1 // ==========================================================================
2 // SeqAn - The Library for Sequence Analysis
3 // ==========================================================================
4 // Copyright (c) 2006-2010, Knut Reinert, FU Berlin
5 // All rights reserved.
6 //
7 // Redistribution and use in source and binary forms, with or without
8 // modification, are permitted provided that the following conditions are met:
9 //
10 // * Redistributions of source code must retain the above copyright
11 // notice, this list of conditions and the following disclaimer.
12 // * Redistributions in binary form must reproduce the above copyright
13 // notice, this list of conditions and the following disclaimer in the
14 // documentation and/or other materials provided with the distribution.
15 // * Neither the name of Knut Reinert or the FU Berlin nor the names of
16 // its contributors may be used to endorse or promote products derived
17 // from this software without specific prior written permission.
18 //
19 // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
20 // AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
21 // IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
22 // ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
23 // FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
24 // DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
25 // SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
26 // CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
27 // LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
28 // OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
29 // DAMAGE.
30 //
31 // ==========================================================================
32
33 #ifndef SEQAN_HEADER_GRAPH_REFINE_ALIGN_H
34 #define SEQAN_HEADER_GRAPH_REFINE_ALIGN_H
35
36
37
38 namespace SEQAN_NAMESPACE_MAIN
39 {
40
41
42 ///////////////////////////////////////////////////////////////////////////////////////////////////////
43 //Functions for Align<TSource,TSpec>
44 //project onto other sequence
45 template<typename TSource,typename TSpec,typename TValue,typename TMap>
46 void
_getOtherSequenceAndProject(Align<TSource,TSpec> & segment,TValue seg_num,TMap & seq_map,TValue,TValue node_i,TValue & seq_j_id,TValue & node_j)47 _getOtherSequenceAndProject(Align<TSource,TSpec> & segment,
48 TValue seg_num,
49 TMap & seq_map,
50 TValue ,
51 TValue node_i,
52 TValue & seq_j_id,
53 TValue & node_j)
54 {
55 SEQAN_CHECKPOINT
56
57 if(seg_num == 0)
58 {
59 seq_j_id = seq_map[id(source(row(segment,1)))];
60 node_j = toSourcePosition(row(segment,1),toViewPosition(row(segment,0),node_i));
61 }
62 else
63 {
64 seq_j_id = seq_map[id(source(row(segment,0)))];
65 node_j = toSourcePosition(row(segment,0),toViewPosition(row(segment,1),node_i));
66 }
67 }
68
69
70 //unspektakul�re funktion, die die int ID zur�ckgibt (braucht man damit es f�r alle alignment typen geht)
71 //template<typename TSource,typename TSpec, typename TValue, typename TSeqMap>
72 //int
73 //_getSeqMapId(TSeqMap & seq_map,
74 // Align<TSource,TSpec> & segment,
75 // TValue seq_i)
76 //{
77 //SEQAN_CHECKPOINT
78 // return seq_map[id(source(row(segment,seq_i)))];
79 //}
80 //
81 //given seq and segment, get the sequenceId (seq_i) and its begin and end
82 //if seq = 0 get first sequence (that takes part in the segment match)
83 //if seq = 1 get second sequence
84 template<typename TAliSource,typename TAliSpec, typename TValue>
85 void
_getSeqBeginAndEnd(Align<TAliSource,TAliSpec> & segment,std::map<const void *,int> & seq_map,TValue & seq_i_id,TValue & begin_i,TValue & end_i,TValue seq)86 _getSeqBeginAndEnd(Align<TAliSource,TAliSpec> & segment,
87 std::map<const void * ,int> & seq_map,
88 TValue & seq_i_id,
89 TValue & begin_i,
90 TValue & end_i,
91 TValue seq)
92 {
93 seq_i_id = seq_map[id(source(row(segment,seq)))];
94 begin_i = clippedBeginPosition(row(segment,seq));
95 end_i = clippedEndPosition(row(segment,seq));
96 }
97
98
99
100 ////////////////////////////////////////////////////////////////////////////////////////
101 // 50000 _getRefinedMatchScore Functions
102 ////////////////////////////////////////////////////////////////////////////////////////
103 ////////////////////////////////
104 //for Align<TAliSource,TAliSpec>
105 //get score for alignment of length len starting at pos_i on first sequence
106 //and pos_j on second sequence
107 template<typename TScoreValue,typename TScoreSpec,typename TStringSet,typename TAliSource,typename TAliSpec,typename TValue>
108 TScoreValue
_getRefinedMatchScore(Score<TScoreValue,TScoreSpec> & score_type,TStringSet &,Align<TAliSource,TAliSpec> & segment,TValue pos_i,TValue pos_j,TValue len,TValue)109 _getRefinedMatchScore(Score<TScoreValue,TScoreSpec> & score_type,
110 TStringSet &,
111 Align<TAliSource,TAliSpec> & segment,
112 TValue pos_i,
113 TValue pos_j,
114 TValue len,
115 TValue)
116 {
117 SEQAN_CHECKPOINT
118 typedef Align<TAliSource,TAliSpec> TAlign;
119 typedef typename Row<TAlign>::Type TRow;
120 // typedef typename Iterator<TRow,GapsIterator<ArrayGaps> >::Type TIterator;
121 typedef typename Iterator<TRow, Rooted>::Type TIterator;
122 TIterator row0_it, row1_it;
123 row0_it = iter(row(segment,0),toViewPosition(row(segment,0),pos_i));
124 row1_it = iter(row(segment,1),toViewPosition(row(segment,1),pos_j));
125 len = toViewPosition(row(segment,0),pos_i + len) - toViewPosition(row(segment,0),pos_i);
126 TValue i = 0;
127 TScoreValue ret_score = 0;
128 while(i < len)
129 {
130 if(isGap(row1_it)||isGap(row0_it))
131 ret_score += scoreGapExtend(score_type);
132 else
133 ret_score += score(score_type,getValue(row0_it),getValue(row1_it));
134 ++i;
135 ++row0_it;
136 ++row1_it;
137 }
138 return ret_score;
139 }
140
141
142 //get score for alignment starting at pos_i on first sequence
143 //and pos_j on second sequence, if len1!=len2 then the refinement
144 //process was stopped (the cut is not exact)
145 //template<typename TScore,typename TStringSet, typename TAliSource,typename TAliSpec,typename TValue>
146 //typename Value<TScore>::Type
147 //_getRefinedMatchScore(TScore & score_type,
148 // TStringSet &,
149 // Align<TAliSource,TAliSpec> & segment,
150 // TValue pos_i,
151 // TValue pos_j,
152 // TValue len1,
153 // TValue len2)
154 //{
155 //SEQAN_CHECKPOINT
156 // typedef Align<TAliSource,TAliSpec> TAlign;
157 // typedef typename Row<TAlign>::Type TRow;
158 // typedef typename Iterator<TRow>::Type TIterator;
159 // TIterator row0_it, row1_it;
160 // TValue len;
161 // row0_it = iter(row(segment,0),toViewPosition(row(segment,0),pos_i));
162 // row1_it = iter(row(segment,1),toViewPosition(row(segment,1),pos_j));
163 // len1 = toViewPosition(row(segment,0),pos_i + len1) - toViewPosition(row(segment,0),pos_i);
164 // len2 = toViewPosition(row(segment,1),pos_j + len2) - toViewPosition(row(segment,1),pos_j);
165 // len = (len1 < len2) ? len1 : len2;
166 // int i = 0;
167 // typename Value<TScore>::Type ret_score = 0;
168 //
169 // //calculate score for aligned region
170 // while(i < len)
171 // {
172 // ret_score += score(score_type,getValue(row0_it),getValue(row1_it));
173 // ++i;
174 // ++row0_it;
175 // ++row1_it;
176 // }
177 // //fill up with gaps if one sequence is longer than the other
178 // len = (len1 > len2) ? len1 : len2;
179 // ret_score += (len - i) * scoreGapExtend(score_type);
180 //
181 // return ret_score;
182 //}
183
184
185 }
186 #endif //#ifndef SEQAN_HEADER_...
187