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