added rjsd calculator. improved work balance load between processors for paralellize...

[mothur.git] / validcalculator.cpp

diff --git a/validcalculator.cpp b/validcalculator.cpp
index 4718e2ff89f96a28013a19dc1ca2f51ae93d924e..98f0d9a2a83f4a5c903756e454cd006354ca721d 100644 (file)
--- a/validcalculator.cpp
+++ b/validcalculator.cpp
@@ -77,6 +77,7 @@
 #include "sharedsobs.h"
 #include "sharednseqs.h"
 #include "sharedjsd.h"
+#include "sharedrjsd.h"
 
 
 /********************************************************************/
@@ -208,6 +209,7 @@ void ValidCalculators::printCitations(vector<string> Estimators) {
                                }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 if (Estimators[i] == "rjsd") { Calculator* temp = new RJSD(); 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(); }
                }
@@ -458,7 +460,8 @@ void ValidCalculators::initialShared() {
                shared["memchord"]                              = "memchord";
                shared["memeuclidean"]                  = "memeuclidean";
                shared["mempearson"]                    = "mempearson";
-        shared["jsd"]                          = "jsd";
+        shared["jsd"]                   = "jsd";
+        shared["rjsd"]                  = "rjsd";
                shared["default"]                   = "default";
        }
        catch(exception& e) {
@@ -572,7 +575,8 @@ void ValidCalculators::initialSharedSummary() {
                sharedsummary["memchord"]                               = "memchord";
                sharedsummary["memeuclidean"]                   = "memeuclidean";
                sharedsummary["mempearson"]                             = "mempearson";
-        sharedsummary["jsd"]                           = "jsd";
+        sharedsummary["jsd"]                    = "jsd";
+        sharedsummary["rjsd"]                   = "rjsd";
                sharedsummary["default"]                                = "default";
        }
        catch(exception& e) {
@@ -730,14 +734,15 @@ void ValidCalculators::initialMatrix() {
                matrix["structchi2"]                            = "structchi2";
                matrix["soergel"]                               = "soergel";
                matrix["spearman"]                              = "spearman";
-               matrix["speciesprofile"]                        = "speciesprofile";
+               matrix["speciesprofile"]                = "speciesprofile";
                matrix["hamming"]                               = "hamming";
                matrix["gower"]                                 = "gower";
                matrix["memchi2"]                               = "memchi2";
                matrix["memchord"]                              = "memchord";
                matrix["memeuclidean"]                  = "memeuclidean";
-               matrix["mempearson"]                            = "mempearson";
-        matrix["jsd"]                          = "jsd";
+               matrix["mempearson"]                    = "mempearson";
+        matrix["rjsd"]                   = "rjsd";
+        matrix["jsd"]                   = "jsd";
                
        }
        catch(exception& e) {