added exponential distributions

example.con.txt

@@ -1,17 +1,17 @@
 # This file demonstrates the format of age constraints used by the script snapp_prep.rb:
 # 
 # - All lines beginning with # are ignored by snapp_prep.rb, as are empty lines.
-# - Lines beginning with "normal", "lognormal", "uniform", or "cladeage" are assumed to
-#   specify age constraints. The clades used for these constraints are always also
-#   constrained to be monophyletic. Clades can also be constrained to be monophyletic
-#   without additional age constraints. These monophyly constraints can be specified with
-#   lines starting with "monophyletic".
+# - Lines beginning with "normal", "lognormal", "uniform", "exponential, "or "cladeage"
+#   are assumed to specify age constraints. The clades used for these constraints are
+#   always also constrained to be monophyletic. Clades can also be constrained to be
+#   monophyletic without additional age constraints. These monophyly constraints can be
+#   specified with lines starting with "monophyletic".
 # - The format for these age constraints consists of three character strings separated
 #   by white space (tabs or spaces).
 # - The first of these three character strings specifies the prior distribution, where
-#   the type of the distribution ("normal", "lognormal", "uniform", or "cladeage") is
-#   followed by the parameters of the distribution, given in parentheses and separated
-#   by commas.
+#   the type of the distribution ("normal", "lognormal", "uniform", "exponential", or
+#   "cladeage") is followed by the parameters of the distribution, given in parentheses
+#   and separated by commas.
 #      For a normal distribution, these parameters are (in this order)
 #        (1.)   offset
 #        (2.)   mean
@@ -23,6 +23,9 @@
 #      For a uniform distribution, these parameters are
 #        (1.)   lower boundary
 #        (2.)   upper boundary
+#      For an exponential distribution, these parameters are
+#        (1.)   offset
+#        (2.)   mean
 #      For a cladeage distribution, these parameters are
 #        (1.)   minimum estimate of fossil age
 #        (2.)   maximum estimate of fossil age
@@ -48,6 +51,7 @@
 # - normal(10,5,1)	crown	speciesA,speciesB,speciesC
 # - lognormal(10,5,1)	stem	speciesA,speciesB,speciesC
 # - uniform(10,15)	crown	speciesA,speciesB,speciesC
+# - exponential(10,5)	crown speciesA,speciesB,speciesC
 # - cladeage(10,11,0.01,0.02,0.2,0.5,0.001,0.01)	stem	speciesA,speciesB,speciesC
 # - monophyletic	NA	speciesA,speciesB,speciesC
 

snapp_prep.rb

@@ -837,9 +837,9 @@
 	else
 		constraint_type = constraint_distribution.split("(")[0].strip
 	end
-	unless ["normal","lognormal","uniform","cladeage","monophyletic"].include?(constraint_type)
-		puts "ERROR: Expected 'normal', 'lognormal', 'uniform', 'cladeage', or 'monophyletic' as part"
-		puts "    of the first character string in '#{c}' but found '#{constraint_type}'!"
+	unless ["normal","lognormal","uniform","exponential","cladeage","monophyletic"].include?(constraint_type)
+		puts "ERROR: Expected 'normal', 'lognormal', 'uniform', 'exponential', 'cladeage', or 'monophyletic'"
+		puts "    as part of the first character string in '#{c}' but found '#{constraint_type}'!"
 		exit(1)
 	end
 	unless constraint_type == "monophyletic"
@@ -857,12 +857,17 @@
 		end
 	elsif constraint_type == "uniform"
 		unless constraint_parameters.size == 2
-			puts "ERROR: Expected 2 parameters for lognormal distribution, but found #{constraint_parameters.size}!"
+			puts "ERROR: Expected 2 parameters for uniform distribution, but found #{constraint_parameters.size}!"
+			exit(1)
+		end
+	elsif constraint_type == "exponential"
+		unless constraint_parameters.size == 2
+			puts "ERROR: Expected 2 parameters for exponential distribution, but found #{constraint_parameters.size}!"
 			exit(1)
 		end
 	elsif constraint_type == "cladeage"
 		unless constraint_parameters.size == 8
-			puts "ERROR: Expected 8 parameters for lognormal distribution, but found #{constraint_parameters.size}!"
+			puts "ERROR: Expected 8 parameters for cladeage distribution, but found #{constraint_parameters.size}!"
 			exit(1)
 		end
 	else
@@ -905,6 +910,8 @@
 		xml_string << "                </LogNormal>\n"
 	elsif constraint_type == "uniform"
 		xml_string << "                <Uniform name=\"distr\" lower=\"#{constraint_parameters[0]}\" upper=\"#{constraint_parameters[1]}\"/>\n"
+	elsif constraint_type == "exponential"
+		xml_string << "                <Exponential name=\"distr\" offset=\"#{constraint_parameters[0]}\" mean=\"#{constraint_parameters[1]}\"/>\n"
 	elsif constraint_type == "cladeage"
 		xml_string << "                <fossilDistr\n"
 		xml_string << "                    id=\"#{constraint_id}\"\n"