Class ClansParams

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

Parameters:

• **kw - parameters as kw[parameter_name] = parameter_value

Raises:

• KeyError - if a supplied parameter name is not known (i.e. it is not a key in _DEFAULTS)

Overrides: object.__init__

(inherited documentation)

Sets the parameters to CLANS default values. See ClansParams._DEFAULTS.

attfactor

factor in the attractive force

raises ValueError if value is not castable to float

Get Method:

unreachable.attfactor(self) - factor in the attractive force

Set Method:

unreachable.attfactor(self, value)

Type:

float

attvalpow

exponent in the attractive force

raises ValueError if value is not castable to float

Get Method:

unreachable.attvalpow(self) - exponent in the attractive force

Set Method:

unreachable.attvalpow(self, value)

Type:

float

avgfoldchange

parameter with unclear function. Check in Clans.

raises ValueError if set to non-boolean value

Get Method:

unreachable.avgfoldchange(self) - parameter with unclear function.

Set Method:

unreachable.avgfoldchange(self, value)

Type:

bool

blastpath

path to the BLAST executable for protein-protein comparisons. BLAST+ is currently not supported by Clans.

raises ValueError if value is not a string

Get Method:

unreachable.blastpath(self) - path to the BLAST executable for protein-protein comparisons.

Set Method:

unreachable.blastpath(self, value)

Type:

str

cluster2d

if True, clustering is done in 2D. Else in 3D.

raises ValueError if set to non-boolean value

Get Method:

unreachable.cluster2d(self) - if True, clustering is done in 2D.

Set Method:

unreachable.cluster2d(self, value)

Type:

bool

colors

colors that define the coloring for different p-values/attractions

raises ValueError if set to s.th. else than a 10-tuple of 2-tuples

Get Method:

unreachable.colors(self) - colors that define the coloring for different p-values/attractions

Set Method:

unreachable.colors(self, value)

Type:

tuple

complexatt

if True, complex attraction computations are used.

raises ValueError if set to non-boolean value

Get Method:

unreachable.complexatt(self) - if True, complex attraction computations are used.

Set Method:

unreachable.complexatt(self, value)

Type:

bool

cooling

parameter with unclear function. Check in Clans.

raises ValueError if value is not castable to float

Get Method:

unreachable.cooling(self) - parameter with unclear function.

Set Method:

unreachable.cooling(self, value)

Type:

float

currcool

parameter with unclear function. Check in Clans.

raises ValueError if value is not castable to float

Get Method:

unreachable.currcool(self) - parameter with unclear function.

Set Method:

unreachable.currcool(self, value)

Type:

float

dampening

parameter with unclear function. Check in Clans.

raises ValueError if value is not castable to float

Get Method:

unreachable.dampening(self) - parameter with unclear function.

Set Method:

unreachable.dampening(self, value)

Type:

float

dotsize

size of the central dot representing each sequence in the clustermap

raises ValueError if value is not castable to int

Get Method:

unreachable.dotsize(self) - size of the central dot representing each sequence in the clustermap

Set Method:

unreachable.dotsize(self, value)

Type:

int

formatdbpath

path to the formatdb executable of BLAST.

raises ValueError if value is not a string

Get Method:

unreachable.formatdbpath(self) - path to the formatdb executable of BLAST.

Set Method:

unreachable.formatdbpath(self, value)

Type:

str

groupsize

default for the size of circles that mark newly created groups

raises ValueError if value is not castable to int

Get Method:

unreachable.groupsize(self) - default for the size of circles that mark newly created groups

Set Method:

unreachable.groupsize(self, value)

Type:

int

maxmove

maximal sequence (i.e. dot in the clustermap) movement per round

raises ValueError if value is not castable to float

Get Method:

unreachable.maxmove(self) - maximal sequence (i.e.

Set Method:

unreachable.maxmove(self, value)

Type:

float

minattract

parameter with unclear function. Check in Clans.

raises ValueError if value is not castable to float

Get Method:

unreachable.minattract(self) - parameter with unclear function.

Set Method:

unreachable.minattract(self, value)

Type:

float

ovalsize

size of the circle around selected sequences

raises ValueError if value not castable to int

Get Method:

unreachable.ovalsize(self) - size of the circle around selected sequences

Set Method:

unreachable.ovalsize(self, value)

Type:

int

pval

p-value cutoff that determines which connections are considered for the attractive force

raises ValueError if value is not castable to float

Get Method:

unreachable.pval(self) - p-value cutoff that determines which connections are considered for the attractive force

Set Method:

unreachable.pval(self, value)

Type:

float

repfactor

factor in the repulsive force

raises ValueError if value is not castable to float

Get Method:

unreachable.repfactor(self) - factor in the repulsive force

Set Method:

unreachable.repfactor(self, value)

Type:

float

repvalpow

exponent in the repulsive force

raises ValueError if value is not castable to float

Get Method:

unreachable.repvalpow(self) - exponent in the repulsive force

Set Method:

unreachable.repvalpow(self, value)

Type:

float

showinfo

if True, additional data (rotation matrix) is shown in the clustring window)

raises ValueError if set to non-boolean value

Get Method:

unreachable.showinfo(self) - if True, additional data (rotation matrix) is shown in the clustring window)

Set Method:

unreachable.showinfo(self, value)

Type:

bool

usefoldchange

parameter with unclear function. Check in Clans.

raises ValueError if set to non-boolean value

Get Method:

unreachable.usefoldchange(self) - parameter with unclear function.

Set Method:

unreachable.usefoldchange(self, value)

Type:

bool

usescval

parameter with unclear function. Check in Clans.

raises ValueError if set to non-boolean value

Get Method:

unreachable.usescval(self) - parameter with unclear function.

Set Method:

unreachable.usescval(self, value)

Type:

bool

zoom

zoom value (1.0 == not zoomed)

raises ValueError if value is not castable to float

Get Method:

unreachable.zoom(self) - zoom value (1.0 == not zoomed)

Set Method:

unreachable.zoom(self, value)

Type:

float