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 a875900411bd5b5b3678927e07acbd4e9cd9b9e6..90257c77eefbc1218698ebcc808e66d4c7bd34e9 100644 (file)
--- a/validcalculator.cpp
+++ b/validcalculator.cpp
@@ -20,6 +20,7 @@ ValidCalculators::ValidCalculators() {
                 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";
@@ -132,6 +133,18 @@ bool ValidCalculators::isValidCalculator(string parameter, string calculator) {
                                }
                                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; }
                
@@ -359,6 +372,31 @@ void ValidCalculators::initialVennShared() {
 }
 
 /********************************************************************/
+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);
+       }       
+}
+
+
+/********************************************************************/
+