1 // ==========================================================================
2 // SeqAn - The Library for Sequence Analysis
3 // ==========================================================================
4 // Copyright (c) 2006-2015, 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
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29 // DAMAGE.
30 //
31 // ==========================================================================
32 // Author: Birte Kehr <birte.kehr@fu-berlin.de>
33 // ==========================================================================
34 // Operations on alignments such as integration
35 // ==========================================================================
36
37 #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_ALIGNMENT_OPERATIONS_H_
38 #define SEQAN_INCLUDE_SEQAN_ALIGN_ALIGNMENT_OPERATIONS_H_
39
40 namespace seqan {
41
42 // ============================================================================
43 // Forwards
44 // ============================================================================
45
46 // ============================================================================
47 // Tags, Classes, Enums
48 // ============================================================================
49
50 // ============================================================================
51 // Metafunctions
52 // ============================================================================
53
54 // ============================================================================
55 // Functions
56 // ============================================================================
57
58 // ----------------------------------------------------------------------------
59 // Function integrateAlign()
60 // ----------------------------------------------------------------------------
61
62 /*!
63 * @fn integrateAlign
64 * @headerfile <seqan/align.h>
65 * @brief Integrates an alignment into another by copying the gaps.
66 *
67 * @signature void integrateAlign(align1, align2[, positions]);
68 *
69 * @param[in,out] align1 Target Alignment object into which align2 is to be integrated.
70 * @param[in] align2 Alignment object that is to be integrated into align1.
71 * @param[in] positions The integration positions in align1 for all rows (view positions), String of positions.
72 *
73 * @section Examples
74 *
75 * @include demos/align/integrate_align.cpp
76 *
77 * The output is as follows:
78 *
79 * @include demos/align/integrate_align.cpp.stdout
80 */
81
82 template <typename TSource1, typename TSpec1, typename TSource2, typename TSpec2, typename TPos>
integrateAlign(Align<TSource1,TSpec1> & align,Align<TSource2,TSpec2> const & infixAlign,String<TPos> const & viewPos)83 void integrateAlign(Align<TSource1, TSpec1> & align,
84 Align<TSource2, TSpec2> const & infixAlign,
85 String<TPos> const & viewPos)
86 {
87 typedef Align<TSource1, TSpec1> TAlign;
88 typedef Align<TSource2, TSpec2> TInfixAlign;
89 typedef typename Size<TAlign>::Type TSize;
90
91 typedef typename Row<TAlign>::Type TRow;
92 typedef typename Row<TInfixAlign const>::Type TInfixRow;
93
94 // Iterators on align and infixAlign.
95 typename Iterator<TRow>::Type it;
96 typedef typename Iterator<TInfixRow, Standard>::Type TInfixRowIt;
97
98
99 for (TSize i = 0; i < length(rows(align)); ++i)
100 {
101 TInfixRow const & infixRow = row(infixAlign, i);
102 // This assertion ensures that the number of sequence characters after viewPos[i] is greater than or equal to
103 // the number of source characters in the clipped infix row.
104 SEQAN_ASSERT_GEQ(endPosition(row(align, i)) - toSourcePosition(row(align, i), viewPos[i]),
105 endPosition(infixRow) - beginPosition(infixRow));
106
107 // init iterators
108 it = iter(row(align, i), value(viewPos, i));
109
110 // walk through Gaps containers and copy gaps
111 for (TInfixRowIt infixIt = begin(infixRow, Standard()); !atEnd(infixIt);)
112 {
113 TSize gapSize = countGaps(infixIt);
114 insertGaps(it, gapSize);
115 goFurther(it, gapSize+1);
116 goFurther(infixIt, gapSize+1);
117 }
118 }
119 }
120
121 template <typename TSource, typename TSpec1, typename TSpec2>
integrateAlign(Align<TSource,TSpec1> & align,Align<typename Infix<TSource>::Type,TSpec2> const & infixAlign)122 void integrateAlign(Align<TSource, TSpec1> & align,
123 Align<typename Infix<TSource>::Type, TSpec2> const & infixAlign)
124 {
125 typedef typename Size<TSource>::Type TSize;
126 typedef typename Position<typename Row<Align<TSource, TSpec1> >::Type>::Type TPos;
127
128 String<TPos> viewPos;
129 TPos pos;
130 for (TSize i = 0; i < length(rows(infixAlign)); ++i)
131 {
132 pos = beginPosition(source(row(infixAlign, i)))
133 - beginPosition(source(row(align, i)))
134 + beginPosition(row(infixAlign, i));
135 appendValue(viewPos, toViewPosition(row(align, i), pos));
136 }
137
138 integrateAlign(align, infixAlign, viewPos);
139 }
140
141 } // namespace seqan
142
143 #endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_ALIGNMENT_OPERATIONS_H_
144