Class: Cassiopee::Crawler

Constants

 METHOD_DIRECT
 METHOD_SUFFIX
 ".sfx"
 ".sfp"
 'suffix_length'

Attributes

ambiguous	[RW]	Ambiguity map (Hash)
comments	[RW]	Array of comment characters to skip lines in input sequence file
file_suffix	[RW]	Suffix files name/path
maxthread	[RW]	Max number fo threads to use (not yet used)
method	[RW]	Method for search FORCE or SUFFIX SUFFIX loads all suffixes and search through them afterwards, interesting for multiple searches (suffixes are reused) FORCE checks matches while crossing the suffixes. Does not keep parsed data for later search FORCE method does not yet support optimal filters
useAmbiguity	[RW]	Use alphabet ambiguity (dna/rna) in search, automatically set with loadAmbiguityFile
useCache	[RW]	Manage basic cache to store previous match
use_store	[RW]	Use persistent suffix file ?

Public Class methods

new()

Public Instance methods

clear()

Clear suffixes in memory If using use_store, clear the store too

extractSuffix(start,len)

Extract un suffix from suffix file based on md5 match

filter(posArray)

Filter the array of positions with defined position filter

filterCost()

filterLength()

filter_position(min,max)

Filter matches to be between min and max start position If not using use_store, search speed is improved but existing indexes are cleared If max=0, then max is string length Must be called after index creation or load

indexFile(f)

Index an input file Clear existing indexes

indexString(s)

Index an input string Clear existing indexes

loadAmbiguityFile(f)

Load ambiguity rules from a file File format should be: