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//![main]
#include <iostream>
#include <seqan/align.h>
using namespace seqan2;
int main()
{
//![main]
//![typedefs]
typedef char TChar; // character type
typedef String<TChar> TSequence; // sequence type
typedef Align<TSequence, ArrayGaps> TAlign; // align type
typedef Row<TAlign>::Type TRow; // gapped sequence type
//![typedefs]
std::cout << "//![output_init]\n";
//![init]
TSequence seq1 = "CDFGDC";
TSequence seq2 = "CDEFGAHGC";
TAlign align;
resize(rows(align), 2);
assignSource(row(align, 0), seq1);
assignSource(row(align, 1), seq2);
std::cout << align;
//![init]
std::cout << "//![output_init]\n";
std::cout << "//![output_manipulation]\n";
//![manipulation]
TRow & row1 = row(align, 0);
TRow & row2 = row(align, 1);
insertGap(row1, 2);
std::cout << align;
insertGaps(row1, 5, 2);
std::cout << align;
//![manipulation]
std::cout << "//![output_manipulation]\n";
std::cout << "//![output_source_positions]\n";
//![printingSourcePos]
std::cout << std::endl << "ViewToSource1: " << std::endl;
for (auto c: row1)
std::cout << c << " ";
std::cout << std::endl;
for (unsigned i = 0; i < length(row1); ++i)
std::cout << toSourcePosition(row1, i) << " ";
std::cout << std::endl;
std::cout << std::endl << "ViewToSource2: " << std::endl;
for (auto c: row2)
std::cout << c << " ";
std::cout << std::endl;
for (unsigned i = 0; i < length(row2); ++i)
std::cout << toSourcePosition(row2, i) << " ";
std::cout << std::endl;
//![printingSourcePos]
std::cout << "//![output_source_positions]\n";
std::cout << "//![output_view_positions]\n";
//![printingViewPos]
std::cout << std::endl << "SourceToView1: " << std::endl;
for (auto c: source(row1))
std::cout << c << " ";
std::cout << std::endl;
for (unsigned i = 0; i < length(source(row1)); ++i)
std::cout << toViewPosition(row1, i) << " ";
std::cout << std::endl;
std::cout << std::endl << "SourceToView2: " << std::endl;
for (auto c: source(row2))
std::cout << c << " ";
std::cout << std::endl;
for (unsigned i = 0; i < length(source(row2)); ++i)
std::cout << toViewPosition(row2, i) << " ";
std::cout << std::endl;
//![printingViewPos]
std::cout << "//![output_view_positions]\n";
std::cout << "//![output_clipping]\n";
//![clipping]
std::cout << std::endl << "Before clipping:\n" << align;
setClippedBeginPosition(row1, 1);
setClippedEndPosition(row1, 7);
setClippedBeginPosition(row2, 1);
setClippedEndPosition(row2, 7);
std::cout << std::endl << "After clipping:\n" << align;
//![clipping]
std::cout << "//![output_clipping]\n";
std::cout << "//![output_clipping_positions]\n";
//![clipping_positions]
std::cout << std::endl << "ViewToSource1: ";
for (unsigned i = 0; i < length(row1); ++i)
std::cout << toSourcePosition(row1, i) << " ";
std::cout << std::endl << "ViewToSource2: ";
for (unsigned i = 0; i < length(row2); ++i)
std::cout << toSourcePosition(row2, i) << " ";
std::cout << std::endl;
std::cout << std::endl << "SourceToView1: ";
for (unsigned i = 0; i < length(source(row1)); ++i)
std::cout << toViewPosition(row1, i) << " ";
std::cout << std::endl << "SourceToView2: ";
for (unsigned i = 0; i < length(source(row2)); ++i)
std::cout << toViewPosition(row2, i) << " ";
std::cout << std::endl;
//![clipping_positions]
std::cout << "//![output_clipping_positions]\n";
std::cout << "//![output_iteratingRowClipped]\n";
//![iteratingRowClipped]
typedef Iterator<TRow>::Type TRowIterator;
TRowIterator it = begin(row1),
itEnd = end(row1);
for (; it != itEnd; ++it)
{
TChar c = isGap(it) ? gapValue<TChar>() : *it;
std::cout << c << " ";
}
std::cout << std::endl;
//![iteratingRowClipped]
std::cout << "//![output_iteratingRowClipped]\n";
std::cout << "//![output_iteratingRowClipped2]\n";
//![iteratingRowClipped2]
clearClipping(row1);
it = begin(row1);
itEnd = end(row1);
for (; it != itEnd; ++it)
{
TChar c = isGap(it) ? gapValue<TChar>() : *it;
std::cout << c << " ";
}
std::cout << std::endl;
//![iteratingRowClipped2]
std::cout << "//![output_iteratingRowClipped2]\n";
//![return]
return 0;
}
//![return]
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