renamed patternmatcher to dynamic

[biopieces.git] / code_ruby / lib / maasha / seq / backtrack.rb

diff --git a/code_ruby/lib/maasha/seq/backtrack.rb b/code_ruby/lib/maasha/seq/backtrack.rb
index 1d09c30702b5250c50074d2ecc1760a8920ab0f7..ab2c00fc7a952fb5c9c6be5c906c96c5690b6cf2 100644 (file)
--- a/code_ruby/lib/maasha/seq/backtrack.rb
+++ b/code_ruby/lib/maasha/seq/backtrack.rb
@@ -40,6 +40,20 @@ module BackTrack
   MAX_INS    = 5 # Maximum number of insertions allowed
   MAX_DEL    = 5 # Maximum number of deletions allowed
 
+  # ------------------------------------------------------------------------------
+  #   str.patmatch(pattern[, start|[start, stop][, max_mis[, max_ins[, max_del]]]])
+  #   -> Match
+  #   str.patmatch(pattern[, start|[start, stop][, max_mis[, max_ins[, max_del]]]]) { |match|
+  #     block
+  #   }
+  #   -> Match
+  #
+  # ------------------------------------------------------------------------------
+  # Method to iterate through a sequence from a given start position to the end of
+  # the sequence or to a given stop position to locate a pattern allowing for a
+  # maximum number of mismatches, insertions, and deletions. Insertions are
+  # nucleotides found in the pattern but not in the sequence. Deletions are
+  # nucleotides found in the sequence but not in the pattern.
   def patmatch(pattern, start = 0, max_mismatches = 0, max_insertions = 0, max_deletions = 0)
     self.patscan(pattern, start, max_mismatches, max_insertions, max_deletions) do |m|
       if block_given?
@@ -59,9 +73,9 @@ module BackTrack
   end
 
   # ------------------------------------------------------------------------------
-  #   str.scan(pattern[, start|[start, stop][, max_mismatches[, max_insertions[, max_deletions]]]])
+  #   str.patscan(pattern[, start|[start, stop][, max_mis[, max_ins[, max_del]]]])
   #   -> Array
-  #   str.scan(pattern[, start|[start, stop][, max_mismatches[, max_insertions[, max_deletions]]]]) { |match|
+  #   str.patscan(pattern[, start|[start, stop][, max_mis[, max_ins[, max_del]]]]) { |match|
   #     block
   #   }
   #   -> Match
@@ -82,11 +96,11 @@ module BackTrack
     end
 
     raise BackTrackError, "Bad pattern: #{pattern}"                                          unless pattern.downcase =~ OK_PATTERN
-#    raise BackTrackError, "start: #{start} out of range (0 .. #{self.length - 1})"           unless (0 .. self.length).include? start
-#    raise BackTrackError, "stop: #{stop} out of range (0 .. #{self.length - 1})"             unless (0 .. self.length).include? stop
-#    raise BackTrackError, "max_mismatches: #{max_mismatches} out of range (0 .. #{MAX_MIS})" unless (0 .. MAX_MIS).include? max_mismatches
-#    raise BackTrackError, "max_insertions: #{max_insertions} out of range (0 .. #{MAX_INS})" unless (0 .. MAX_INS).include? max_insertions
-#    raise BackTrackError, "max_deletions: #{max_deletions} out of range (0 .. #{MAX_DEL})"   unless (0 .. MAX_DEL).include? max_deletions
+    raise BackTrackError, "start: #{start} out of range (0 .. #{self.length - 1})"           unless (0 .. self.length).include? start
+    raise BackTrackError, "stop: #{stop} out of range (0 .. #{self.length - 1})"             unless (0 .. self.length).include? stop
+    raise BackTrackError, "max_mismatches: #{max_mismatches} out of range (0 .. #{MAX_MIS})" unless (0 .. MAX_MIS).include? max_mismatches
+    raise BackTrackError, "max_insertions: #{max_insertions} out of range (0 .. #{MAX_INS})" unless (0 .. MAX_INS).include? max_insertions
+    raise BackTrackError, "max_deletions: #{max_deletions} out of range (0 .. #{MAX_DEL})"   unless (0 .. MAX_DEL).include? max_deletions
 
     matches = []