added shannonrange calc.

[mothur.git] / validcalculator.cpp

diff --git a/validcalculator.cpp b/validcalculator.cpp
index 7df7c4e28d65cb2f7853500728075e8edc161723..f5f6562f37b0d9f16bed2271f92a6b497a822d4b 100644 (file)
--- a/validcalculator.cpp
+++ b/validcalculator.cpp
@@ -76,6 +76,9 @@
 #include "mempearson.h"
 #include "sharedsobs.h"
 #include "sharednseqs.h"
+#include "sharedjsd.h"
+#include "sharedrjsd.h"
+#include "shannonrange.h"
 
 
 /********************************************************************/
@@ -137,6 +140,7 @@ void ValidCalculators::printCitations(vector<string> Estimators) {
                                }else if (Estimators[i] == "jack") { Calculator* temp = new Jackknife(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
                                }else if (Estimators[i] == "shannon") { Calculator* temp = new Shannon(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
                                }else if (Estimators[i] == "shannoneven") { Calculator* temp = new ShannonEven(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+                }else if (Estimators[i] == "shannonrange") { Calculator* temp = new RangeShannon(0); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
                                }else if (Estimators[i] == "npshannon") { Calculator* temp = new NPShannon(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
                                }else if (Estimators[i] == "heip") { Calculator* temp = new Heip(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp; 
                                
@@ -206,6 +210,8 @@ 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 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(); }
                }
@@ -388,6 +394,7 @@ void ValidCalculators::initialSingle() {
                single["shannon"]           = "shannon";
                single["npshannon"]     = "npshannon";
                single["shannoneven"]   = "shannoneven";
+        single["shannonrange"] = "shannonrange";
                single["smithwilson"]   = "smithwilson";
                single["heip"]                  = "heip";
                single["simpson"]           = "simpson";
@@ -456,6 +463,8 @@ void ValidCalculators::initialShared() {
                shared["memchord"]                              = "memchord";
                shared["memeuclidean"]                  = "memeuclidean";
                shared["mempearson"]                    = "mempearson";
+        shared["jsd"]                   = "jsd";
+        shared["rjsd"]                  = "rjsd";
                shared["default"]                   = "default";
        }
        catch(exception& e) {
@@ -476,6 +485,7 @@ void ValidCalculators::initialRarefaction() {
                rarefaction["heip"]                     = "heip";
                rarefaction["npshannon"]        = "npshannon";
                rarefaction["shannoneven"]      = "shannoneven";
+        rarefaction["shannonrange"]    = "shannonrange";
                rarefaction["simpson"]          = "simpson";
                rarefaction["invsimpson"]       = "invsimpson";
                rarefaction["simpsoneven"]      = "simpsoneven";
@@ -504,6 +514,7 @@ void ValidCalculators::initialSummary() {
                summary["smithwilson"]  = "smithwilson";
                summary["invsimpson"]   = "invsimpson";
                summary["npshannon"]    = "npshannon";
+        summary["shannonrange"]        = "shannonrange";
                summary["simpson"]              = "simpson";
                summary["simpsoneven"]  = "simpsoneven";
                summary["bergerparker"] = "bergerparker";
@@ -569,6 +580,8 @@ void ValidCalculators::initialSharedSummary() {
                sharedsummary["memchord"]                               = "memchord";
                sharedsummary["memeuclidean"]                   = "memeuclidean";
                sharedsummary["mempearson"]                             = "mempearson";
+        sharedsummary["jsd"]                    = "jsd";
+        sharedsummary["rjsd"]                   = "rjsd";
                sharedsummary["default"]                                = "default";
        }
        catch(exception& e) {
@@ -726,13 +739,15 @@ 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["mempearson"]                    = "mempearson";
+        matrix["rjsd"]                   = "rjsd";
+        matrix["jsd"]                   = "jsd";
                
        }
        catch(exception& e) {