added cluster.split command

[mothur.git] / sharedjclass.cpp

diff --git a/sharedjclass.cpp b/sharedjclass.cpp
index 2c7d8c9422d4c4c95b74374f05e5f7b0291aa2d9..d44f22f17645b4e373404d33a60509574a0ef392 100644 (file)
--- a/sharedjclass.cpp
+++ b/sharedjclass.cpp
@@ -11,7 +11,7 @@
 
 /***********************************************************************/
 
-EstOutput SharedJclass::getValues(SharedRAbundVector* shared1, SharedRAbundVector* shared2) {
+EstOutput Jclass::getValues(vector<SharedRAbundVector*> shared) {
        try {
                int S1, S2, S12, tempA, tempB;
                S1 = 0; S2 = 0; S12 = 0; tempA = 0; tempB = 0; 
@@ -21,10 +21,10 @@ EstOutput SharedJclass::getValues(SharedRAbundVector* shared1, SharedRAbundVecto
 
                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);
                        
                        //find number of bins in shared1 and shared2
                        if (tempA != 0) { S1++; }
@@ -41,13 +41,9 @@ EstOutput SharedJclass::getValues(SharedRAbundVector* shared1, SharedRAbundVecto
                return data;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedJclass class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               m->errorOut(e, "Jclass", "getValues");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedJclass class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }       
 }
 
 /***********************************************************************/