altered venn command to make use of sharedchao for any number of groups, fixed window...

[mothur.git] / validcalculator.cpp

diff --git a/validcalculator.cpp b/validcalculator.cpp
index f6fe280a86474ea35e78a18245ac24a0ba5e5349..14fa775e7398d4be2b5b13a02f111303093c9e9d 100644 (file)
--- a/validcalculator.cpp
+++ b/validcalculator.cpp
@@ -22,6 +22,7 @@ ValidCalculators::ValidCalculators() {
                 initialVennShared();
                 initialTreeGroups();
                 initialBoot();
+                initialDistance();
        }
        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";
@@ -139,7 +140,7 @@ 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.shared command in shared mode and will be disregarded. Valid estimators are ";
+                               cout << calculator << " is not a valid estimator for the tree.shared command and will be disregarded. Valid estimators are ";
                                for (it = treegroup.begin(); it != treegroup.end(); it++) {
                                        cout << it->first << ", ";
                                }
@@ -150,12 +151,23 @@ bool ValidCalculators::isValidCalculator(string parameter, string calculator) {
                        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 ";
+                               cout << calculator << " is not a valid estimator for the bootstrap.shared command and will be disregarded. Valid estimators are ";
                                for (it = boot.begin(); it != boot.end(); it++) {
                                        cout << it->first << ", ";
                                }
                                cout << endl;
                                return false; }
+               }else if (parameter == "distance") {
+                       //is it valid
+                       if ((distance.find(calculator)) != (distance.end())) {
+                               return true;
+                       }else { 
+                               cout << calculator << " is not a valid estimator for the distance command and will be disregarded. Valid calculators are ";
+                               for (it = distance.begin(); it != distance.end(); it++) {
+                                       cout << it->first << ", ";
+                               }
+                               cout << endl;
+                               return false; }
                //not a valid parameter
                }else { return false; }
                
@@ -208,7 +220,7 @@ void ValidCalculators::initialShared() {
                shared["sharedchao"]                    = "sharedchao";
                shared["sharedace"]                             = "sharedace";
                shared["jabund"]                                = "jabund";
-               shared["sorabund"]                      = "sorabund";
+               shared["sorabund"]                              = "sorabund";
                shared["jclass"]                                = "jclass";
                shared["sorclass"]                              = "sorclass";
                shared["jest"]                                  = "jest";
@@ -391,7 +403,7 @@ void ValidCalculators::initialVennShared() {
 void ValidCalculators::initialTreeGroups() {
        try {   
                treegroup["jabund"]                                     = "jabund";
-               treegroup["sorabund"]                   = "sorabund";
+               treegroup["sorabund"]                           = "sorabund";
                treegroup["jclass"]                                     = "jclass";
                treegroup["sorclass"]                           = "sorclass";
                treegroup["jest"]                                       = "jest";
@@ -399,7 +411,7 @@ void ValidCalculators::initialTreeGroups() {
                treegroup["thetayc"]                            = "thetayc";
                treegroup["thetan"]                                     = "thetan";
                treegroup["morisitahorn"]                       = "morisitahorn";
-               treegroup["braycurtis"]                 = "braycurtis";
+               treegroup["braycurtis"]                         = "braycurtis";
        }
        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";
@@ -414,7 +426,7 @@ void ValidCalculators::initialTreeGroups() {
 void ValidCalculators::initialBoot() {
        try {   
                boot["jabund"]                          = "jabund";
-               boot["sorabund"]                = "sorabund";
+               boot["sorabund"]                        = "sorabund";
                boot["jclass"]                          = "jclass";
                boot["sorclass"]                        = "orclass";
                boot["jest"]                            = "jest";
@@ -433,6 +445,22 @@ void ValidCalculators::initialBoot() {
                exit(1);
        }       
 }
+/********************************************************************/
+void ValidCalculators::initialDistance() {
+       try {   
+               distance["nogaps"]              = "nogaps";
+               distance["eachgap"]             = "eachgap";
+               distance["onegap"]              = "onegap";
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialDistance. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the ValidCalculator class function initialDistance. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }       
+}
 
 /********************************************************************/
 void ValidCalculators::printCalc(string parameter, ostream& out) {
@@ -483,7 +511,12 @@ void ValidCalculators::printCalc(string parameter, ostream& out) {
                        for (it = boot.begin(); it != boot.end(); it++) {
                                out << it->first << ", ";
                        }
+               }else if (parameter == "distance") {
+                       for (it = distance.begin(); it != distance.end(); it++) {
+                               out << it->first << ", ";
+                       }
                }
+
                out << endl;
        }
        catch(exception& e) {