created mothurOut class to handle logfiles

[mothur.git] / validparameter.cpp

diff --git a/validparameter.cpp b/validparameter.cpp
index a978f0fae0f4e357978898bb218adae100e51111..0c32a3e1c7b00e9fa90c8a5e4ca7fb759238c9e2 100644 (file)
--- a/validparameter.cpp
+++ b/validparameter.cpp
@@ -13,10 +13,11 @@
 
 ValidParameters::ValidParameters() {
        try {
+               m = MothurOut::getInstance();
                initParameterRanges();
        }
        catch(exception& e) {
-               errorOut(e, "ValidParameters", "ValidParameters");
+               m->errorOut(e, "ValidParameters", "ValidParameters");
                exit(1);
        }
 }
@@ -38,11 +39,11 @@ bool ValidParameters::isValidParameter(string parameter, vector<string> cParams,
                        }
                }
                if(!valid) {
-                       mothurOut(parameter + " is not a valid parameter."); mothurOutEndLine();
-                       mothurOut("The valid parameters are: ");
+                       m->mothurOut(parameter + " is not a valid parameter."); m->mothurOutEndLine();
+                       m->mothurOut("The valid parameters are: ");
                        for(int i = 0; i < numParams-1; i++)
-                               mothurOut(cParams.at(i) + ", ");
-                       mothurOut("and " + cParams.at(numParams-1) + ".\n");
+                               m->mothurOut(cParams.at(i) + ", ");
+                       m->mothurOut("and " + cParams.at(numParams-1) + ".\n");
                        return false;
                }
                
@@ -73,7 +74,7 @@ bool ValidParameters::isValidParameter(string parameter, vector<string> cParams,
                                double logNum = log10((double)pVal);
                                double diff = (double)((int)logNum - logNum);
                                if(diff != 0) {
-                                       mothurOut("The precision parameter can only take powers of 10 as a value (e.g. 10,1000,1000, etc.)\n");
+                                       m->mothurOut("The precision parameter can only take powers of 10 as a value (e.g. 10,1000,1000, etc.)\n");
                                        return false;
                                }
                        }
@@ -99,7 +100,7 @@ bool ValidParameters::isValidParameter(string parameter, vector<string> cParams,
                        else if(range.at(4).compare("only") == 0)
                                c = 1;
                        else {
-                               mothurOut("The range can only be 'between' or 'only' the bounding numbers.\n");
+                               m->mothurOut("The range can only be 'between' or 'only' the bounding numbers.\n");
                                return false;
                        }
                        
@@ -108,7 +109,7 @@ bool ValidParameters::isValidParameter(string parameter, vector<string> cParams,
                        else if(range.at(0).compare(">=") == 0 || range[3].compare("=>") == 0)
                                d = 1;
                        else {
-                               mothurOut("The parameter value can only be '>', '>=', or '=>' the lower bounding number.\n");
+                               m->mothurOut("The parameter value can only be '>', '>=', or '=>' the lower bounding number.\n");
                                return false;
                        }
                        
@@ -117,7 +118,7 @@ bool ValidParameters::isValidParameter(string parameter, vector<string> cParams,
                        else if(range.at(2).compare("<=") == 0 || range[4].compare("=<") == 0)
                                e = 1;
                        else {
-                               mothurOut("The parameter value can only be '<', '<=', or '=<' the upper bounding number.\n");
+                               m->mothurOut("The parameter value can only be '<', '<=', or '=<' the upper bounding number.\n");
                                return false;
                        }
                        
@@ -161,25 +162,25 @@ bool ValidParameters::isValidParameter(string parameter, vector<string> cParams,
                        
                        
                        if(!valid) {
-                               mothurOut("The '" + parameter + "' parameter needs to be ");
+                               m->mothurOut("The '" + parameter + "' parameter needs to be ");
                                if(c == 1)
-                                       mothurOut("either '" + toString(a) + "' or '" + toString(b) + "'.\n");
+                                       m->mothurOut("either '" + toString(a) + "' or '" + toString(b) + "'.\n");
                                else {
                                        if(a != piSentinel) {
-                                               mothurOut(">");
+                                               m->mothurOut(">");
                                                if(d != 0)
-                                                       mothurOut("=");
-                                               mothurOut(" '" + toString(a) + "'");
+                                                       m->mothurOut("=");
+                                               m->mothurOut(" '" + toString(a) + "'");
                                        }
                                        if(b == piSentinel)
-                                               mothurOut( "'.\n");
+                                               m->mothurOut( "'.\n");
                                        else if(a != piSentinel)
-                                               mothurOut(" and ");
+                                               m->mothurOut(" and ");
                                        if(b != piSentinel) {
-                                               mothurOut("<");
+                                               m->mothurOut("<");
                                                if(e != 0)
-                                                       mothurOut("=");
-                                               mothurOut(" '" + toString(b) + "'.\n");
+                                                       m->mothurOut("=");
+                                               m->mothurOut(" '" + toString(b) + "'.\n");
                                        }
                                }
                                return false;
@@ -188,7 +189,7 @@ bool ValidParameters::isValidParameter(string parameter, vector<string> cParams,
                return true;
        }
        catch(exception& e) {
-               errorOut(e, "ValidParameters", "isValidParameters");
+               m->errorOut(e, "ValidParameters", "isValidParameters");
                exit(1);
        }
 }
@@ -218,7 +219,7 @@ string ValidParameters::validFile(map<string, string> container, string paramete
        
        }
        catch(exception& e) {
-               errorOut(e, "ValidParameters", "validFile");
+               m->errorOut(e, "ValidParameters", "validFile");
                exit(1);
        }
 }
@@ -263,7 +264,7 @@ void ValidParameters::initParameterRanges() {
                parameterRanges["size"] = addParameters(sizeArray, rangeSize);
        }
        catch(exception& e) {
-               errorOut(e, "ValidParameters", "initParameterRanges");
+               m->errorOut(e, "ValidParameters", "initParameterRanges");
                exit(1);
        }
 }
@@ -277,7 +278,7 @@ vector<string> ValidParameters::addParameters(string parameters[], int size) {
                return pVector;
        }
        catch(exception& e) {
-               errorOut(e, "ValidParameters", "addParameters");
+               m->errorOut(e, "ValidParameters", "addParameters");
                exit(1);
        }
 }