Package csb :: Package bio :: Package io :: Module clans :: Class ClansParams

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# Class ClansParams

source code

    object --+
             |
            ClansParams

Class for handling Clans parameters. See ClansParams._DEFAULTS for accepted parameter names.

Instance Methods

__init__(self, strict=True, **kw) x.__init__(...) initializes x; see help(type(x)) for signature | source code

set_default_params(self) Sets the parameters to CLANS default values. | source code

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

Properties
float | attfactor factor in the attractive force
float | attvalpow exponent in the attractive force
bool | avgfoldchange parameter with unclear function.
str | blastpath path to the BLAST executable for protein-protein comparisons.
bool | cluster2d if True, clustering is done in 2D.
tuple | colors colors that define the coloring for different p-values/attractions
bool | complexatt if True, complex attraction computations are used.
float | cooling parameter with unclear function.
float | currcool parameter with unclear function.
float | dampening parameter with unclear function.
int | dotsize size of the central dot representing each sequence in the clustermap
str | formatdbpath path to the formatdb executable of BLAST.
int | groupsize default for the size of circles that mark newly created groups
float | maxmove maximal sequence (i.e.
float | minattract parameter with unclear function.
int | ovalsize size of the circle around selected sequences
float | pval p-value cutoff that determines which connections are considered for the attractive force
float | repfactor factor in the repulsive force
float | repvalpow exponent in the repulsive force
bool | showinfo if True, additional data (rotation matrix) is shown in the clustring window)
bool | usefoldchange parameter with unclear function.
bool | usescval parameter with unclear function.
float | zoom zoom value (1.0 == not zoomed)
Inherited from `object`: `__class__`

Method Details

### __init__(self, strict=True, **kw)
(Constructor)

source code

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)

### set_default_params(self)

source code

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

Property Details

### 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