lib/genevalidator/exceptions.rb in genevalidator-1.6.1 vs lib/genevalidator/exceptions.rb in genevalidator-1.6.2

@@ -1,13 +1,18 @@
 module GeneValidator
   # Exception raised when BLAST path is not added to the CLASSPATH
   class ClasspathError < Exception
   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
+    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
   end
@@ -16,44 +21,66 @@
   class QueryError < Exception
   end
 
   # Exception raised when a validation class is not instance of ValidationTest
   class ValidationClassError < Exception
+    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
+  # Exception raised when a validation report class is not instance of
+  #   ValidationReport
   class ReportClassError < Exception
+    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 statisticl validation
+  # Exception raised when there are not enough blast hits to make a statistical
+  #   validation
   class NotEnoughHitsError < Exception
   end
 
-  # Exception raised when function dependig on the internet connection raise Exception
+  # Exception raised when function dependig on the internet connection raise
+  #   Exception
   class NoInternetError < Exception
   end
 
   # Exception raised when the alignment initialization raises exception
   class NoMafftInstallationError < Exception
   end
 
   # Exception raised when the -v argument didn't filter any validatio test
   class NoValidationError < Exception
+    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
+    def to_s
+      "\nAlias Duplication error: Possible cause: At least two validations" \
+      " have the same CLI alias\n"
+    end
   end
 
   # Exception raised when the are alias duplications
   class NoPIdentError < Exception
   end
 
-  # Exception raised when the tabular format does not correspond to the tabular argumet
+  # Exception raised when the tabular format does not correspond to the tabular
+  #   argument
   class InconsistentTabularFormat < Exception
   end
 
-  # Exception raised when there are more than one reading frame among the hits of one prediction
+  # Exception raised when there are more than one reading frame among the hits
+  #   of one prediction
   class ReadingFrameError < Exception
   end
 
   class OtherError < Exception
   end