HappyDoc Generated Documentation Class: Interface

mabslib / Interface.py / Interface 

This class provides most of the functionality.

Most of the UI commands are related to methods of this class. Especially align and getTFBS functions are important.

Methods   
  showMoreAlignments 
showMoreAlignments ( self,  count=1 )

Gets more alignments but doesn't display them

  savematch 
savematch ( self,  filename='' )

Saves the results. (possibly gziped)

  savealignGFF 
savealignGFF ( self,  filename="" )

Saves the results in GFF format

  showalignSTDO 
showalignSTDO ( self )

Prints the alignment to standart out

  getSeqNames 
getSeqNames ( self )

returns the sequence names

  savealign 
savealign ( self,  filename='' )

Saves the results

  addSequence 
addSequence ( self,  filenames )

adds sequences from files in FASTA format

  removeMatrix 
removeMatrix ( self,  index )

removes matrix given by index

  resetMatrices 
resetMatrices ( self )

resets the list of matrices

  resetSequences 
resetSequences ( self )

resets the sequences

  __init__ 
__init__ ( self )
  printMatrices 
printMatrices ( self )

prints matrices to standard out

  quit 
quit ( self )

Exits the program

  savealignAnchor 
savealignAnchor ( self,  filename="" )

Saves the results in Anchor format

  printMatrixWeights 
printMatrixWeights ( self )

prints matrix weights to standard out

  moreAlignments 
moreAlignments ( self,  num_of_align=1 )

Fetch more alignments from previously run alignment matrix

  removeSequence 
removeSequence ( self,  name )

removes sequences given by name

  align 
align (
        self,
        filename='.',
        num_of_align=3,
        Lambda=1.0,
        xi=1.0,
        mu=0.5,
        nu=1.0,
        nuc_per_rotation=10.4,
        )

aligns the computed BS or some given in file

  addMatrix 
addMatrix ( self,  filenames )

adds new matrices from given files

  getTFBS 
getTFBS (
        self,
        bound=0.1,
        absCutoff=None,
        )

computes the possible TFBS

  showmatch 
showmatch ( self )

Prints the results to standard out

  getTFBSAbsolute 
getTFBSAbsolute ( self,  cutoff=9.0 )

computes the possible TFBS

  about 
about ( self )

Information about the program

  storeTmpGFF 
storeTmpGFF ( self )

Open temporary file and store BS data to it

  finalTmpGFF 
finalTmpGFF ( self )

Store BS data to temporary file and close it


This document was automatically generated Thu Feb 19 15:16:16 2004 by HappyDoc version 3.0.a1