X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=validcalculator.cpp;h=b9075414a456c8abc5aa14fbd382dc5c48a0dcb3;hb=a89c6295ae9a35fcaaab7fa50dcb68360dd543b0;hp=a22ece24c3c83943d90971f51026ddeb6ddd3c73;hpb=8f7f4fc08b8c70d9ef0f79607813dba4e926e102;p=mothur.git

diff --git a/validcalculator.cpp b/validcalculator.cpp
index a22ece2..b907541 100644
--- 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; 
 				
@@ -177,7 +181,7 @@ void ValidCalculators::printCitations(vector<string> Estimators) {
 				}else if (Estimators[i] == "ochiai") { Calculator* temp = new Ochiai(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp; 
 				
 				}else if (Estimators[i] == "anderberg") { Calculator* temp = new Anderberg(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp; 
-				}else if (Estimators[i] == "skulczynski") { Calculator* temp = new Kulczynski(); 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] == "kulczynskicody") { Calculator* temp = new KulczynskiCody(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp; 
 				}else if (Estimators[i] == "lennon") { Calculator* temp = new Lennon(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 				}else if (Estimators[i] == "morisitahorn") { Calculator* temp = new MorHorn(); 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) {
@@ -662,6 +675,8 @@ void ValidCalculators::initialTreeGroups() {
 		treegroup["gower"]					= "gower";
 		treegroup["memchi2"]				= "memchi2";
 		treegroup["memchord"]				= "memchord";
+        treegroup["jsd"]                    = "jsd";
+        treegroup["rjsd"]                   = "rjsd";
 		treegroup["memeuclidean"]			= "memeuclidean";
 		treegroup["mempearson"]				= "mempearson";
 		
@@ -726,13 +741,15 @@ 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) {