working on pam

[mothur.git] / validcalculator.cpp

diff --git a/validcalculator.cpp b/validcalculator.cpp
index 7df7c4e28d65cb2f7853500728075e8edc161723..4718e2ff89f96a28013a19dc1ca2f51ae93d924e 100644 (file)
--- a/validcalculator.cpp
+++ b/validcalculator.cpp
@@ -76,6 +76,7 @@
 #include "mempearson.h"
 #include "sharedsobs.h"
 #include "sharednseqs.h"
+#include "sharedjsd.h"
 
 
 /********************************************************************/
@@ -206,6 +207,7 @@ void ValidCalculators::printCitations(vector<string> Estimators) {
                                }else if (Estimators[i] == "mempearson") { Calculator* temp = new MemPearson(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
                                }else if (Estimators[i] == "sharedobserved") { Calculator* temp = new SharedSobs(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
                                }else if (Estimators[i] == "kulczynski") { Calculator* temp = new Kulczynski(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+                }else if (Estimators[i] == "jsd") { Calculator* temp = new JSD(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
                                }else { m->mothurOut("[ERROR]: Missing else if for " + Estimators[i] + " in printCitations."); m->mothurOutEndLine(); }
                        }else { m->mothurOut(Estimators[i] + " is not a valid calculator, no citation will be given."); m->mothurOutEndLine(); }
                }
@@ -456,6 +458,7 @@ void ValidCalculators::initialShared() {
                shared["memchord"]                              = "memchord";
                shared["memeuclidean"]                  = "memeuclidean";
                shared["mempearson"]                    = "mempearson";
+        shared["jsd"]                          = "jsd";
                shared["default"]                   = "default";
        }
        catch(exception& e) {
@@ -569,6 +572,7 @@ void ValidCalculators::initialSharedSummary() {
                sharedsummary["memchord"]                               = "memchord";
                sharedsummary["memeuclidean"]                   = "memeuclidean";
                sharedsummary["mempearson"]                             = "mempearson";
+        sharedsummary["jsd"]                           = "jsd";
                sharedsummary["default"]                                = "default";
        }
        catch(exception& e) {
@@ -733,6 +737,7 @@ void ValidCalculators::initialMatrix() {
                matrix["memchord"]                              = "memchord";
                matrix["memeuclidean"]                  = "memeuclidean";
                matrix["mempearson"]                            = "mempearson";
+        matrix["jsd"]                          = "jsd";
                
        }
        catch(exception& e) {