|
/ . / MultAlignViewer / MAViewer.py / MAViewer
|
Methods
|
|
|
|
disassociate
|
disassociate ( self, mol )
|
|
|
assessMatch
|
assessMatch (
self,
refMol,
evalMols,
attrName,
)
|
|
|
usePhylogenyFile
|
usePhylogenyFile ( self, phylogenyFile )
|
Exceptions
|
|
|
UserError("No trees in '%s' have the same number" " of leaf nodes as the number of sequences" " in the alignment\n(tree: %s; alignment: %d)" %(phylogenyFile, ",".join([ str(t.countNodes( "leaf" ) ) for t in fileTrees ] ), len( self.seqs ) ) )
UserError( v )
UserError( "No tree chosen" )
UserError( "Must choose only one tree" )
|
|
|
|
save
|
save ( self, modal=None )
|
|
|
match
|
match (
self,
refMol,
matchMols,
createRegion=None,
makePseudobonds=None,
matchConserved=None,
matchActive=None,
iterate=None,
iterateCutoff=None,
)
|
Exceptions
|
|
|
ValueError, "%s not associated" " with any sequence" % matchMol.name
ValueError, "%s not associated with any sequence" % refMol.name
|
|
|
|
addHeaders
|
addHeaders ( self, headers )
|
|
|
useColoringFile
|
useColoringFile (
self,
colorFileName,
makeDefault=None,
)
|
|
|
saveAssocInfo
|
saveAssocInfo (
self,
fileName,
namingStyle=None,
)
|
|
|
saveHeader
|
saveHeader (
self,
fileName,
header,
omitNoValue=None,
)
|
|
|
showHeaders
|
showHeaders ( self, headers )
|
|
|
realign
|
realign (
self,
input,
fileType=None,
offset=None,
startOffset=None,
markEdited=None,
)
|
|
|
saveEPS
|
saveEPS (
self,
fileName,
colorMode=None,
rotate=None,
extent=None,
hideNodes=None,
)
|
|
|
alignSeq
|
alignSeq (
self,
newSeq,
displayName=None,
matrix=None,
gapChar=None,
**kw,
)
|
|
|
associate
|
associate (
self,
models,
seq=None,
force=None,
minLength=None,
showMatches=None,
showErrors=None,
)
|
|
|
readHeaderFile
|
readHeaderFile ( self, fileName )
|
Exceptions
|
|
|
UserError("Non-floating" " point value (%s)" " given on data line %d" %( val, ln + 1 ) )
UserError("RGB color on" " data line %d" " is not 3" " numbers" %( ln + 1 ) )
UserError( v )
UserError("Non-numeric" " color RGB" " color value" " given on data" " line %d" %( ln + 1 ) )
UserError( "No name for header line given in file" )
UserError("Unknown style (%s)." "Legal styles are: %s." %(style, ", ".join( styles ) ) )
UserError("Unknown color" " name (%s) on" " data line %d" %( color, ln + 1 ) )
UserError("RGB" " color values" " on data line" " %d not in the" " range zero to" " one" %( ln + 1 ) )
UserError("Value on data" " line %d is not a" " single character" " ('%s')" %( ln + 1, val ) )
UserError("Non-integer position" " (%s) on data line %d" %( pos, ln + 1 ) )
UserError("Position (%d) is less" " than one or greater than" " alignment length on data line" " %d" %( pos, ln + 1 ) )
UserError("Data line %d" " is neither position/" "value nor position/" "value/color" %( ln + 1 ) )
|
|
|
|
insertGap
|
insertGap (
self,
amount,
column,
gapChar=None,
)
|
|
|
refreshHeader
|
refreshHeader (
self,
header,
**kw,
)
|
|
|
deleteHeaders
|
deleteHeaders ( self, headers )
|
|
|
setLeftNumberingDisplay
|
setLeftNumberingDisplay ( self, showNumbering=None )
|
|
|
saveInfo
|
saveInfo ( self )
|
|
|
useTree
|
useTree ( self, tree )
|
|
|
customUI
|
customUI ( self, parent )
|
|
|
newRegion
|
newRegion ( self, **kw )
|
|
|
setResidueAttrs
|
setResidueAttrs ( self )
|
|
|
addSeqs
|
addSeqs (
self,
seqs,
reassociate=None,
)
|
|
|
expandSelectionByColumns
|
expandSelectionByColumns ( self )
|
|
|
molName
|
molName ( self, mol )
|
|
|
deleteSeqs
|
deleteSeqs ( self, delSeqs )
|
Exceptions
|
|
|
UserError( "Must leave at least two sequences in" " alignment!" )
|
|
|
|
reorder
|
reorder ( self, seqs )
|
|
|
deleteAllGaps
|
deleteAllGaps ( self )
|
|
|
__init__
|
__init__ (
self,
fileNameOrSeqs,
fileType=None,
autoAssociate=None,
title=None,
quitCB=None,
frame=None,
numberingDisplay=None,
)
|
|
|
updateNumberings
|
updateNumberings ( self )
|
|
|
setRulerDisplay
|
setRulerDisplay ( self, showRuler=None )
|
|
|
extractSubalignment
|
extractSubalignment ( self )
|
|
|
readFile
|
readFile (
self,
fileName,
fileType,
)
|
Exceptions
|
|
|
UserError( "Found no sequences in file %s" % fileName )
|
|
|
|
fillInUI
|
fillInUI ( self, parent )
|
|
|
destroy
|
destroy ( self, *args )
|
|
|
hideHeaders
|
hideHeaders ( self, headers )
|
|
|
setRightNumberingDisplay
|
setRightNumberingDisplay ( self, showNumbering=None )
|
|
|