+ fixed a bug in the C++ interface
[qpalma.git] / standalone / palma / alignment_tool.py
1 # This file was automatically generated by SWIG (http://www.swig.org).
2 # Version 1.3.31
3 #
4 # Don't modify this file, modify the SWIG interface instead.
5 # This file is compatible with both classic and new-style classes.
6
7 import _alignment_tool
8 import new
9 new_instancemethod = new.instancemethod
10 try:
11 _swig_property = property
12 except NameError:
13 pass # Python < 2.2 doesn't have 'property'.
14 def _swig_setattr_nondynamic(self,class_type,name,value,static=1):
15 if (name == "thisown"): return self.this.own(value)
16 if (name == "this"):
17 if type(value).__name__ == 'PySwigObject':
18 self.__dict__[name] = value
19 return
20 method = class_type.__swig_setmethods__.get(name,None)
21 if method: return method(self,value)
22 if (not static) or hasattr(self,name):
23 self.__dict__[name] = value
24 else:
25 raise AttributeError("You cannot add attributes to %s" % self)
26
27 def _swig_setattr(self,class_type,name,value):
28 return _swig_setattr_nondynamic(self,class_type,name,value,0)
29
30 def _swig_getattr(self,class_type,name):
31 if (name == "thisown"): return self.this.own()
32 method = class_type.__swig_getmethods__.get(name,None)
33 if method: return method(self)
34 raise AttributeError,name
35
36 def _swig_repr(self):
37 try: strthis = "proxy of " + self.this.__repr__()
38 except: strthis = ""
39 return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
40
41 import types
42 try:
43 _object = types.ObjectType
44 _newclass = 1
45 except AttributeError:
46 class _object : pass
47 _newclass = 0
48 del types
49
50
51 new_intArray = _alignment_tool.new_intArray
52 delete_intArray = _alignment_tool.delete_intArray
53 intArray_getitem = _alignment_tool.intArray_getitem
54 intArray_setitem = _alignment_tool.intArray_setitem
55 new_doubleArray = _alignment_tool.new_doubleArray
56 delete_doubleArray = _alignment_tool.delete_doubleArray
57 doubleArray_getitem = _alignment_tool.doubleArray_getitem
58 doubleArray_setitem = _alignment_tool.doubleArray_setitem
59 class MyAlignException(_object):
60 __swig_setmethods__ = {}
61 __setattr__ = lambda self, name, value: _swig_setattr(self, MyAlignException, name, value)
62 __swig_getmethods__ = {}
63 __getattr__ = lambda self, name: _swig_getattr(self, MyAlignException, name)
64 __repr__ = _swig_repr
65 def __init__(self, *args):
66 this = _alignment_tool.new_MyAlignException(*args)
67 try: self.this.append(this)
68 except: self.this = this
69 __swig_destroy__ = _alignment_tool.delete_MyAlignException
70 __del__ = lambda self : None;
71 MyAlignException_swigregister = _alignment_tool.MyAlignException_swigregister
72 MyAlignException_swigregister(MyAlignException)
73
74 class penalty(_object):
75 __swig_setmethods__ = {}
76 __setattr__ = lambda self, name, value: _swig_setattr(self, penalty, name, value)
77 __swig_getmethods__ = {}
78 __getattr__ = lambda self, name: _swig_getattr(self, penalty, name)
79 __repr__ = _swig_repr
80 __swig_setmethods__["len"] = _alignment_tool.penalty_len_set
81 __swig_getmethods__["len"] = _alignment_tool.penalty_len_get
82 if _newclass:len = _swig_property(_alignment_tool.penalty_len_get, _alignment_tool.penalty_len_set)
83 __swig_setmethods__["limits"] = _alignment_tool.penalty_limits_set
84 __swig_getmethods__["limits"] = _alignment_tool.penalty_limits_get
85 if _newclass:limits = _swig_property(_alignment_tool.penalty_limits_get, _alignment_tool.penalty_limits_set)
86 __swig_setmethods__["penalties"] = _alignment_tool.penalty_penalties_set
87 __swig_getmethods__["penalties"] = _alignment_tool.penalty_penalties_get
88 if _newclass:penalties = _swig_property(_alignment_tool.penalty_penalties_get, _alignment_tool.penalty_penalties_set)
89 __swig_setmethods__["name"] = _alignment_tool.penalty_name_set
90 __swig_getmethods__["name"] = _alignment_tool.penalty_name_get
91 if _newclass:name = _swig_property(_alignment_tool.penalty_name_get, _alignment_tool.penalty_name_set)
92 __swig_setmethods__["max_len"] = _alignment_tool.penalty_max_len_set
93 __swig_getmethods__["max_len"] = _alignment_tool.penalty_max_len_get
94 if _newclass:max_len = _swig_property(_alignment_tool.penalty_max_len_get, _alignment_tool.penalty_max_len_set)
95 __swig_setmethods__["min_len"] = _alignment_tool.penalty_min_len_set
96 __swig_getmethods__["min_len"] = _alignment_tool.penalty_min_len_get
97 if _newclass:min_len = _swig_property(_alignment_tool.penalty_min_len_get, _alignment_tool.penalty_min_len_set)
98 __swig_setmethods__["transform"] = _alignment_tool.penalty_transform_set
99 __swig_getmethods__["transform"] = _alignment_tool.penalty_transform_get
100 if _newclass:transform = _swig_property(_alignment_tool.penalty_transform_get, _alignment_tool.penalty_transform_set)
101 def __init__(self, *args):
102 this = _alignment_tool.new_penalty(*args)
103 try: self.this.append(this)
104 except: self.this = this
105 __swig_destroy__ = _alignment_tool.delete_penalty
106 __del__ = lambda self : None;
107 penalty_swigregister = _alignment_tool.penalty_swigregister
108 penalty_swigregister(penalty)
109
110 class align_info(_object):
111 __swig_setmethods__ = {}
112 __setattr__ = lambda self, name, value: _swig_setattr(self, align_info, name, value)
113 __swig_getmethods__ = {}
114 __getattr__ = lambda self, name: _swig_getattr(self, align_info, name)
115 __repr__ = _swig_repr
116 __swig_setmethods__["splice_align"] = _alignment_tool.align_info_splice_align_set
117 __swig_getmethods__["splice_align"] = _alignment_tool.align_info_splice_align_get
118 if _newclass:splice_align = _swig_property(_alignment_tool.align_info_splice_align_get, _alignment_tool.align_info_splice_align_set)
119 __swig_setmethods__["est_align"] = _alignment_tool.align_info_est_align_set
120 __swig_getmethods__["est_align"] = _alignment_tool.align_info_est_align_get
121 if _newclass:est_align = _swig_property(_alignment_tool.align_info_est_align_get, _alignment_tool.align_info_est_align_set)
122 __swig_setmethods__["mmatrix_param"] = _alignment_tool.align_info_mmatrix_param_set
123 __swig_getmethods__["mmatrix_param"] = _alignment_tool.align_info_mmatrix_param_get
124 if _newclass:mmatrix_param = _swig_property(_alignment_tool.align_info_mmatrix_param_get, _alignment_tool.align_info_mmatrix_param_set)
125 __swig_setmethods__["alignment_scores"] = _alignment_tool.align_info_alignment_scores_set
126 __swig_getmethods__["alignment_scores"] = _alignment_tool.align_info_alignment_scores_get
127 if _newclass:alignment_scores = _swig_property(_alignment_tool.align_info_alignment_scores_get, _alignment_tool.align_info_alignment_scores_set)
128 __swig_setmethods__["alignment_length"] = _alignment_tool.align_info_alignment_length_set
129 __swig_getmethods__["alignment_length"] = _alignment_tool.align_info_alignment_length_get
130 if _newclass:alignment_length = _swig_property(_alignment_tool.align_info_alignment_length_get, _alignment_tool.align_info_alignment_length_set)
131 __swig_setmethods__["aligned_dna"] = _alignment_tool.align_info_aligned_dna_set
132 __swig_getmethods__["aligned_dna"] = _alignment_tool.align_info_aligned_dna_get
133 if _newclass:aligned_dna = _swig_property(_alignment_tool.align_info_aligned_dna_get, _alignment_tool.align_info_aligned_dna_set)
134 __swig_setmethods__["aligned_est"] = _alignment_tool.align_info_aligned_est_set
135 __swig_getmethods__["aligned_est"] = _alignment_tool.align_info_aligned_est_get
136 if _newclass:aligned_est = _swig_property(_alignment_tool.align_info_aligned_est_get, _alignment_tool.align_info_aligned_est_set)
137 def __init__(self, *args):
138 this = _alignment_tool.new_align_info(*args)
139 try: self.this.append(this)
140 except: self.this = this
141 __swig_destroy__ = _alignment_tool.delete_align_info
142 __del__ = lambda self : None;
143 align_info_swigregister = _alignment_tool.align_info_swigregister
144 align_info_swigregister(align_info)
145
146 myalign = _alignment_tool.myalign
147 def createDoubleArrayFromList(list):
148 array = new_doubleArray(len(list))
149 for i in range(len(list)):
150 doubleArray_setitem(array, i, list[i])
151 return array
152
153 def createListFromIntArray(array, array_len):
154 list = [0]*array_len
155 for i in range(array_len):
156 list[i] = intArray_getitem(array,i)
157 return list
158
159 def createListFromDoubleArray(array, array_len):
160 list = [0]*array_len
161 for i in range(array_len):
162 list[i] = doubleArray_getitem(array,i)
163 return list
164
165
166
167