Generated by Cython 0.29.32
Yellow lines hint at Python interaction.
Click on a line that starts with a "+
" to see the C code that Cython generated for it.
Raw output: _insert.c
+001: # encoding: utf-8
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002: # cython: profile=False, boundscheck=False, wraparound=False
003:
004: from ._bp cimport BP
+005: from . import to_skbio_treenode
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+006: import pandas as pd
__pyx_t_2 = __Pyx_Import(__pyx_n_s_pandas, 0, -1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 6, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_2); if (PyDict_SetItem(__pyx_d, __pyx_n_s_pd, __pyx_t_2) < 0) __PYX_ERR(0, 6, __pyx_L1_error) __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+007: import json
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+008: import skbio
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009: cimport cython
010:
011:
012: # see the comment in _insert_setup. Avoid the use of invalidate_caches as it
013: # is very expensive for tree mutation operations
+014: class TreeNodeNoValidate(skbio.TreeNode):
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+015: def invalidate_caches(self):
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016: pass
017:
018:
019: # our noop used when monkey patching invalidate_caches
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021: pass
022:
023:
024: # pandas apply functions for preallocation of objects in bulk
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027:
028:
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031:
032:
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034: # insertion setup addresses:
035: # * treenode caching
036: # * placement ordering
037: # * preallocation of objects where "easy"
038:
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061: # length. Ties are handled arbitrarily.
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071:
072:
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+076: placements['parent'] = placements.apply(_preallocate_empty, axis=1)
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080:
081: # pd.DataFrame is not a resolved type so we cannot use it here for cython
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083: """Update the backbone, fully resolving edges with multiple queries
084:
085: Parameters
086: ----------
087: placements : pd.DataFrame
088: jplace data represented as a DataFrame
089: bptree : bp.BP
090: An instance of a BP tree, this is expected to contain edge numbers
091: and correspond to the backbone for the jplace data
092:
093: Returns
094: -------
095: skbio.TreeNode
096: A tree with the fragments placed
097: """
098: # TODO: profile, type and re-profile
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__pyx_t_1 = __Pyx_PyObject_Dict_GetItem(__pyx_v_fragment, __pyx_n_s_parent); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 114, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); __Pyx_XDECREF_SET(__pyx_v_fragment_parent, __pyx_t_1); __pyx_t_1 = 0;
115:
116: # update branch lengths
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__pyx_t_1 = PyNumber_Subtract(__pyx_v_existing_length, __pyx_v_distal_length); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 117, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); if (__Pyx_PyObject_SetAttrStr(__pyx_v_fragment_parent, __pyx_n_s_length, __pyx_t_1) < 0) __PYX_ERR(0, 117, __pyx_L1_error) __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+118: existing_length = distal_length
__Pyx_INCREF(__pyx_v_distal_length); __Pyx_DECREF_SET(__pyx_v_existing_length, __pyx_v_distal_length);
119:
120: # attach the nodes
+121: fragment_parent.append(fragment_node)
__pyx_t_13 = __Pyx_PyObject_Append(__pyx_v_fragment_parent, __pyx_v_fragment_node); if (unlikely(__pyx_t_13 == ((int)-1))) __PYX_ERR(0, 121, __pyx_L1_error)
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__pyx_t_13 = __Pyx_PyObject_Append(__pyx_v_current_parent, __pyx_v_fragment_parent); if (unlikely(__pyx_t_13 == ((int)-1))) __PYX_ERR(0, 122, __pyx_L1_error)
123:
124: # update
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__Pyx_INCREF(__pyx_v_fragment_parent); __Pyx_DECREF_SET(__pyx_v_current_parent, __pyx_v_fragment_parent);
126:
+127: existing_node.length = existing_length
if (__Pyx_PyObject_SetAttrStr(__pyx_v_existing_node, __pyx_n_s_length, __pyx_v_existing_length) < 0) __PYX_ERR(0, 127, __pyx_L1_error)
+128: current_parent.append(existing_node)
__pyx_t_13 = __Pyx_PyObject_Append(__pyx_v_current_parent, __pyx_v_existing_node); if (unlikely(__pyx_t_13 == ((int)-1))) __PYX_ERR(0, 128, __pyx_L1_error)
+129: existing_node.length = distal_length
if (unlikely(!__pyx_v_distal_length)) { __Pyx_RaiseUnboundLocalError("distal_length"); __PYX_ERR(0, 129, __pyx_L1_error) } if (__Pyx_PyObject_SetAttrStr(__pyx_v_existing_node, __pyx_n_s_length, __pyx_v_distal_length) < 0) __PYX_ERR(0, 129, __pyx_L1_error)
130:
+131: return sktree
__Pyx_XDECREF(__pyx_r); __Pyx_INCREF(__pyx_v_sktree); __pyx_r = __pyx_v_sktree; goto __pyx_L0;