Package csb :: Package bio :: Package fragments :: Module hhsites :: Class HMMFragmentWrapper

Class HMMFragmentWrapper

       object --+            
                |            
   hmm.ProfileHMM --+        
                    |        
hmm.ProfileHMMSegment --+    
                        |    
              HMMFragment --+
                            |
                           HMMFragmentWrapper

Describes a HMM segment which can be slid over a subject profile. Wraps an existing ProfileHMMSegment to decorate it with a slide_over method.

Instance Methods

__init__(self, hmm_segment)
x.__init__(...) initializes x; see help(type(x)) for signature

source code

list

slide_over(self, other)
Find instances of self by sliding it over other and computing emission vector similarity and RSMD.

source code

Inherited from hmm.ProfileHMM: add_emission_pseudocounts, add_transition_pseudocounts, chain, convert_scores, emission_profile, emission_similarity, segment, serialize, structure, subregion, to_hmm

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__