took out debugging output code from distance calculators

[mothur.git] / validcalculator.cpp

diff --git a/validcalculator.cpp b/validcalculator.cpp
index 504eb7103ee7e59c998cb438f520f3204a970c29..bc8c4b8d7ab4b753cfa3f75a7c7da0b8ba740bc0 100644 (file)
--- a/validcalculator.cpp
+++ b/validcalculator.cpp
@@ -12,6 +12,8 @@
 /********************************************************************/
 ValidCalculators::ValidCalculators() {
        try {
+                m = MothurOut::getInstance();
+               
                 initialSingle();
                 initialShared();
                 initialRarefaction();
@@ -27,7 +29,7 @@ ValidCalculators::ValidCalculators() {
                 initialHeat();
        }
        catch(exception& e) {
-               errorOut(e, "ValidCalculator", "ValidCalculator");
+               m->errorOut(e, "ValidCalculator", "ValidCalculator");
                exit(1);
        }
 }
@@ -46,11 +48,11 @@ bool ValidCalculators::isValidCalculator(string parameter, string calculator) {
                        if ((single.find(calculator)) != (single.end())) {
                                return true;
                        }else { 
-                               mothurOut(calculator + " is not a valid estimator for the collect.single command and will be disregarded. Valid estimators are ");
+                               m->mothurOut(calculator + " is not a valid estimator for the collect.single command and will be disregarded. Valid estimators are ");
                                for (it = single.begin(); it != single.end(); it++) {
-                                       mothurOut(it->first + ", ");
+                                       m->mothurOut(it->first + ", ");
                                }
-                               mothurOutEndLine();
+                               m->mothurOutEndLine();
                                return false; }
                //are you looking for a calculator for a shared parameter
                }else if (parameter == "shared") {
@@ -58,11 +60,11 @@ bool ValidCalculators::isValidCalculator(string parameter, string calculator) {
                        if ((shared.find(calculator)) != (shared.end())) {
                                return true;
                        }else { 
-                               mothurOut(calculator +  " is not a valid estimator for the collect.shared command and will be disregarded.  Valid estimators are ");
+                               m->mothurOut(calculator +  " is not a valid estimator for the collect.shared command and will be disregarded.  Valid estimators are ");
                                for (it = shared.begin(); it != shared.end(); it++) {
-                                       mothurOut(it->first + ", ");
+                                       m->mothurOut(it->first + ", ");
                                }
-                               mothurOutEndLine();
+                               m->mothurOutEndLine();
                                return false; }
                //are you looking for a calculator for a rarefaction parameter
                }else if (parameter == "rarefaction") {
@@ -70,11 +72,11 @@ bool ValidCalculators::isValidCalculator(string parameter, string calculator) {
                        if ((rarefaction.find(calculator)) != (rarefaction.end())) {
                                return true;
                        }else { 
-                               mothurOut(calculator + " is not a valid estimator for the rarefaction.single command and will be disregarded. Valid estimators are ");
+                               m->mothurOut(calculator + " is not a valid estimator for the rarefaction.single command and will be disregarded. Valid estimators are ");
                                for (it = rarefaction.begin(); it != rarefaction.end(); it++) {
-                                       mothurOut(it->first + ", ");
+                                       m->mothurOut(it->first + ", ");
                                }
-                               mothurOutEndLine();
+                               m->mothurOutEndLine();
                                return false; }
                //are you looking for a calculator for a summary parameter
                }else if (parameter == "summary") {
@@ -82,11 +84,11 @@ bool ValidCalculators::isValidCalculator(string parameter, string calculator) {
                        if ((summary.find(calculator)) != (summary.end())) {
                                return true;
                        }else { 
-                               mothurOut(calculator + " is not a valid estimator for the summary.shared command and will be disregarded. Valid estimators are ");
+                               m->mothurOut(calculator + " is not a valid estimator for the summary.shared command and will be disregarded. Valid estimators are ");
                                for (it = summary.begin(); it != summary.end(); it++) {
-                                       mothurOut(it->first + ", ");
+                                       m->mothurOut(it->first + ", ");
                                }
-                               mothurOutEndLine();
+                               m->mothurOutEndLine();
                                return false; }
                //are you looking for a calculator for a sharedsummary parameter
                }else if (parameter == "sharedsummary") {
@@ -94,106 +96,106 @@ bool ValidCalculators::isValidCalculator(string parameter, string calculator) {
                        if ((sharedsummary.find(calculator)) != (sharedsummary.end())) {
                                return true;
                        }else { 
-                               mothurOut(calculator +  " is not a valid estimator for the summary.shared command and will be disregarded. Valid estimators are ");
+                               m->mothurOut(calculator +  " is not a valid estimator for the summary.shared command and will be disregarded. Valid estimators are ");
                                for (it = sharedsummary.begin(); it != sharedsummary.end(); it++) {
-                                       mothurOut(it->first + ", ");
+                                       m->mothurOut(it->first + ", ");
                                }
-                               mothurOutEndLine();
+                               m->mothurOutEndLine();
                                return false; }
                }else if (parameter == "sharedrarefaction") {
                        //is it valid
                        if ((sharedrarefaction.find(calculator)) != (sharedrarefaction.end())) {
                                return true;
                        }else { 
-                               mothurOut(calculator + " is not a valid estimator for the rarefaction.shared command and will be disregarded. Valid estimator is ");
+                               m->mothurOut(calculator + " is not a valid estimator for the rarefaction.shared command and will be disregarded. Valid estimator is ");
                                for (it = sharedrarefaction.begin(); it != sharedrarefaction.end(); it++) {
-                                       mothurOut(it->first + ", ");
+                                       m->mothurOut(it->first + ", ");
                                }
-                               mothurOutEndLine();
+                               m->mothurOutEndLine();
                                return false; }
                }else if (parameter == "vennsingle") {
                        //is it valid
                        if ((vennsingle.find(calculator)) != (vennsingle.end())) {
                                return true;
                        }else { 
-                               mothurOut(calculator + " is not a valid estimator for the venn command in single mode and will be disregarded. Valid estimators are ");
+                               m->mothurOut(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++) {
-                                       mothurOut(it->first + ", ");
+                                       m->mothurOut(it->first + ", ");
                                }
-                               mothurOutEndLine();
+                               m->mothurOutEndLine();
                                return false; }
                }else if (parameter == "vennshared") {
                        //is it valid
                        if ((vennshared.find(calculator)) != (vennshared.end())) {
                                return true;
                        }else { 
-                               mothurOut(calculator + " is not a valid estimator for the venn command in shared mode and will be disregarded. Valid estimators are ");
+                               m->mothurOut(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++) {
-                                       mothurOut(it->first + ", ");
+                                       m->mothurOut(it->first + ", ");
                                }
-                               mothurOutEndLine();
+                               m->mothurOutEndLine();
                                return false; }
                }else if (parameter == "treegroup") {
                        //is it valid
                        if ((treegroup.find(calculator)) != (treegroup.end())) {
                                return true;
                        }else { 
-                               mothurOut(calculator + " is not a valid estimator for the tree.shared command and will be disregarded. Valid estimators are ");
+                               m->mothurOut(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++) {
-                                       mothurOut(it->first + ", ");
+                                       m->mothurOut(it->first + ", ");
                                }
-                               mothurOutEndLine();
+                               m->mothurOutEndLine();
                                return false; }
                }else if (parameter == "matrix") {
                        //is it valid
                        if ((matrix.find(calculator)) != (matrix.end())) {
                                return true;
                        }else { 
-                               mothurOut(calculator +  " is not a valid estimator for the matrix.output command and will be disregarded. Valid estimators are ");
+                               m->mothurOut(calculator +  " is not a valid estimator for the matrix.output command and will be disregarded. Valid estimators are ");
                                for (it = matrix.begin(); it != matrix.end(); it++) {
-                                       mothurOut(it->first + ", ");
+                                       m->mothurOut(it->first + ", ");
                                }
-                               mothurOutEndLine();
+                               m->mothurOutEndLine();
                                return false; }
                }else if (parameter == "heat") {
                        //is it valid
                        if ((heat.find(calculator)) != (heat.end())) {
                                return true;
                        }else { 
-                               mothurOut(calculator + " is not a valid estimator for the heatmap.sim command and will be disregarded. Valid estimators are ");
+                               m->mothurOut(calculator + " is not a valid estimator for the heatmap.sim command and will be disregarded. Valid estimators are ");
                                for (it = heat.begin(); it != heat.end(); it++) {
-                                       mothurOut(it->first + ", ");
+                                       m->mothurOut(it->first + ", ");
                                }
-                               mothurOutEndLine();
+                               m->mothurOutEndLine();
                                return false; }
                }else if (parameter == "boot") {
                        //is it valid
                        if ((boot.find(calculator)) != (boot.end())) {
                                return true;
                        }else { 
-                               mothurOut(calculator + " is not a valid estimator for the bootstrap.shared command and will be disregarded. Valid estimators are ");
+                               m->mothurOut(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++) {
-                                       mothurOut(it->first + ", ");
+                                       m->mothurOut(it->first + ", ");
                                }
-                               mothurOutEndLine();
+                               m->mothurOutEndLine();
                                return false; }
                }else if (parameter == "distance") {
                        //is it valid
                        if ((distance.find(calculator)) != (distance.end())) {
                                return true;
                        }else { 
-                               mothurOut(calculator +  " is not a valid estimator for the distance command and will be disregarded. Valid calculators are ");
+                               m->mothurOut(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++) {
-                                       mothurOut(it->first + ", ");
+                                       m->mothurOut(it->first + ", ");
                                }
-                               mothurOutEndLine();
+                               m->mothurOutEndLine();
                                return false; }
                //not a valid parameter
                }else { return false; }
                
        }
        catch(exception& e) {
-               errorOut(e, "ValidCalculator", "isValidCalculator");
+               m->errorOut(e, "ValidCalculator", "isValidCalculator");
                exit(1);
        }
 }
@@ -207,11 +209,16 @@ void ValidCalculators::initialSingle() {
                single["jack"]              = "jack";
                single["shannon"]           = "shannon";
                single["npshannon"]     = "npshannon";
+               single["shannoneven"]   = "shannoneven";
+               single["smithwilson"]   = "smithwilson";
+               single["heip"]                  = "heip";
                single["simpson"]           = "simpson";
+               single["simpsoneven"]   = "simpsoneven";
+               single["invsimpson"]    = "invsimpson";
                single["bergerparker"]  = "bergerparker";
                single["bootstrap"]     = "bootstrap";
                single["geometric"]     = "geometric";
-               single["logseries"]         = "logseries";
+               single["logseries"]             = "logseries";
                single["qstat"]         = "qstat";
                single["bstick"]        = "bstick";
                single["goodscoverage"] = "goodscoverage";
@@ -224,7 +231,7 @@ void ValidCalculators::initialSingle() {
                single["default"]           = "default";
        }
        catch(exception& e) {
-               errorOut(e, "ValidCalculator", "initialSingle");
+               m->errorOut(e, "ValidCalculator", "initialSingle");
                exit(1);
        }
 }
@@ -256,7 +263,7 @@ void ValidCalculators::initialShared() {
                shared["default"]                   = "default";
        }
        catch(exception& e) {
-               errorOut(e, "ValidCalculator", "initialShared");
+               m->errorOut(e, "ValidCalculator", "initialShared");
                exit(1);
        }
 }
@@ -269,15 +276,20 @@ void ValidCalculators::initialRarefaction() {
                rarefaction["ace"]                      = "ace";
                rarefaction["jack"]                     = "jack";
                rarefaction["shannon"]          = "shannon";
+               rarefaction["smithwilson"]      = "smithwilson";
+               rarefaction["heip"]                     = "heip";
                rarefaction["npshannon"]        = "npshannon";
+               rarefaction["shannoneven"]      = "shannoneven";
                rarefaction["simpson"]          = "simpson";
+               rarefaction["invsimpson"]       = "invsimpson";
+               rarefaction["simpsoneven"]      = "simpsoneven";
                rarefaction["bootstrap"]        = "bootstrap";
                rarefaction["nseqs"]            = "nseqs";
                rarefaction["coverage"]         = "coverage";
                rarefaction["default"]      = "default";
        }
        catch(exception& e) {
-               errorOut(e, "ValidCalculator", "initialRarefaction");
+               m->errorOut(e, "ValidCalculator", "initialRarefaction");
                exit(1);
        }
 }
@@ -291,8 +303,13 @@ void ValidCalculators::initialSummary() {
                summary["ace"]                  = "ace";
                summary["jack"]                 = "jack";
                summary["shannon"]              = "shannon";
+               summary["heip"]                 = "heip";
+               summary["shannoneven"]  = "shannoneven";
+               summary["smithwilson"]  = "smithwilson";
+               summary["invsimpson"]   = "invsimpson";
                summary["npshannon"]    = "npshannon";
                summary["simpson"]              = "simpson";
+               summary["simpsoneven"]  = "simpsoneven";
                summary["bergerparker"] = "bergerparker";
                summary["geometric"]    = "geometric";
                summary["bootstrap"]    = "bootstrap";
@@ -309,7 +326,7 @@ void ValidCalculators::initialSummary() {
                summary["default"]          = "default";
        }
        catch(exception& e) {
-               errorOut(e, "ValidCalculator", "initialSummary");
+               m->errorOut(e, "ValidCalculator", "initialSummary");
                exit(1);
        }
 }
@@ -341,7 +358,7 @@ void ValidCalculators::initialSharedSummary() {
                sharedsummary["default"]                                = "default";
        }
        catch(exception& e) {
-               errorOut(e, "ValidCalculator", "initialSharedSummary");
+               m->errorOut(e, "ValidCalculator", "initialSharedSummary");
                exit(1);
        }
 }
@@ -356,7 +373,7 @@ void ValidCalculators::initialSharedRarefact() {
                sharedrarefaction["default"]        = "default";
        }
        catch(exception& e) {
-               errorOut(e, "ValidCalculator", "initialSharedRarefact");
+               m->errorOut(e, "ValidCalculator", "initialSharedRarefact");
                exit(1);
        }
 }
@@ -372,7 +389,7 @@ void ValidCalculators::initialVennSingle() {
                vennsingle["default"]           = "default";
        }
        catch(exception& e) {
-               errorOut(e, "ValidCalculator", "initialVennSingle");
+               m->errorOut(e, "ValidCalculator", "initialVennSingle");
                exit(1);
        }
 }
@@ -386,7 +403,7 @@ void ValidCalculators::initialVennShared() {
                vennshared["default"]           = "default";
        }
        catch(exception& e) {
-               errorOut(e, "ValidCalculator", "initialVennShared");
+               m->errorOut(e, "ValidCalculator", "initialVennShared");
                exit(1);
        }
 }
@@ -406,7 +423,7 @@ void ValidCalculators::initialTreeGroups() {
                treegroup["braycurtis"]                         = "braycurtis";
        }
        catch(exception& e) {
-               errorOut(e, "ValidCalculator", "initialTreeGroups");
+               m->errorOut(e, "ValidCalculator", "initialTreeGroups");
                exit(1);
        }
 }
@@ -425,7 +442,7 @@ void ValidCalculators::initialHeat() {
                heat["braycurtis"]                      = "braycurtis";
        }
        catch(exception& e) {
-               errorOut(e, "ValidCalculator", "initialHeat");
+               m->errorOut(e, "ValidCalculator", "initialHeat");
                exit(1);
        }
 }
@@ -445,7 +462,7 @@ void ValidCalculators::initialMatrix() {
                matrix["braycurtis"]                    = "braycurtis";
        }
        catch(exception& e) {
-               errorOut(e, "ValidCalculator", "initialMatrix");
+               m->errorOut(e, "ValidCalculator", "initialMatrix");
                exit(1);
        }
 }
@@ -465,7 +482,7 @@ void ValidCalculators::initialBoot() {
                boot["braycurtis"]                      = "braycurtis";
        }
        catch(exception& e) {
-               errorOut(e, "ValidCalculator", "initialBoot");
+               m->errorOut(e, "ValidCalculator", "initialBoot");
                exit(1);
        }
 }
@@ -477,7 +494,7 @@ void ValidCalculators::initialDistance() {
                distance["onegap"]              = "onegap";
        }
        catch(exception& e) {
-               errorOut(e, "ValidCalculator", "initialDistance");
+               m->errorOut(e, "ValidCalculator", "initialDistance");
                exit(1);
        }
 }
@@ -548,7 +565,7 @@ void ValidCalculators::printCalc(string parameter, ostream& out) {
                out << endl;
        }
        catch(exception& e) {
-               errorOut(e, "ValidCalculator", "printCalc");
+               m->errorOut(e, "ValidCalculator", "printCalc");
                exit(1);
        }
 }