started shared utilities, updates to venn and heatmap added tree.groups command

[mothur.git] / validcalculator.cpp

diff --git a/validcalculator.cpp b/validcalculator.cpp
index b29ff5797f9db61b3c3cb31e32628cc251c3b95e..90257c77eefbc1218698ebcc808e66d4c7bd34e9 100644 (file)
--- a/validcalculator.cpp
+++ b/validcalculator.cpp
@@ -18,6 +18,9 @@ ValidCalculators::ValidCalculators() {
                 initialSharedRarefact();
                 initialSummary();
                 initialSharedSummary();
+                initialVennSingle();
+                initialVennShared();
+                initialTreeGroups();
        }
        catch(exception& e) {
                cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function ValidCalculator. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
@@ -108,7 +111,41 @@ bool ValidCalculators::isValidCalculator(string parameter, string calculator) {
                                }
                                cout << endl;
                                return false; }
-               //not a valid paramter
+               }else if (parameter == "vennsingle") {
+                       //is it valid
+                       if ((vennsingle.find(calculator)) != (vennsingle.end())) {
+                               return true;
+                       }else { 
+                               cout << calculator << " is not a valid estimator for the venn command in single mode and will be disregarded. Valid estimators are ";
+                               for (it = vennsingle.begin(); it != vennsingle.end(); it++) {
+                                       cout << it->first << ", ";
+                               }
+                               cout << endl;
+                               return false; }
+               }else if (parameter == "vennshared") {
+                       //is it valid
+                       if ((vennshared.find(calculator)) != (vennshared.end())) {
+                               return true;
+                       }else { 
+                               cout << calculator << " is not a valid estimator for the venn command in shared mode and will be disregarded. Valid estimators are ";
+                               for (it = vennshared.begin(); it != vennshared.end(); it++) {
+                                       cout << it->first << ", ";
+                               }
+                               cout << endl;
+                               return false; }
+               }else if (parameter == "treegroup") {
+                       //is it valid
+                       if ((treegroup.find(calculator)) != (treegroup.end())) {
+                               return true;
+                       }else { 
+                               cout << calculator << " is not a valid estimator for the tree.groups command in shared mode and will be disregarded. Valid estimators are ";
+                               for (it = treegroup.begin(); it != treegroup.end(); it++) {
+                                       cout << it->first << ", ";
+                               }
+                               cout << endl;
+                               return false; }
+
+               //not a valid parameter
                }else { return false; }
                
        }
@@ -125,17 +162,21 @@ bool ValidCalculators::isValidCalculator(string parameter, string calculator) {
 /********************************************************************/
 void ValidCalculators::initialSingle() {
        try {   
-       
-               single["sobs"]          = "sobs";
-               single["chao"]          = "chao";
-               single["ace"]           = "ace";
-               single["jack"]          = "jack";
-               single["shannon"]       = "shannon";
-               single["npshannon"]     = "npshannon";
-               single["simpson"]       = "simpson";
-               single["bootstrap"]     = "bootstrap";
-               single["default"]       = "default";
+               single["sobs"]          = "sobs";
+               single["chao"]              = "chao";
+               single["ace"]               = "ace";
+               single["jack"]              = "jack";
+               single["shannon"]           = "shannon";
+               single["npshannon"]     = "npshannon";
+               single["simpson"]           = "simpson";
+               single["bergerparker"]  = "bergerparker";
+               single["bootstrap"]     = "bootstrap";
+               single["geom"]          = "geom";
+               single["logsd"]         = "logsd";
+               single["qstat"]         = "qstat";
+               single["bstick"]        = "bstick";
                single["nseqs"]         = "nseqs";
+               single["default"]           = "default";
        }
        catch(exception& e) {
                cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSingle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
@@ -161,9 +202,16 @@ void ValidCalculators::initialShared() {
                shared["sharedsorest"]                  = "sharedsorest";
                shared["sharedthetayc"]                 = "sharedthetayc";
                shared["sharedthetan"]                  = "sharedthetan";
+               shared["sharedkstest"]          = "sharedkstest";
+               shared["sharedbdiversity"]      = "sharedbdiversity";
                shared["sharednseqs"]                   = "sharednseqs";
                shared["sharedochiai"]                  = "sharedochiai";
                shared["sharedanderberg"]               = "sharedanderberg";
+               shared["sharedkulczynski"]              = "sharedkulczynski";
+               shared["sharedkulczynskicody"]  = "sharedkulczynskicody";
+               shared["sharedlennon"]                  = "sharedlennon";
+               shared["sharedmorisitahorn"]    = "sharedmorisitahorn";
+               shared["sharedbraycurtis"]              = "sharedbraycurtis";
                shared["default"]                   = "default";
        }
        catch(exception& e) {
@@ -211,7 +259,12 @@ void ValidCalculators::initialSummary() {
                summary["shannon"]              = "shannon";
                summary["npshannon"]    = "npshannon";
                summary["simpson"]              = "simpson";
+               summary["bergerparker"] = "bergerparker";
+               summary["geom"]         = "geom";
                summary["bootstrap"]    = "bootstrap";
+               summary["logsd"]        = "logsd";
+               summary["qstat"]        = "qstat";
+               summary["bstick"]       = "bstick";
                summary["nseqs"]                = "nseqs";
                summary["default"]          = "default";
        }
@@ -239,9 +292,16 @@ void ValidCalculators::initialSharedSummary() {
                sharedsummary["sharedsorest"]                   = "sharedsorest";
                sharedsummary["sharedthetayc"]                  = "sharedthetayc";
                sharedsummary["sharedthetan"]                   = "sharedthetan";
+               sharedsummary["sharedkstest"]           = "sharedkstest";
+               sharedsummary["sharedbdiversity"]       = "sharedbdiversity";
                sharedsummary["sharednseqs"]                    = "sharednseqs";
                sharedsummary["sharedochiai"]                   = "sharedochiai";
                sharedsummary["sharedanderberg"]                = "sharedanderberg";
+               sharedsummary["sharedkulczynski"]               = "sharedkulczynski";
+               sharedsummary["sharedkulczynskicody"]   = "sharedkulczynskicody";
+               sharedsummary["sharedlennon"]                   = "sharedlennon";
+               sharedsummary["sharedmorisitahorn"]             = "sharedmorisitahorn";
+               sharedsummary["sharedbraycurtis"]               = "sharedbraycurtis";
                sharedsummary["default"]                                = "default";
        }
        catch(exception& e) {
@@ -273,7 +333,70 @@ void ValidCalculators::initialSharedRarefact() {
        }       
 }
 
+
+/********************************************************************/
+void ValidCalculators::initialVennSingle() {
+       try {
+               vennsingle["sobs"]              = "sobs";
+               vennsingle["chao"]                  = "chao";
+               vennsingle["ace"]                               = "ace";
+               vennsingle["jack"]                  = "jack";
+               vennsingle["default"]                   = "default";
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSingle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the ValidCalculator class function initialSingle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }       
+}
+
 /********************************************************************/
+void ValidCalculators::initialVennShared() {
+       try {
+               vennshared["sharedsobs"]        = "sharedsobs";
+               vennshared["sharedchao"]        = "sharedchao";
+               vennshared["sharedace"]         = "sharedace";
+               vennshared["default"]           = "default";
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSingle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the ValidCalculator class function initialSingle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }       
+}
+
+/********************************************************************/
+void ValidCalculators::initialTreeGroups() {
+       try {   
+               treegroup["sharedjabund"]                       = "sharedjabund";
+               treegroup["sharedsorensonabund"]        = "sharedsorensonabund";
+               treegroup["sharedjclass"]                       = "sharedjclass";
+               treegroup["sharedsorclass"]                     = "sharedsorclass";
+               treegroup["sharedjest"]                         = "sharedjest";
+               treegroup["sharedsorest"]                       = "sharedsorest";
+               treegroup["sharedthetayc"]                      = "sharedthetayc";
+               treegroup["sharedthetan"]                       = "sharedthetan";
+               treegroup["sharedmorisitahorn"]         = "sharedmorisitahorn";
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialTreeGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the ValidCalculator class function initialTreeGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }       
+}
+
+
+/********************************************************************/
+