remove.rare command

[mothur.git] / validcalculator.cpp

diff --git a/validcalculator.cpp b/validcalculator.cpp
index cf783f30f82db5a0b5e3c2fa040775fb85463f46..f8c7cc3352e9281defb720c24d15ebda4337a44d 100644 (file)
--- a/validcalculator.cpp
+++ b/validcalculator.cpp
@@ -260,6 +260,24 @@ void ValidCalculators::initialShared() {
                shared["lennon"]                                = "lennon";
                shared["morisitahorn"]                  = "morisitahorn";
                shared["braycurtis"]                    = "braycurtis";
+               shared["odum"]                                  = "odum";
+               shared["canberra"]                              = "canberra";
+               shared["structeuclidean"]               = "structeuclidean";
+               shared["structchord"]                   = "structchord";
+               shared["hellinger"]                             = "hellinger";
+               shared["manhattan"]                             = "manhattan";
+               shared["structpearson"]                 = "structpearson";
+               shared["soergel"]                               = "soergel";
+               shared["spearman"]                              = "spearman";
+               shared["structkulczynski"]              = "structkulczynski";
+               shared["structchi2"]                    = "structchi2";
+               shared["speciesprofile"]                = "speciesprofile";
+               shared["hamming"]                               = "hamming";
+               shared["gower"]                                 = "gower";
+               shared["memchi2"]                               = "memchi2";
+               shared["memchord"]                              = "memchord";
+               shared["memeuclidean"]                  = "memeuclidean";
+               shared["mempearson"]                    = "mempearson";
                shared["default"]                   = "default";
        }
        catch(exception& e) {
@@ -338,7 +356,7 @@ void ValidCalculators::initialSharedSummary() {
                sharedsummary["sharedchao"]                             = "sharedchao";
                sharedsummary["sharedace"]                              = "sharedace";
                sharedsummary["jabund"]                                 = "jabund";
-               sharedsummary["sorabund"]                       = "sorabund";
+               sharedsummary["sorabund"]                               = "sorabund";
                sharedsummary["jclass"]                                 = "jclass";
                sharedsummary["sorclass"]                               = "sorclass";
                sharedsummary["jest"]                                   = "jest";
@@ -355,6 +373,24 @@ void ValidCalculators::initialSharedSummary() {
                sharedsummary["lennon"]                                 = "lennon";
                sharedsummary["morisitahorn"]                   = "morisitahorn";
                sharedsummary["braycurtis"]                             = "braycurtis";
+               sharedsummary["odum"]                                   = "odum";
+               sharedsummary["canberra"]                               = "canberra";
+               sharedsummary["structeuclidean"]                = "structeuclidean";
+               sharedsummary["structchord"]                    = "structchord";
+               sharedsummary["hellinger"]                              = "hellinger";
+               sharedsummary["manhattan"]                              = "manhattan";
+               sharedsummary["structpearson"]                  = "structpearson";
+               sharedsummary["structkulczynski"]               = "structkulczynski";
+               sharedsummary["structchi2"]                             = "structchi2";
+               sharedsummary["soergel"]                                = "soergel";
+               sharedsummary["spearman"]                               = "spearman";
+               sharedsummary["speciesprofile"]                 = "speciesprofile";
+               sharedsummary["hamming"]                                = "hamming";
+               sharedsummary["gower"]                                  = "gower";
+               sharedsummary["memchi2"]                                = "memchi2";
+               sharedsummary["memchord"]                               = "memchord";
+               sharedsummary["memeuclidean"]                   = "memeuclidean";
+               sharedsummary["mempearson"]                             = "mempearson";
                sharedsummary["default"]                                = "default";
        }
        catch(exception& e) {
@@ -386,7 +422,6 @@ void ValidCalculators::initialVennSingle() {
                vennsingle["chao"]                  = "chao";
                vennsingle["ace"]                       = "ace";
                vennsingle["jack"]                  = "jack";
-               vennsingle["nseqs"]                 = "nseqs";
                vennsingle["default"]           = "default";
        }
        catch(exception& e) {
@@ -401,7 +436,6 @@ void ValidCalculators::initialVennShared() {
                vennshared["sharedsobs"]        = "sharedsobs";
                vennshared["sharedchao"]        = "sharedchao";
                vennshared["sharedace"]         = "sharedace";
-               vennshared["nseqs"]                     = "nseqs";
                vennshared["default"]           = "default";
        }
        catch(exception& e) {
@@ -413,6 +447,9 @@ void ValidCalculators::initialVennShared() {
 /********************************************************************/
 void ValidCalculators::initialTreeGroups() {
        try {   
+               treegroup["sharedsobs"]                         = "sharedsobs";
+               treegroup["sharedchao"]                         = "sharedchao";
+               treegroup["sharedace"]                          = "sharedace";
                treegroup["jabund"]                                     = "jabund";
                treegroup["sorabund"]                           = "sorabund";
                treegroup["jclass"]                                     = "jclass";
@@ -421,8 +458,35 @@ void ValidCalculators::initialTreeGroups() {
                treegroup["sorest"]                                     = "sorest";
                treegroup["thetayc"]                            = "thetayc";
                treegroup["thetan"]                                     = "thetan";
+               treegroup["kstest"]                                     = "kstest";
+               treegroup["whittaker"]                          = "whittaker";
+               treegroup["sharednseqs"]                        = "sharednseqs";
+               treegroup["ochiai"]                                     = "ochiai";
+               treegroup["anderberg"]                          = "anderberg";
+               treegroup["kulczynski"]                         = "kulczynski";
+               treegroup["kulczynskicody"]                     = "kulczynskicody";
+               treegroup["lennon"]                                     = "lennon";
                treegroup["morisitahorn"]                       = "morisitahorn";
                treegroup["braycurtis"]                         = "braycurtis";
+               treegroup["odum"]                                       = "odum";
+               treegroup["canberra"]                           = "canberra";
+               treegroup["structeuclidean"]            = "structeuclidean";
+               treegroup["structchord"]                        = "structchord";
+               treegroup["hellinger"]                          = "hellinger";
+               treegroup["manhattan"]                          = "manhattan";
+               treegroup["structpearson"]                      = "structpearson";
+               treegroup["structkulczynski"]           = "structkulczynski";
+               treegroup["structchi2"]                         = "structchi2";
+               treegroup["soergel"]                            = "soergel";
+               treegroup["spearman"]                           = "spearman";
+               treegroup["speciesprofile"]                     = "speciesprofile";
+               treegroup["hamming"]                            = "hamming";
+               treegroup["gower"]                                      = "gower";
+               treegroup["memchi2"]                            = "memchi2";
+               treegroup["memchord"]                           = "memchord";
+               treegroup["memeuclidean"]                       = "memeuclidean";
+               treegroup["mempearson"]                         = "mempearson";
+               
        }
        catch(exception& e) {
                m->errorOut(e, "ValidCalculator", "initialTreeGroups");
@@ -452,16 +516,46 @@ void ValidCalculators::initialHeat() {
 /********************************************************************/
 void ValidCalculators::initialMatrix() {
        try {   
-               matrix["jabund"]                                = "jabund";
+               matrix["sharedsobs"]                            = "sharedsobs";
+               matrix["sharedchao"]                            = "sharedchao";
+               matrix["sharedace"]                             = "sharedace";
+               matrix["jabund"]                                        = "jabund";
                matrix["sorabund"]                              = "sorabund";
-               matrix["jclass"]                                = "jclass";
+               matrix["jclass"]                                        = "jclass";
                matrix["sorclass"]                              = "sorclass";
                matrix["jest"]                                  = "jest";
-               matrix["sorest"]                                = "sorest";
+               matrix["sorest"]                                        = "sorest";
                matrix["thetayc"]                               = "thetayc";
-               matrix["thetan"]                                = "thetan";
+               matrix["thetan"]                                        = "thetan";
+               matrix["kstest"]                                        = "kstest";
+               matrix["whittaker"]                             = "whittaker";
+               matrix["sharednseqs"]                   = "sharednseqs";
+               matrix["ochiai"]                                        = "ochiai";
+               matrix["anderberg"]                             = "anderberg";
+               matrix["kulczynski"]                            = "kulczynski";
+               matrix["kulczynskicody"]                        = "kulczynskicody";
+               matrix["lennon"]                                        = "lennon";
                matrix["morisitahorn"]                  = "morisitahorn";
-               matrix["braycurtis"]                    = "braycurtis";
+               matrix["braycurtis"]                            = "braycurtis";
+               matrix["odum"]                                  = "odum";
+               matrix["canberra"]                              = "canberra";
+               matrix["structeuclidean"]               = "structeuclidean";
+               matrix["structchord"]                   = "structchord";
+               matrix["hellinger"]                             = "hellinger";
+               matrix["manhattan"]                             = "manhattan";
+               matrix["structpearson"]                 = "structpearson";
+               matrix["structkulczynski"]              = "structkulczynski";
+               matrix["structchi2"]                            = "structchi2";
+               matrix["soergel"]                               = "soergel";
+               matrix["spearman"]                              = "spearman";
+               matrix["speciesprofile"]                        = "speciesprofile";
+               matrix["hamming"]                               = "hamming";
+               matrix["gower"]                                 = "gower";
+               matrix["memchi2"]                               = "memchi2";
+               matrix["memchord"]                              = "memchord";
+               matrix["memeuclidean"]                  = "memeuclidean";
+               matrix["mempearson"]                            = "mempearson";
+               
        }
        catch(exception& e) {
                m->errorOut(e, "ValidCalculator", "initialMatrix");