baba5d336d9 100644 (file)
--- a/sharedrabundvector.cpp
+++ b/sharedrabundvector.cpp
@@ -72,7 +72,7 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0),
                //are we at the beginning of the file??
                if (m->saveNextLabel == "") {  
                        f >> label; 
-       
+            
                        //is this a shared file that has headers
                        if (label == "label") { 
                                //gets "group"
@@ -120,6 +120,8 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0),
             
             //read in first row since you know there is at least 1 group.
             f >> groupN >> num;
+            
+            if (m->debug) { m->mothurOut("[DEBUG]: "+ groupN + '\t' + toString(num)); }
         }
                
                //reset labels, currentLabels may have gotten changed as otus were eliminated because of group choices or sampling
@@ -138,6 +140,7 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0),
                //fill vector.  data = first sharedrabund in file
                for(int i=0;i<num;i++){
                        f >> inputData;
+            if (m->debug) { m->mothurOut("[DEBUG]: OTU" + toString(i+1)+ '\t' +toString(inputData)); }
                        
                        lookup[0]->push_back(inputData, groupN); //abundance, bin, group
                        push_back(inputData, groupN);
@@ -152,6 +155,7 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0),
                //read the rest of the groups info in
                while ((nextLabel == holdLabel) && (f.eof() != true)) {
                        f >> groupN >> num;
+            if (m->debug) { m->mothurOut("[DEBUG]: "+ groupN + '\t' + toString(num)); }
                        count++;
                        
                        allGroups.push_back(groupN);
@@ -165,6 +169,7 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0),
                        //fill vector.  
                        for(int i=0;i<num;i++){
                                f >> inputData;
+                if (m->debug) { m->mothurOut("[DEBUG]: OTU" + toString(i+1)+ '\t' +toString(inputData)); }
                                
                                lookup[count]->push_back(inputData, groupN); //abundance, bin, group
                        }
@@ -211,6 +216,18 @@ 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(){