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// ==========================================================================
// SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2026, Knut Reinert, FU Berlin
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
// * Neither the name of Knut Reinert or the FU Berlin nor the names of
// its contributors may be used to endorse or promote products derived
// from this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
// DAMAGE.
//
// ==========================================================================
// Author: Rene Rahn <rene.rahn@fu-berlin.de>
// ==========================================================================
// Mock generator for the journaled string tree.
// ==========================================================================
#ifndef TESTS_JOURNALED_STRING_TREE_TEST_JOURNALED_STRING_TREE_MOCK_H_
#define TESTS_JOURNALED_STRING_TREE_TEST_JOURNALED_STRING_TREE_MOCK_H_
#include <vector>
#include <seqan/sequence.h>
using namespace seqan2;
struct TestJstPosConfig_
{
typedef uint16_t TDeltaPos;
typedef Dna TSnpValue;
typedef uint16_t TDelValue;
typedef String<Dna> TInsValue;
typedef Pair<TDelValue, TInsValue> TSVValue;
};
template <typename TString, typename TRef, typename TDeltaMap>
inline void
_createJournaledStrings(StringSet<TString> & set,
TRef const & source,
TDeltaMap const & map,
unsigned const dim)
{
for (unsigned seqId = 0; seqId < dim; ++seqId)
{
TString seq = source;
auto it = end(map, Standard());
auto itBegin = begin(map, Standard());
while (it != itBegin)
{
--it;
if (!getDeltaCoverage(*it)[seqId])
continue;
switch (getDeltaType(*it))
{
case DELTA_TYPE_SNP:
{
erase(seq, getDeltaPosition(*it));
insertValue(seq, getDeltaPosition(*it), deltaValue(it, DeltaTypeSnp()));
break;
}
case DELTA_TYPE_DEL:
{
if((*it).deltaTypeEnd != DeltaEndType::IS_RIGHT)
erase(seq, getDeltaPosition(*it), getDeltaPosition(*it)+ deltaValue(it, DeltaTypeDel()));
break;
}
case DELTA_TYPE_INS:
{
insert(seq, getDeltaPosition(*it), deltaValue(it, DeltaTypeIns()));
break;
}
case DELTA_TYPE_SV:
{
if((*it).deltaTypeEnd != DeltaEndType::IS_RIGHT)
{
erase(seq, getDeltaPosition(*it), getDeltaPosition(*it) + deltaValue(it, DeltaTypeSV()).i1);
insert(seq, getDeltaPosition(*it), deltaValue(it, DeltaTypeSV()).i2);
}
break;
}
}
}
appendValue(set, seq);
}
}
class JstMockGenerator
{
public:
template <typename TJst>
static TJst _createSimpleJst()
{
typename Host<typename Member<TJst, JstSourceMember>::Type>::Type const seq = "AGATCGAGCGAGCTAGCGACTCAG";
TJst jst(seq, 100);
String<unsigned> ids;
appendValue(ids, 0);
appendValue(ids, 3);
appendValue(ids, 9);
appendValue(ids, 99);
insert(jst, 1, 3, ids, DeltaTypeDel());
insert(jst, 8, "CGTA", ids, DeltaTypeIns());
insert(jst, 10, 'C', ids, DeltaTypeSnp());
insert(jst, 15, 2, ids, DeltaTypeDel());
insert(jst, 20, 'A', ids, DeltaTypeSnp());
return jst;
}
template <typename TJst>
static TJst _createComplexJst()
{
// POS TYPE S0 S1 S2 S3 S4 S5 S6 S7 S8 S9 MOD
// 0 SNP 0 1 0 1 0 1 1 1 0 0 C
// 0 INS 1 0 1 0 0 0 0 0 0 0 TTG
// 0 DEL 0 0 0 0 1 0 0 0 0 1 2
// 1 SNP 0 1 1 1 0 0 0 1 0 0 G
// 5 STV 1 0 0 0 1 0 0 1 0 0 3,CTC
// 6 INS 0 1 1 0 0 0 1 0 0 0 GGTAGACAACG
// 8 DEL 1 0 0 0 0 0 1 1 0 1 10
// 8 DEL 0 1 0 0 1 0 0 0 0 0 5
// 10 SNP 0 0 1 0 0 1 0 0 0 0 G
// 13 DEL 0 1 0 0 0 0 0 0 0 0 5
// 13 DEL 0 0 0 0 1 1 0 0 0 0 8
// 20 SNP 1 1 0 0 0 0 1 0 0 0 T
// 40 INS 1 0 1 0 0 0 1 0 1 0 TGAC
// 41 INS 1 0 1 0 0 0 0 1 0 1 GTAGA
// 41 STV 0 1 0 0 0 1 1 0 0 0 5,A
// 58 DEL 1 0 0 0 0 0 0 0 1 1 10
// 60 SNP 0 1 1 1 1 1 1 1 0 0 G
// 61 STV 0 0 1 0 0 1 1 1 0 0 2,TA
// 63 DEL 0 0 0 1 0 1 0 1 0 0 3
// 66 INS 0 0 0 0 1 0 1 1 0 0 AGGTA
// 90 DEL 1 0 0 0 0 0 0 0 0 0 9
// 90 DEL 0 1 0 0 0 0 0 0 0 0 10
// 99 SNP 0 0 1 0 0 0 0 0 0 0 T
// 100 INS 0 0 0 1 0 0 0 0 0 0 CCT
typename Host<typename Member<TJst, JstSourceMember>::Type>::Type const seq = "ACGTGGGATTACGGACGAGCGGACTGATTTAGGAGGACAGTACGGGACTACGGACGTACTACGAGCGACTATCGACGAGAGGAGATCAGGCATTAAGCCC";
// 01234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890
// 0 1 2 3 4 5 6 7 8 9 10
TJst jst(std::move(seq), 10);
insert(jst, 0, 'C', std::vector<unsigned>{1, 3, 5, 6, 7}, DeltaTypeSnp());
insert(jst, 0, "TTG", std::vector<unsigned>{0, 2}, DeltaTypeIns());
insert(jst, 0, 2, std::vector<unsigned>{4, 9}, DeltaTypeDel());
insert(jst, 1, 'G', std::vector<unsigned>{1, 2, 3, 7}, DeltaTypeSnp());
insert(jst, 5, Pair<unsigned, DnaString>(3, "CTC"), std::vector<unsigned>{0, 4, 7}, DeltaTypeSV());
insert(jst, 6, "GGTAGACAACG", std::vector<unsigned>{1, 2, 6}, DeltaTypeIns());
insert(jst, 8, 10, std::vector<unsigned>{0, 6, 7, 9}, DeltaTypeDel());
insert(jst, 8, 5, std::vector<unsigned>{1, 4}, DeltaTypeDel());
insert(jst, 10, 'G', std::vector<unsigned>{2, 5}, DeltaTypeSnp());
insert(jst, 13, 5, std::vector<unsigned>{1}, DeltaTypeDel());
insert(jst, 13, 8, std::vector<unsigned>{4, 5}, DeltaTypeDel());
insert(jst, 20, 'T', std::vector<unsigned>{0, 1, 6}, DeltaTypeSnp());
insert(jst, 40, "TGAC", std::vector<unsigned>{0, 2, 6, 8}, DeltaTypeIns());
insert(jst, 41, "GTAGA", std::vector<unsigned>{0, 2, 7, 9}, DeltaTypeIns());
insert(jst, 41, Pair<unsigned, DnaString>(5, "A"), std::vector<unsigned>{1, 5, 6}, DeltaTypeSV());
insert(jst, 58, 10, std::vector<unsigned>{0, 8, 9}, DeltaTypeDel());
insert(jst, 60, 'G', std::vector<unsigned>{1, 2, 3, 4, 5, 6, 7}, DeltaTypeSnp());
insert(jst, 61, Pair<unsigned, DnaString>(2, "TA"), std::vector<unsigned>{2, 5, 6, 7}, DeltaTypeSV());
insert(jst, 63, 3, std::vector<unsigned>{3, 5, 7}, DeltaTypeDel());
insert(jst, 66, "AGGTA", std::vector<unsigned>{4, 6, 7}, DeltaTypeIns());
insert(jst, 90, 9, std::vector<unsigned>{0}, DeltaTypeDel());
insert(jst, 90, 10, std::vector<unsigned>{1}, DeltaTypeDel());
insert(jst, 99, 'T', std::vector<unsigned>{2}, DeltaTypeSnp());
insert(jst, 100, "CCT", std::vector<unsigned>{3}, DeltaTypeIns());
return jst;
}
static StringSet<DnaString> _createComplexTestSet()
{
StringSet<DnaString> set;
appendValue(set, "TTGACGTGCTCGCTGACTGATTTAGGAGGACAGTGACTGTAGAACGGGACTACGGACGTACTATCGACGAGAGGAGATCAGGC");
appendValue(set, "CGGTGGGGTAGACAACGGAGCTGACTGATTTAGGAGGACAGTAACTACGGACGTACTGCGAGCGACTATCGACGAGAGGAGATCAGG");
appendValue(set, "TTGAGGTGGGGTAGACAACGGATTGCGGACGAGCGGACTGATTTAGGAGGACAGTGACTGTAGAACGGGACTACGGACGTACTGTAAGCGACTATCGACGAGAGGAGATCAGGCATTAAGCCT");
appendValue(set, "CGGTGGGATTACGGACGAGCGGACTGATTTAGGAGGACAGTACGGGACTACGGACGTACTGCGGACTATCGACGAGAGGAGATCAGGCATTAAGCCCCCT");
appendValue(set, "GTGCTCGACTGATTTAGGAGGACAGTACGGGACTACGGACGTACTGCGAGCAGGTAGACTATCGACGAGAGGAGATCAGGCATTAAGCCC");
appendValue(set, "CCGTGGGATTGCGGACTGATTTAGGAGGACAGTAACTACGGACGTACTGTAGACTATCGACGAGAGGAGATCAGGCATTAAGCCC");
appendValue(set, "CCGTGGGGTAGACAACGGAGCTGACTGATTTAGGAGGACAGTGACTAACTACGGACGTACTGTAAGCAGGTAGACTATCGACGAGAGGAGATCAGGCATTAAGCCC");
appendValue(set, "CGGTGCTCGCGGACTGATTTAGGAGGACAGTGTAGAACGGGACTACGGACGTACTGTAAGGTAGACTATCGACGAGAGGAGATCAGGCATTAAGCCC");
appendValue(set, "ACGTGGGATTACGGACGAGCGGACTGATTTAGGAGGACAGTGACTACGGGACTACGGACGTACTATCGACGAGAGGAGATCAGGCATTAAGCCC");
appendValue(set, "GTGGGAGCGGACTGATTTAGGAGGACAGTGTAGAACGGGACTACGGACGTACTATCGACGAGAGGAGATCAGGCATTAAGCCC");
return set;
}
static StringSet<DnaString> generateNeedles()
{
std::vector<unsigned> ndlLengths = {5, 12, 23, 32, 66};
StringSet<DnaString> ndlSet;
auto set = _createComplexTestSet();
for (unsigned id = 0; id < length(set); ++id)
{
for (unsigned pos = 0; pos < length(set[id]) - 5; ++pos)
{
auto ndlSize = ndlLengths[pos % length(ndlLengths)];
ndlSize = _min(ndlSize, length(set[id]) - pos);
appendValue(ndlSet, infix(set[id], pos, pos + ndlSize));
}
}
return ndlSet;
}
};
#endif // TESTS_JOURNALED_STRING_TREE_TEST_JOURNALED_STRING_TREE_MOCK_H_
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