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// Demo program for clipping with Gaps objects.
#include <iostream>
#include <seqan/sequence.h>
#include <seqan/align.h>
using namespace seqan;
int main()
{
// Create sequence variable and gaps basd on sequence.
CharString seq("ABCDEFGHIJ");
Gaps<CharString> gaps(seq);
// Insert gaps, the positions are in (clipped) view space.
insertGaps(gaps, 2, 2);
insertGap(gaps, 6);
insertGap(gaps, 10);
// Print to stdout.
std::cout << "gaps\t" << gaps << "\n"
<< "seq \t" << seq << "\n\n";
// Print the begin and end positions in sequence space and the clipped
// begin and end positions in gap space. We have no clipping, so no
// surprises here.
std::cout << "beginPosition(gaps) == " << beginPosition(gaps) << "\n"
<< "endPosition(gaps) == " << endPosition(gaps) << "\n"
<< "clippedBeginPosition(gaps) == " << clippedBeginPosition(gaps) << "\n"
<< "clippedEndPosition(gaps) == " << clippedEndPosition(gaps) << "\n\n";
// Now, clip the alignment and again print the gaps, sequence and begin/end
// positions. Note that the clipping positions are relative to the unclipped
// view.
setClippedBeginPosition(gaps, 3);
setClippedEndPosition(gaps, 10);
std::cout << "gaps\t" << gaps << "\n"
<< "seq \t" << infix(seq, beginPosition(gaps), endPosition(gaps)) << "\n\n";
std::cout << "beginPosition(gaps) == " << beginPosition(gaps) << "\n"
<< "endPosition(gaps) == " << endPosition(gaps) << "\n"
<< "clippedBeginPosition(gaps) == " << clippedBeginPosition(gaps) << "\n"
<< "clippedEndPosition(gaps) == " << clippedEndPosition(gaps) << "\n\n";
// We can translate between the (clipped) gapped position (aka view) and
// the unclipped ungapped positions (aka) source using toSourcePosition()
// and toViewPosition(). Note that because of projection to the right of
// gaps, these operations are not symmetric.
std::cout << "4 view position => " << toSourcePosition(gaps, 4) << " source position\n"
<< "2 source position => " << toViewPosition(gaps, 2) << " view position\n\n";
// Translating between clipped gapped and unclipped gapped position can
// be done by adding/subtracting clippedBeginPosition(gaps).
std::cout << "3 clipped gapped => " << 3 + clippedBeginPosition(gaps) << " unclipped gapped\n"
<< "6 unclipped gapped => " << 5 - clippedBeginPosition(gaps) << " clipped gapped\n\n";
// Translating between clipped ungapped and unclipped ungapped position can
// be done by adding/subtracing beginPosition(gaps). Since there are no
// gaps, this operation is symmetric.
std::cout << "3 clipped ungapped => " << 3 + beginPosition(gaps) << " unclipped ungapped\n"
<< "5 unclipped ungapped => " << 5 - beginPosition(gaps) << " clipped ungapped\n\n";
// Translating between gapped clipped position and ungapped clipped
// position and between gapped unclipped and ungapped unclipped positions
// has to be done using the translations above.
std::cout << "3 clipped gapped => " << toSourcePosition(gaps, 3) - beginPosition(gaps) << " clipped ungapped\n"
<< "4 unclipped ungapped => " << toViewPosition(gaps, 4) + clippedBeginPosition(gaps) << " unclipped gapped\n";
return 0;
}
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