Quit ( self )

saveHeader (
        self,
        fileName,
        header,
        omitNoValue=True,
        )

Hide ( self )

disassociate ( self,  mol )

customUI ( self,  parent )

Function to allow customization of the interface

parent is the interior frame of the dialog. It can be populated with custom widgets as desired. A frame should be returned by this function, in which the MAViewer UI will be placed.

useTree ( self,  tree )

usePhylogenyFile ( self,  phylogenyFile )

showHeaders ( self,  headers )

show previously-added header sequences

readFile (
        self,
        fileName,
        fileType,
        )

newRegion ( self,  **kw )

assessMatch (
        self,
        refMol,
        evalMols,
        attrName,
        )

deleteAllGaps ( self )

delete all-gap columns

__init__ (
        self,
        fileNameOrSeqs,
        fileType=None,
        autoAssociate=1,
        title=None,
        quitCB=None,
        frame=None,
        numberingDisplay=None,
        )

updateNumberings ( self )

setRulerDisplay ( self,  showRuler=None )

emHide ( self )

Extension manager method

setLeftNumberingDisplay ( self,  showNumbering=None )

useColoringFile (
        self,
        colorFileName,
        makeDefault=False,
        )

extractSubalignment ( self )

addSeqs (
        self,
        seqs,
        reassociate=True,
        )

realign (
        self,
        input,
        fileType=None,
        offset=None,
        startOffset=0,
        markEdited=False,
        )

Switch to a different alignment of the same sequences

input is list of Sequences or file name

setRightNumberingDisplay ( self,  showNumbering=None )

fillInUI ( self,  parent )

setResidueAttrs ( self )

expandSelectionByColumns ( self )

destroy ( self,  *args )

molName ( self,  mol )

deleteSeqs ( self,  delSeqs )

saveEPS (
        self,
        fileName,
        colorMode="color",
        rotate=False,
        extent="all",
        hideNodes=True,
        )

hideHeaders ( self,  headers )

hide header sequences

match (
        self,
        refMol,
        matchMols,
        createRegion=False,
        makePseudobonds=False,
        matchConserved=False,
        matchActive=False,
        iterate=False,
        iterateCutoff=5.0,
        )

match models to a reference model

refMol is the reference model matchMols is a list of models to match createRegion indicates if a region on the alignment should be created to indicate which residues were involved in matching makePseudobonds indicates if pseudobonds should be created between matched atoms matchConserved restricts matching to "highly" conserved (capitalized) residues only matchActive restricts matching to the currently active region iterate indicates if the matching should iterate, pruning poorly-matching residues at each pass iterateCutoff controls when iteration stops: it stops when no pair exceeds the cutoff

addHeaders ( self,  headers )

add header sequences

implies show

alignSeq (
        self,
        newSeq,
        matrix="BLOSUM-62",
        gapChar='.',
        **kw,
        )

align in a new sequence

associate (
        self,
        models,
        seq=None,
        force=True,
        minLength=10,
        showMatches=None,
        showErrors=None,
        )

associate models with sequences

models is normally a list of models, but it can be a Sequence instance or None. If it's a Sequence, it should be a Sequence of a particular chain of a model. If None, then some or all of the alignment sequences have residues attributes indicating their corresponding model; set up the proper associations.

if seq is given, associate only with that sequence, otherwise consider all sequences in alignment. If a non-empty list of models is provided and force is False, then it is assumed that the seq has just been added to the alignment and that associations are being re-evaluated.

If force is True, then if no association meets the built-in association criteria, then use Needleman- Wunsch to force an association with at least one sequence.

If a chain is less than minLength residues, ignore it.

showMatches and showErrors control whether regions will be created indicating matches and errors. A complete, error-free matchup will not have regions created regardless. Values of None indicate that the user preference should be used.

emRaise ( self )

Extension manager method

emQuit ( self )

Extension manager method

saveString ( self )

returns a string that can be used by restoreMAV()

insertGap (
        self,
        amount,
        column,
        gapChar='.',
        )

insert a gap into the alignment

amount is the size of the gap column is the column after which the gap is inserted (so zero would put it in front of the alignment) gapChar is what to fill the gap with

saveAssocInfo (
        self,
        fileName,
        namingStyle="simple",
        )

save ( self,  modal=False )

deleteHeaders ( self,  headers )

delete header sequences

emName ( self )

Extension manager method

readHeaderFile ( self,  fileName )

reorder ( self,  seqs )