TAMO.MD.MDsupport
index
/home/David_Gordon/docs/TAMO/MD/MDsupport.py

# This file was created automatically by SWIG.
# Don't modify this file, modify the SWIG interface instead.
# This file is compatible with both classic and new-style classes.

 
Modules
       
TAMO.MD._MDsupport
types

 
Classes
       
__builtin__.object
DoubleVector
DoubleVectorPtr
IntVector
IntVectorPtr
Probe
ProbePtr
Probelist
ProbelistPtr
Probelist_str
Probelist_strPtr
SeqMat
SeqMatPtr

 
class DoubleVector(__builtin__.object)
     Methods defined here:
__del__(self, destroy=<built-in function delete_DoubleVector>)
__delitem__(*args)
__delslice__(*args)
__getattr__ lambda self, name
__getitem__(*args)
__getslice__(*args)
__init__(self, *args)
__len__(*args)
__nonzero__(*args)
__repr__(self)
__setattr__ lambda self, name, value
__setitem__(*args)
__setslice__(*args)
append(*args)
clear(*args)
pop(*args)

Data and other attributes defined here:
__dict__ = <dictproxy object>
dictionary for instance variables (if defined)
__swig_getmethods__ = {}
__swig_setmethods__ = {}
__weakref__ = <attribute '__weakref__' of 'DoubleVector' objects>
list of weak references to the object (if defined)

 
class DoubleVectorPtr(DoubleVector)
    
Method resolution order:
DoubleVectorPtr
DoubleVector
__builtin__.object

Methods defined here:
__init__(self, this)

Methods inherited from DoubleVector:
__del__(self, destroy=<built-in function delete_DoubleVector>)
__delitem__(*args)
__delslice__(*args)
__getattr__ lambda self, name
__getitem__(*args)
__getslice__(*args)
__len__(*args)
__nonzero__(*args)
__repr__(self)
__setattr__ lambda self, name, value
__setitem__(*args)
__setslice__(*args)
append(*args)
clear(*args)
pop(*args)

Data and other attributes inherited from DoubleVector:
__dict__ = <dictproxy object>
dictionary for instance variables (if defined)
__swig_getmethods__ = {}
__swig_setmethods__ = {}
__weakref__ = <attribute '__weakref__' of 'DoubleVector' objects>
list of weak references to the object (if defined)

 
class IntVector(__builtin__.object)
     Methods defined here:
__del__(self, destroy=<built-in function delete_IntVector>)
__delitem__(*args)
__delslice__(*args)
__getattr__ lambda self, name
__getitem__(*args)
__getslice__(*args)
__init__(self, *args)
__len__(*args)
__nonzero__(*args)
__repr__(self)
__setattr__ lambda self, name, value
__setitem__(*args)
__setslice__(*args)
append(*args)
clear(*args)
pop(*args)

Data and other attributes defined here:
__dict__ = <dictproxy object>
dictionary for instance variables (if defined)
__swig_getmethods__ = {}
__swig_setmethods__ = {}
__weakref__ = <attribute '__weakref__' of 'IntVector' objects>
list of weak references to the object (if defined)

 
class IntVectorPtr(IntVector)
    
Method resolution order:
IntVectorPtr
IntVector
__builtin__.object

Methods defined here:
__init__(self, this)

Methods inherited from IntVector:
__del__(self, destroy=<built-in function delete_IntVector>)
__delitem__(*args)
__delslice__(*args)
__getattr__ lambda self, name
__getitem__(*args)
__getslice__(*args)
__len__(*args)
__nonzero__(*args)
__repr__(self)
__setattr__ lambda self, name, value
__setitem__(*args)
__setslice__(*args)
append(*args)
clear(*args)
pop(*args)

Data and other attributes inherited from IntVector:
__dict__ = <dictproxy object>
dictionary for instance variables (if defined)
__swig_getmethods__ = {}
__swig_setmethods__ = {}
__weakref__ = <attribute '__weakref__' of 'IntVector' objects>
list of weak references to the object (if defined)

 
class Probe(__builtin__.object)
     Methods defined here:
__del__(self, destroy=<built-in function delete_Probe>)
__getattr__ lambda self, name
__init__(self, *args)
__repr__(self)
__setattr__ lambda self, name, value

Properties defined here:
Zs
get = Probe_Zs_get(...)
set = Probe_Zs_set(...)
iseq
get = Probe_iseq_get(...)
set = Probe_iseq_set(...)
len
get = Probe_len_get(...)
set = Probe_len_set(...)
probebg
get = Probe_probebg_get(...)
set = Probe_probebg_set(...)
wmerbgs
get = Probe_wmerbgs_get(...)
set = Probe_wmerbgs_set(...)

Data and other attributes defined here:
__dict__ = <dictproxy object>
dictionary for instance variables (if defined)
__swig_getmethods__ = {'Zs': <built-in function Probe_Zs_get>, 'iseq': <built-in function Probe_iseq_get>, 'len': <built-in function Probe_len_get>, 'probebg': <built-in function Probe_probebg_get>, 'wmerbgs': <built-in function Probe_wmerbgs_get>}
__swig_setmethods__ = {'Zs': <built-in function Probe_Zs_set>, 'iseq': <built-in function Probe_iseq_set>, 'len': <built-in function Probe_len_set>, 'probebg': <built-in function Probe_probebg_set>, 'wmerbgs': <built-in function Probe_wmerbgs_set>}
__weakref__ = <attribute '__weakref__' of 'Probe' objects>
list of weak references to the object (if defined)

 
class ProbePtr(Probe)
    
Method resolution order:
ProbePtr
Probe
__builtin__.object

Methods defined here:
__init__(self, this)

Methods inherited from Probe:
__del__(self, destroy=<built-in function delete_Probe>)
__getattr__ lambda self, name
__repr__(self)
__setattr__ lambda self, name, value

Properties inherited from Probe:
Zs
get = Probe_Zs_get(...)
set = Probe_Zs_set(...)
iseq
get = Probe_iseq_get(...)
set = Probe_iseq_set(...)
len
get = Probe_len_get(...)
set = Probe_len_set(...)
probebg
get = Probe_probebg_get(...)
set = Probe_probebg_set(...)
wmerbgs
get = Probe_wmerbgs_get(...)
set = Probe_wmerbgs_set(...)

Data and other attributes inherited from Probe:
__dict__ = <dictproxy object>
dictionary for instance variables (if defined)
__swig_getmethods__ = {'Zs': <built-in function Probe_Zs_get>, 'iseq': <built-in function Probe_iseq_get>, 'len': <built-in function Probe_len_get>, 'probebg': <built-in function Probe_probebg_get>, 'wmerbgs': <built-in function Probe_wmerbgs_get>}
__swig_setmethods__ = {'Zs': <built-in function Probe_Zs_set>, 'iseq': <built-in function Probe_iseq_set>, 'len': <built-in function Probe_len_set>, 'probebg': <built-in function Probe_probebg_set>, 'wmerbgs': <built-in function Probe_wmerbgs_set>}
__weakref__ = <attribute '__weakref__' of 'Probe' objects>
list of weak references to the object (if defined)

 
class Probelist(__builtin__.object)
     Methods defined here:
__del__(self, destroy=<built-in function delete_Probelist>)
__getattr__ lambda self, name
__init__(self, *args)
__repr__(self)
__setattr__ lambda self, name, value
append(*args)
get_Z(*args)
get_Zlist(*args)

Properties defined here:
count
get = Probelist_count_get(...)
set = Probelist_count_set(...)
probes
get = Probelist_probes_get(...)
set = Probelist_probes_set(...)

Data and other attributes defined here:
__dict__ = <dictproxy object>
dictionary for instance variables (if defined)
__swig_getmethods__ = {'count': <built-in function Probelist_count_get>, 'probes': <built-in function Probelist_probes_get>}
__swig_setmethods__ = {'count': <built-in function Probelist_count_set>, 'probes': <built-in function Probelist_probes_set>}
__weakref__ = <attribute '__weakref__' of 'Probelist' objects>
list of weak references to the object (if defined)

 
class ProbelistPtr(Probelist)
    
Method resolution order:
ProbelistPtr
Probelist
__builtin__.object

Methods defined here:
__init__(self, this)

Methods inherited from Probelist:
__del__(self, destroy=<built-in function delete_Probelist>)
__getattr__ lambda self, name
__repr__(self)
__setattr__ lambda self, name, value
append(*args)
get_Z(*args)
get_Zlist(*args)

Properties inherited from Probelist:
count
get = Probelist_count_get(...)
set = Probelist_count_set(...)
probes
get = Probelist_probes_get(...)
set = Probelist_probes_set(...)

Data and other attributes inherited from Probelist:
__dict__ = <dictproxy object>
dictionary for instance variables (if defined)
__swig_getmethods__ = {'count': <built-in function Probelist_count_get>, 'probes': <built-in function Probelist_probes_get>}
__swig_setmethods__ = {'count': <built-in function Probelist_count_set>, 'probes': <built-in function Probelist_probes_set>}
__weakref__ = <attribute '__weakref__' of 'Probelist' objects>
list of weak references to the object (if defined)

 
class Probelist_str(__builtin__.object)
     Methods defined here:
__del__(self, destroy=<built-in function delete_Probelist_str>)
__getattr__ lambda self, name
__init__(self, *args)
__repr__(self)
__setattr__ lambda self, name, value
append(*args)
count_re_matches(*args)

Properties defined here:
count
get = Probelist_str_count_get(...)
set = Probelist_str_count_set(...)
probes
get = Probelist_str_probes_get(...)
set = Probelist_str_probes_set(...)

Data and other attributes defined here:
__dict__ = <dictproxy object>
dictionary for instance variables (if defined)
__swig_getmethods__ = {'count': <built-in function Probelist_str_count_get>, 'probes': <built-in function Probelist_str_probes_get>}
__swig_setmethods__ = {'count': <built-in function Probelist_str_count_set>, 'probes': <built-in function Probelist_str_probes_set>}
__weakref__ = <attribute '__weakref__' of 'Probelist_str' objects>
list of weak references to the object (if defined)

 
class Probelist_strPtr(Probelist_str)
    
Method resolution order:
Probelist_strPtr
Probelist_str
__builtin__.object

Methods defined here:
__init__(self, this)

Methods inherited from Probelist_str:
__del__(self, destroy=<built-in function delete_Probelist_str>)
__getattr__ lambda self, name
__repr__(self)
__setattr__ lambda self, name, value
append(*args)
count_re_matches(*args)

Properties inherited from Probelist_str:
count
get = Probelist_str_count_get(...)
set = Probelist_str_count_set(...)
probes
get = Probelist_str_probes_get(...)
set = Probelist_str_probes_set(...)

Data and other attributes inherited from Probelist_str:
__dict__ = <dictproxy object>
dictionary for instance variables (if defined)
__swig_getmethods__ = {'count': <built-in function Probelist_str_count_get>, 'probes': <built-in function Probelist_str_probes_get>}
__swig_setmethods__ = {'count': <built-in function Probelist_str_count_set>, 'probes': <built-in function Probelist_str_probes_set>}
__weakref__ = <attribute '__weakref__' of 'Probelist_str' objects>
list of weak references to the object (if defined)

 
class SeqMat(__builtin__.object)
     Methods defined here:
EMstep(*args)
__del__(self, destroy=<built-in function delete_SeqMat>)
__getattr__ lambda self, name
__init__(self, *args)
__repr__(self)
__setattr__ lambda self, name, value
compute_ambig(*args)
get(*args)
get_c(*args)
loglikelihood(*args)
matchstarts(*args)
scanbest(*args)
score(*args)
score_probe(*args)
set(*args)
setBg(*args)
setmask(*args)
sumscoresabove(*args)

Properties defined here:
beta
get = SeqMat_beta_get(...)
set = SeqMat_beta_set(...)
bg
get = SeqMat_bg_get(...)
set = SeqMat_bg_set(...)
deltamin
get = SeqMat_deltamin_get(...)
set = SeqMat_deltamin_set(...)
gamma
get = SeqMat_gamma_get(...)
set = SeqMat_gamma_set(...)
gamma_wt
get = SeqMat_gamma_wt_get(...)
set = SeqMat_gamma_wt_set(...)
joint
get = SeqMat_joint_get(...)
set = SeqMat_joint_set(...)
mask
get = SeqMat_mask_get(...)
set = SeqMat_mask_set(...)
width
get = SeqMat_width_get(...)
set = SeqMat_width_set(...)

Data and other attributes defined here:
__dict__ = <dictproxy object>
dictionary for instance variables (if defined)
__swig_getmethods__ = {'beta': <built-in function SeqMat_beta_get>, 'bg': <built-in function SeqMat_bg_get>, 'deltamin': <built-in function SeqMat_deltamin_get>, 'gamma': <built-in function SeqMat_gamma_get>, 'gamma_wt': <built-in function SeqMat_gamma_wt_get>, 'joint': <built-in function SeqMat_joint_get>, 'mask': <built-in function SeqMat_mask_get>, 'width': <built-in function SeqMat_width_get>}
__swig_setmethods__ = {'beta': <built-in function SeqMat_beta_set>, 'bg': <built-in function SeqMat_bg_set>, 'deltamin': <built-in function SeqMat_deltamin_set>, 'gamma': <built-in function SeqMat_gamma_set>, 'gamma_wt': <built-in function SeqMat_gamma_wt_set>, 'joint': <built-in function SeqMat_joint_set>, 'mask': <built-in function SeqMat_mask_set>, 'width': <built-in function SeqMat_width_set>}
__weakref__ = <attribute '__weakref__' of 'SeqMat' objects>
list of weak references to the object (if defined)

 
class SeqMatPtr(SeqMat)
    
Method resolution order:
SeqMatPtr
SeqMat
__builtin__.object

Methods defined here:
__init__(self, this)

Methods inherited from SeqMat:
EMstep(*args)
__del__(self, destroy=<built-in function delete_SeqMat>)
__getattr__ lambda self, name
__repr__(self)
__setattr__ lambda self, name, value
compute_ambig(*args)
get(*args)
get_c(*args)
loglikelihood(*args)
matchstarts(*args)
scanbest(*args)
score(*args)
score_probe(*args)
set(*args)
setBg(*args)
setmask(*args)
sumscoresabove(*args)

Properties inherited from SeqMat:
beta
get = SeqMat_beta_get(...)
set = SeqMat_beta_set(...)
bg
get = SeqMat_bg_get(...)
set = SeqMat_bg_set(...)
deltamin
get = SeqMat_deltamin_get(...)
set = SeqMat_deltamin_set(...)
gamma
get = SeqMat_gamma_get(...)
set = SeqMat_gamma_set(...)
gamma_wt
get = SeqMat_gamma_wt_get(...)
set = SeqMat_gamma_wt_set(...)
joint
get = SeqMat_joint_get(...)
set = SeqMat_joint_set(...)
mask
get = SeqMat_mask_get(...)
set = SeqMat_mask_set(...)
width
get = SeqMat_width_get(...)
set = SeqMat_width_set(...)

Data and other attributes inherited from SeqMat:
__dict__ = <dictproxy object>
dictionary for instance variables (if defined)
__swig_getmethods__ = {'beta': <built-in function SeqMat_beta_get>, 'bg': <built-in function SeqMat_bg_get>, 'deltamin': <built-in function SeqMat_deltamin_get>, 'gamma': <built-in function SeqMat_gamma_get>, 'gamma_wt': <built-in function SeqMat_gamma_wt_get>, 'joint': <built-in function SeqMat_joint_get>, 'mask': <built-in function SeqMat_mask_get>, 'width': <built-in function SeqMat_width_get>}
__swig_setmethods__ = {'beta': <built-in function SeqMat_beta_set>, 'bg': <built-in function SeqMat_bg_set>, 'deltamin': <built-in function SeqMat_deltamin_set>, 'gamma': <built-in function SeqMat_gamma_set>, 'gamma_wt': <built-in function SeqMat_gamma_wt_set>, 'joint': <built-in function SeqMat_joint_set>, 'mask': <built-in function SeqMat_mask_set>, 'width': <built-in function SeqMat_width_set>}
__weakref__ = <attribute '__weakref__' of 'SeqMat' objects>
list of weak references to the object (if defined)

 
Functions
       
Motif2c_PSSM(motif)
list2double(...)
log2_sum(...)
print_seq(...)
printdouble(...)
seq2int(...)