added bootstrap.shared command and fixed some bugs with heatmap

[mothur.git] / validcalculator.cpp

diff --git a/validcalculator.cpp b/validcalculator.cpp
index 4c05e4a8e466e2a99a2628e0ca7e1cf31c5e4bfe..7d3477f68c2c8eb71c5c42ab27b1aceb7eb81472 100644 (file)
--- a/validcalculator.cpp
+++ b/validcalculator.cpp
@@ -21,6 +21,7 @@ ValidCalculators::ValidCalculators() {
                 initialVennSingle();
                 initialVennShared();
                 initialTreeGroups();
+                initialBoot();
        }
        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";
@@ -138,13 +139,23 @@ bool ValidCalculators::isValidCalculator(string parameter, string calculator) {
                        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 ";
+                               cout << calculator << " is not a valid estimator for the tree.shared 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; }
-
+               }else if (parameter == "boot") {
+                       //is it valid
+                       if ((boot.find(calculator)) != (boot.end())) {
+                               return true;
+                       }else { 
+                               cout << calculator << " is not a valid estimator for the bootstrap.shared command in shared mode and will be disregarded. Valid estimators are ";
+                               for (it = boot.begin(); it != boot.end(); it++) {
+                                       cout << it->first << ", ";
+                               }
+                               cout << endl;
+                               return false; }
                //not a valid parameter
                }else { return false; }
                
@@ -393,10 +404,90 @@ void ValidCalculators::initialTreeGroups() {
                exit(1);
        }       
 }
-
-
 /********************************************************************/
+void ValidCalculators::initialBoot() {
+       try {   
+               boot["jabund"]                          = "jabund";
+               boot["sorensonabund"]           = "sorensonabund";
+               boot["jclass"]                          = "jclass";
+               boot["sorclass"]                        = "orclass";
+               boot["jest"]                            = "jest";
+               boot["sorest"]                          = "sorest";
+               boot["thetayc"]                         = "thetayc";
+               boot["thetan"]                          = "thetan";
+               boot["morisitahorn"]            = "morisitahorn";
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialBoot. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the ValidCalculator class function initialBoot. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }       
+}
 
+/********************************************************************/
+void ValidCalculators::printCalc(string parameter, ostream& out) {
+       try{
+               out << "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++) {
+                               out << it->first << ", ";
+                       }
+               //are you looking for a calculator for a shared parameter
+               }else if (parameter == "shared") {
+                       for (it = shared.begin(); it != shared.end(); it++) {
+                               out << it->first << ", ";
+                       }
+               //are you looking for a calculator for a rarefaction parameter
+               }else if (parameter == "rarefaction") {
+                       for (it = rarefaction.begin(); it != rarefaction.end(); it++) {
+                               out << it->first << ", ";
+                       }
+               //are you looking for a calculator for a summary parameter
+               }else if (parameter == "summary") {
+                       for (it = summary.begin(); it != summary.end(); it++) {
+                               out << it->first << ", ";
+                       }
+               //are you looking for a calculator for a sharedsummary parameter
+               }else if (parameter == "sharedsummary") {
+                       for (it = sharedsummary.begin(); it != sharedsummary.end(); it++) {
+                               out << it->first << ", ";
+                       }
+               }else if (parameter == "sharedrarefaction") {
+                       for (it = sharedrarefaction.begin(); it != sharedrarefaction.end(); it++) {
+                               out << it->first << ", ";
+                       }
+               }else if (parameter == "vennsingle") {
+                       for (it = vennsingle.begin(); it != vennsingle.end(); it++) {
+                               out << it->first << ", ";
+                       }
+               }else if (parameter == "vennshared") {
+                       for (it = vennshared.begin(); it != vennshared.end(); it++) {
+                               out << it->first << ", ";
+                       }
+               }else if (parameter == "treegroup") {
+                       for (it = treegroup.begin(); it != treegroup.end(); it++) {
+                               out << it->first << ", ";
+                       }
+               }else if (parameter == "boot") {
+                       for (it = boot.begin(); it != boot.end(); it++) {
+                               out << it->first << ", ";
+                       }
+               }
+               out << endl;
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function printCalc. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the ValidCalculator class function printCalc. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }       
 
-
+}
+/********************************************************************/