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SegmentLoss.h
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1 /*
2  * This program is free software; you can redistribute it and/or modify
3  * it under the terms of the GNU General Public License as published by
4  * the Free Software Foundation; either version 3 of the License, or
5  * (at your option) any later version.
6  *
7  * Written (W) 2009 Jonas Behr
8  * Copyright (C) 2009 Fraunhofer Institute FIRST and Max-Planck-Society
9  */
10 #ifndef __SEGMENT_LOSS__
11 #define __SEGMENT_LOSS__
12 
13 #include <shogun/lib/config.h>
14 
15 #include <shogun/lib/common.h>
16 #include <shogun/base/SGObject.h>
18 
19 
20 namespace shogun
21 {
22  template <class T> class CDynamicArray;
24 class CSegmentLoss : public CSGObject
25 {
26  public:
27 
30  CSegmentLoss();
31 
32  virtual ~CSegmentLoss();
33 
40  float32_t get_segment_loss(int32_t from_pos, int32_t to_pos, int32_t segment_id);
41 
48  float32_t get_segment_loss_extend(int32_t from_pos, int32_t to_pos, int32_t segment_id);
49 
56  void set_segment_loss(float64_t* segment_loss, int32_t m, int32_t n);
57 
62  void set_segment_ids(CDynamicArray<int32_t>* segment_ids);
63 
70  void set_segment_mask(CDynamicArray<float64_t>* segment_mask);
71 
76  void set_num_segment_types(int32_t num_segment_types)
77  {
78  m_num_segment_types = num_segment_types;
79  }
80 
86  void compute_loss(int32_t* all_pos, int32_t len);
87 
91  virtual const char* get_name() const { return "SegmentLoss"; }
92  protected:
93 
96 
102 
105 
108 
111 };
112 
113 inline float32_t CSegmentLoss::get_segment_loss(int32_t from_pos, int32_t to_pos, int32_t segment_id)
114 {
115 
116  /* int32_t from_pos_shift = from_pos ;
117  if (print)
118  SG_PRINT("# pos=%i,%i segment_id=%i, m_segment_ids[from-2]=%i (%1.1f), m_segment_ids[from-1]=%i (%1.1f), m_segment_ids[from]=%i (%1.1f), m_segment_ids[from+1]=%i (%1.1f), \n",
119  from_pos_shift, to_pos, segment_id,
120  m_segment_ids->element(from_pos_shift-2), m_segment_loss_matrix.element(segment_id, from_pos_shift-2)-m_segment_loss_matrix.element(segment_id, to_pos),
121  m_segment_ids->element(from_pos_shift-1), m_segment_loss_matrix.element(segment_id, from_pos_shift-1)-m_segment_loss_matrix.element(segment_id, to_pos),
122  m_segment_ids->element(from_pos_shift), m_segment_loss_matrix.element(segment_id, from_pos_shift)-m_segment_loss_matrix.element(segment_id, to_pos),
123  m_segment_ids->element(from_pos_shift+1), m_segment_loss_matrix.element(segment_id, from_pos_shift+1)-m_segment_loss_matrix.element(segment_id, to_pos)) ;
124  while(1)
125  {
126  while (m_segment_ids->element(from_pos_shift)==m_segment_ids->element(from_pos_shift+1) && from_pos_shift<to_pos)
127  from_pos_shift++ ;
128  if (print)
129  SG_PRINT("# pos=%i,%i segment_id=%i, m_segment_ids[from-2]=%i (%1.1f), m_segment_ids[from-1]=%i (%1.1f), m_segment_ids[from]=%i (%1.1f), m_segment_ids[from+1]=%i (%1.1f), \n",
130  from_pos_shift, to_pos, segment_id,
131  m_segment_ids->element(from_pos_shift-2), m_segment_loss_matrix.element(segment_id, from_pos_shift-2)-m_segment_loss_matrix.element(segment_id, to_pos),
132  m_segment_ids->element(from_pos_shift-1), m_segment_loss_matrix.element(segment_id, from_pos_shift-1)-m_segment_loss_matrix.element(segment_id, to_pos),
133  m_segment_ids->element(from_pos_shift), m_segment_loss_matrix.element(segment_id, from_pos_shift)-m_segment_loss_matrix.element(segment_id, to_pos),
134  m_segment_ids->element(from_pos_shift+1), m_segment_loss_matrix.element(segment_id, from_pos_shift+1)-m_segment_loss_matrix.element(segment_id, to_pos)) ;
135 
136  if (from_pos_shift>=to_pos)
137  {
138  //SG_PRINT("break")
139  break ;
140  }
141  else from_pos_shift++ ;
142  }
143  if (print)
144  SG_PRINT("break\n") */
145 
146  float32_t diff_contrib = m_segment_loss_matrix.element(segment_id, from_pos)-m_segment_loss_matrix.element(segment_id, to_pos);
147  diff_contrib += m_segment_mask->element(to_pos-1)*m_segment_loss.element(segment_id, m_segment_ids->element(to_pos-1), 0);
148  return diff_contrib;
149 }
150 
151 inline float32_t CSegmentLoss::get_segment_loss_extend(int32_t from_pos, int32_t to_pos, int32_t segment_id)
152 {
153  int32_t from_pos_shift = from_pos ;
154 
155  /*SG_PRINT("segment_id=%i, m_segment_ids[from-2]=%i (%1.1f), m_segment_ids[from-1]=%i (%1.1f), m_segment_ids[from]=%i (%1.1f), m_segment_ids[from+1]=%i (%1.1f), \n",
156  segment_id,
157  m_segment_ids->element(from_pos_shift-2), m_segment_loss_matrix.element(segment_id, from_pos_shift-2)-m_segment_loss_matrix.element(segment_id, to_pos),
158  m_segment_ids->element(from_pos_shift-1), m_segment_loss_matrix.element(segment_id, from_pos_shift-1)-m_segment_loss_matrix.element(segment_id, to_pos),
159  m_segment_ids->element(from_pos_shift), m_segment_loss_matrix.element(segment_id, from_pos_shift)-m_segment_loss_matrix.element(segment_id, to_pos),
160  m_segment_ids->element(from_pos_shift+1), m_segment_loss_matrix.element(segment_id, from_pos_shift+1)-m_segment_loss_matrix.element(segment_id, to_pos)) ;*/
161 
162  while (from_pos_shift<to_pos && m_segment_ids->element(from_pos_shift)==m_segment_ids->element(from_pos_shift+1))
163  from_pos_shift++ ;
164 
165  /*SG_PRINT("segment_id=%i, m_segment_ids[from-2]=%i (%1.1f), m_segment_ids[from-1]=%i (%1.1f), m_segment_ids[from]=%i (%1.1f), m_segment_ids[from+1]=%i (%1.1f), \n",
166  segment_id,
167  m_segment_ids->element(from_pos_shift-2), m_segment_loss_matrix.element(segment_id, from_pos_shift-2)-m_segment_loss_matrix.element(segment_id, to_pos),
168  m_segment_ids->element(from_pos_shift-1), m_segment_loss_matrix.element(segment_id, from_pos_shift-1)-m_segment_loss_matrix.element(segment_id, to_pos),
169  m_segment_ids->element(from_pos_shift), m_segment_loss_matrix.element(segment_id, from_pos_shift)-m_segment_loss_matrix.element(segment_id, to_pos),
170  m_segment_ids->element(from_pos_shift+1), m_segment_loss_matrix.element(segment_id, from_pos_shift+1)-m_segment_loss_matrix.element(segment_id, to_pos)) ;*/
171 
172  float32_t diff_contrib = m_segment_loss_matrix.element(segment_id, from_pos_shift)-m_segment_loss_matrix.element(segment_id, to_pos);
173  //diff_contrib += m_segment_mask->element(to_pos)*m_segment_loss.element(segment_id, m_segment_ids->element(to_pos), 0);
174 
175  //if (from_pos_shift!=from_pos)
176  // SG_PRINT("shifting from %i to %i, to_pos=%i, loss=%1.1f\n", from_pos, from_pos_shift, to_pos, diff_contrib)
177 
178  return diff_contrib;
179 }
180 }
181 #endif
virtual const char * get_name() const
Definition: SegmentLoss.h:91
float32_t get_segment_loss(int32_t from_pos, int32_t to_pos, int32_t segment_id)
Definition: SegmentLoss.h:113
CDynamicArray< int32_t > * m_segment_ids
Definition: SegmentLoss.h:104
void compute_loss(int32_t *all_pos, int32_t len)
Definition: SegmentLoss.cpp:47
class IntronList
Definition: SegmentLoss.h:24
float32_t get_segment_loss_extend(int32_t from_pos, int32_t to_pos, int32_t segment_id)
Definition: SegmentLoss.h:151
Class SGObject is the base class of all shogun objects.
Definition: SGObject.h:115
void set_segment_ids(CDynamicArray< int32_t > *segment_ids)
Definition: SegmentLoss.cpp:37
double float64_t
Definition: common.h:50
void set_num_segment_types(int32_t num_segment_types)
Definition: SegmentLoss.h:76
float float32_t
Definition: common.h:49
all of classes and functions are contained in the shogun namespace
Definition: class_list.h:18
CDynamicArray< float64_t > * m_segment_mask
Definition: SegmentLoss.h:107
CDynamicArray< float64_t > m_segment_loss
Definition: SegmentLoss.h:101
const T & element(int32_t idx1, int32_t idx2=0, int32_t idx3=0) const
Definition: DynamicArray.h:224
CDynamicArray< float32_t > m_segment_loss_matrix
Definition: SegmentLoss.h:95
int32_t m_num_segment_types
Definition: SegmentLoss.h:110
void set_segment_loss(float64_t *segment_loss, int32_t m, int32_t n)
Definition: SegmentLoss.cpp:26
void set_segment_mask(CDynamicArray< float64_t > *segment_mask)
Definition: SegmentLoss.cpp:42

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