added calcs to tree.shared. working on remove.rare command

[mothur.git] / validcalculator.cpp

diff --git a/validcalculator.cpp b/validcalculator.cpp
index 0ade87338bb9c2b264f99200a3c7e09fac3fdd12..6583bbefc9564d17959d4b1240fc589fea54751d 100644 (file)
--- a/validcalculator.cpp
+++ b/validcalculator.cpp
@@ -209,11 +209,16 @@ void ValidCalculators::initialSingle() {
                single["jack"]              = "jack";
                single["shannon"]           = "shannon";
                single["npshannon"]     = "npshannon";
+               single["shannoneven"]   = "shannoneven";
+               single["smithwilson"]   = "smithwilson";
+               single["heip"]                  = "heip";
                single["simpson"]           = "simpson";
+               single["simpsoneven"]   = "simpsoneven";
+               single["invsimpson"]    = "invsimpson";
                single["bergerparker"]  = "bergerparker";
                single["bootstrap"]     = "bootstrap";
                single["geometric"]     = "geometric";
-               single["logseries"]         = "logseries";
+               single["logseries"]             = "logseries";
                single["qstat"]         = "qstat";
                single["bstick"]        = "bstick";
                single["goodscoverage"] = "goodscoverage";
@@ -255,6 +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) {
@@ -271,8 +294,13 @@ void ValidCalculators::initialRarefaction() {
                rarefaction["ace"]                      = "ace";
                rarefaction["jack"]                     = "jack";
                rarefaction["shannon"]          = "shannon";
+               rarefaction["smithwilson"]      = "smithwilson";
+               rarefaction["heip"]                     = "heip";
                rarefaction["npshannon"]        = "npshannon";
+               rarefaction["shannoneven"]      = "shannoneven";
                rarefaction["simpson"]          = "simpson";
+               rarefaction["invsimpson"]       = "invsimpson";
+               rarefaction["simpsoneven"]      = "simpsoneven";
                rarefaction["bootstrap"]        = "bootstrap";
                rarefaction["nseqs"]            = "nseqs";
                rarefaction["coverage"]         = "coverage";
@@ -293,8 +321,13 @@ void ValidCalculators::initialSummary() {
                summary["ace"]                  = "ace";
                summary["jack"]                 = "jack";
                summary["shannon"]              = "shannon";
+               summary["heip"]                 = "heip";
+               summary["shannoneven"]  = "shannoneven";
+               summary["smithwilson"]  = "smithwilson";
+               summary["invsimpson"]   = "invsimpson";
                summary["npshannon"]    = "npshannon";
                summary["simpson"]              = "simpson";
+               summary["simpsoneven"]  = "simpsoneven";
                summary["bergerparker"] = "bergerparker";
                summary["geometric"]    = "geometric";
                summary["bootstrap"]    = "bootstrap";
@@ -323,7 +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";
@@ -340,6 +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) {
@@ -396,6 +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";
@@ -404,8 +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");