working on slayer bug

[mothur.git] / validcalculator.cpp

diff --git a/validcalculator.cpp b/validcalculator.cpp
index 6583bbefc9564d17959d4b1240fc589fea54751d..2798b53ba50c8f3ffd50a20fcaa7462d62a071a7 100644 (file)
--- a/validcalculator.cpp
+++ b/validcalculator.cpp
@@ -516,16 +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");
@@ -636,4 +666,79 @@ void ValidCalculators::printCalc(string parameter, ostream& out) {
        }
 }
 /********************************************************************/
+string ValidCalculators::printCalc(string parameter) {
+       try{
+               string output = "The available estimators for calc are ";
+               //are you looking for a calculator for a single parameter
+               if (parameter == "single") {
+                       for (it = single.begin(); it != single.end(); it++) {
+                               output += it->first + ", ";
+                       }
+                       //are you looking for a calculator for a shared parameter
+               }else if (parameter == "shared") {
+                       for (it = shared.begin(); it != shared.end(); it++) {
+                               output += it->first + ", ";
+                       }
+                       //are you looking for a calculator for a rarefaction parameter
+               }else if (parameter == "rarefaction") {
+                       for (it = rarefaction.begin(); it != rarefaction.end(); it++) {
+                               output += it->first + ", ";
+                       }
+                       //are you looking for a calculator for a summary parameter
+               }else if (parameter == "summary") {
+                       for (it = summary.begin(); it != summary.end(); it++) {
+                               output += it->first + ", ";
+                       }
+                       //are you looking for a calculator for a sharedsummary parameter
+               }else if (parameter == "sharedsummary") {
+                       for (it = sharedsummary.begin(); it != sharedsummary.end(); it++) {
+                               output += it->first + ", ";
+                       }
+               }else if (parameter == "sharedrarefaction") {
+                       for (it = sharedrarefaction.begin(); it != sharedrarefaction.end(); it++) {
+                               output += it->first + ", ";
+                       }
+               }else if (parameter == "vennsingle") {
+                       for (it = vennsingle.begin(); it != vennsingle.end(); it++) {
+                               output += it->first + ", ";
+                       }
+               }else if (parameter == "vennshared") {
+                       for (it = vennshared.begin(); it != vennshared.end(); it++) {
+                               output += it->first + ", ";
+                       }
+               }else if (parameter == "treegroup") {
+                       for (it = treegroup.begin(); it != treegroup.end(); it++) {
+                               output += it->first + ", ";
+                       }
+               }else if (parameter == "matrix") {
+                       for (it = matrix.begin(); it != matrix.end(); it++) {
+                               output += it->first + ", ";
+                       }
+               }else if (parameter == "heat") {
+                       for (it = heat.begin(); it != heat.end(); it++) {
+                               output += it->first + ", ";
+                       }
+               }else if (parameter == "boot") {
+                       for (it = boot.begin(); it != boot.end(); it++) {
+                               output += it->first + ", ";
+                       }
+               }else if (parameter == "distance") {
+                       for (it = distance.begin(); it != distance.end(); it++) {
+                               output += it->first + ", ";
+                       }
+               }
+               
+               //rip off comma
+               output = output.substr(0, output.length()-1);
+               output += "\n";
+               
+               return output;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ValidCalculator", "printCalc");
+               exit(1);
+       }
+}
+/********************************************************************/
+