lib/genevalidator/exceptions.rb in genevalidator-1.6.12 vs lib/genevalidator/exceptions.rb in genevalidator-2.1.3

@@ -1,95 +1,95 @@
 module GeneValidator
   # Exception raised when BLAST path is not added to the CLASSPATH
-  class ClasspathError < Exception
+  class ClasspathError < RuntimeError
   end
 
   # Exception raised when the command line type argument
   # does not corrsepond to the type of the sequences in the fasta file
-  class SequenceTypeError < Exception
+  class SequenceTypeError < RuntimeError
     def to_s
       "\nSequence Type error: Possible cause include that the blast output" \
       " was not obtained against a protein database.\n"
     end
   end
 
   # Exception raised when an unexisting file is accessed
-  class FileNotFoundException < Exception
+  class FileNotFoundException < RuntimeError
   end
 
   # Exception raised when blast does not find any hit
-  class QueryError < Exception
+  class QueryError < RuntimeError
   end
 
   # Exception raised when a validation class is not instance of ValidationTest
-  class ValidationClassError < Exception
+  class ValidationClassError < RuntimeError
     def to_s
       "\nClass Type error: Possible cause include that one of the validations" \
       " is not a sub-class of ValidationTest\n"
     end
   end
 
   # Exception raised when a validation report class is not instance of
   #   ValidationReport
-  class ReportClassError < Exception
+  class ReportClassError < RuntimeError
     def to_s
       "\nClass Type error: Possible causes include that the type of one of" \
       ' the validation reports is not a subclass of the ValidationReport' \
       " class.\n"
     end
   end
 
   # Exception raised when there are not enough blast hits to make a statistical
   #   validation
-  class NotEnoughHitsError < Exception
+  class NotEnoughHitsError < RuntimeError
   end
 
   # Exception raised when function dependig on the internet connection raise
   #   Exception
-  class NoInternetError < Exception
+  class NoInternetError < RuntimeError
   end
 
   # Exception raised when the alignment initialization raises exception
-  class NoMafftInstallationError < Exception
+  class NoMafftInstallationError < RuntimeError
   end
 
   # Exception raised when the -v argument didn't filter any validatio test
-  class NoValidationError < Exception
+  class NoValidationError < RuntimeError
     def to_s
       "\nValidation error: Possible cause inlcude that the -v arguments" \
       " supplied is not valid\n"
     end
   end
 
   # Exception raised when the are alias duplications
-  class AliasDuplicationError < Exception
+  class AliasDuplicationError < RuntimeError
     def to_s
       "\nAlias Duplication error: Possible cause: At least two validations" \
       " have the same CLI alias\n"
     end
   end
 
   # Exception raised when the BLAST is not set up with the '-parse-seqids' arg.
-  class BLASTDBError < Exception
+  class BLASTDBError < RuntimeError
   end
 
   # Error raised by QI Validation when the query does not have QI tag
-  class NotEnoughEvidence < Exception
+  class NotEnoughEvidence < RuntimeError
   end
 
   # Exception raised when the are alias duplications
-  class NoPIdentError < Exception
+  class NoPIdentError < RuntimeError
   end
 
   # Exception raised when the tabular format does not correspond to the tabular
   #   argument
-  class InconsistentTabularFormat < Exception
+  class InconsistentTabularFormat < RuntimeError
   end
 
   # Exception raised when there are more than one reading frame among the hits
   #   of one prediction
-  class ReadingFrameError < Exception
+  class ReadingFrameError < RuntimeError
   end
 
-  class OtherError < Exception
+  class OtherError < RuntimeError
   end
 end