fixed bug with trim.seqs- when a file is blank for a grouping mothur removed it,...

[mothur.git] / sharedkulczynski.cpp

diff --git a/sharedkulczynski.cpp b/sharedkulczynski.cpp
index 30c8c7a34a9b1d79f99637fa6c1874df2dd0f3d9..c19df537a4f382f5404d8d2c643725599fba2478 100644 (file)
--- a/sharedkulczynski.cpp
+++ b/sharedkulczynski.cpp
@@ -2,7 +2,7 @@
  *  sharedkulczynski.cpp
  *  Mothur
  *
- *  Created by John Westcott on 3/24/09.
+ *  Created by Sarah Westcott on 3/24/09.
  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
  *
  */
@@ -11,9 +11,9 @@
 
 /***********************************************************************/
 
-EstOutput SharedKulczynski::getValues(SharedRAbundVector* shared1, SharedRAbundVector* shared2) {
+EstOutput Kulczynski::getValues(vector<SharedRAbundVector*> shared) {
        try {
-               int S1, S2, S12, tempA, tempB;
+               double S1, S2, S12, tempA, tempB;
                S1 = 0; S2 = 0; S12 = 0; tempA = 0; tempB = 0; 
                
                /*S1, S2 = number of OTUs observed or estimated in A and B 
@@ -21,10 +21,10 @@ EstOutput SharedKulczynski::getValues(SharedRAbundVector* shared1, SharedRAbundV
 
                data.resize(1,0);
                
-               for (int i = 0; i < shared1->size(); i++) {
+               for (int i = 0; i < shared[0]->size(); i++) {
                        //store in temps to avoid multiple repetitive function calls
-                       tempA = shared1->getAbundance(i);
-                       tempB = shared2->getAbundance(i);
+                       tempA = shared[0]->getAbundance(i);
+                       tempB = shared[1]->getAbundance(i);
                        
                        if (tempA != 0) { S1++; }
                        if (tempB != 0) { S2++; } 
@@ -40,13 +40,9 @@ EstOutput SharedKulczynski::getValues(SharedRAbundVector* shared1, SharedRAbundV
                return data;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedKulczynski class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               m->errorOut(e, "Kulczynski", "getValues");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedKulczynski class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }       
 }
 
 /***********************************************************************/