added sequence name to error string in fastq.info. Changed np_shannon to npshannon.

[mothur.git] / mothurout.cpp

diff --git a/mothurout.cpp b/mothurout.cpp
index c58e634500270cce359470ebc56f7244ef994c8c..20a7b5235029b6d7908ca0f23f119c3c38d095f1 100644 (file)
--- a/mothurout.cpp
+++ b/mothurout.cpp
@@ -1514,6 +1514,84 @@ int MothurOut::mothurRemove(string filename){
                exit(1);
        }
 }
+/***********************************************************************/
+bool MothurOut::mothurConvert(string item, int& num){
+       try {
+               bool error = false;
+               
+               if (isNumeric1(item)) {
+                       convert(item, num);
+               }else {
+                       num = 0;
+                       error = true;
+                       mothurOut("[ERROR]: cannot convert " + item + " to an integer."); mothurOutEndLine();
+                       commandInputsConvertError = true;
+               }
+               
+               return error;
+       }
+       catch(exception& e) {
+               errorOut(e, "MothurOut", "mothurConvert");
+               exit(1);
+       }
+}
+/***********************************************************************/
+bool MothurOut::isNumeric1(string stringToCheck){
+       try {
+               bool numeric = false;
+               
+               if(stringToCheck.find_first_not_of("0123456789.-") == string::npos) { numeric = true; }
+                       
+               return numeric;
+       }
+       catch(exception& e) {
+               errorOut(e, "MothurOut", "isNumeric1");
+               exit(1);
+       }
+       
+}
+/***********************************************************************/
+bool MothurOut::mothurConvert(string item, float& num){
+       try {
+               bool error = false;
+               
+               if (isNumeric1(item)) {
+                       convert(item, num);
+               }else {
+                       num = 0;
+                       error = true;
+                       mothurOut("[ERROR]: cannot convert " + item + " to a float."); mothurOutEndLine();
+                       commandInputsConvertError = true;
+               }
+               
+               return error;
+       }
+       catch(exception& e) {
+               errorOut(e, "MothurOut", "mothurConvert");
+               exit(1);
+       }
+}
+/***********************************************************************/
+bool MothurOut::mothurConvert(string item, double& num){
+       try {
+               bool error = false;
+               
+               if (isNumeric1(item)) {
+                       convert(item, num);
+               }else {
+                       num = 0;
+                       error = true;
+                       mothurOut("[ERROR]: cannot convert " + item + " to a double."); mothurOutEndLine();
+                       commandInputsConvertError = true;
+               }
+               
+               return error;
+       }
+       catch(exception& e) {
+               errorOut(e, "MothurOut", "mothurConvert");
+               exit(1);
+       }
+}
 /**************************************************************************************************/
 
 vector<vector<double> > MothurOut::binomial(int maxOrder){
@@ -2074,7 +2152,7 @@ int MothurOut::removeConfidences(string& tax) {
                                int pos2 = taxon.find_last_of(')');
                                if (pos2 != -1) {
                                        string confidenceScore = taxon.substr(pos+1, (pos2-(pos+1)));
-                                       if (isContainingOnlyDigits(confidenceScore)) {
+                                       if (isNumeric1(confidenceScore)) {
                                                taxon = taxon.substr(0, pos); //rip off confidence 
                                        }
                                }