Adapt the free end gap configuration of the alignment

[rrahn]

Description

Following the discussion on #131 adapt the free end configuration.

seqan3::align_cfg::method_global:    [required]

construction

seqan3::align_cfg::method_global global
{
seqan3::align_cfg::free_end_gaps_sequence1_leading{true},
seqan3::align_cfg::free_end_gaps_sequence2_leading{true},
seqan3::align_cfg::free_end_gaps_sequence1_trailing{true},
seqan3::align_cfg::free_end_gaps_sequence2_trailing{true}
}; // verbose has constructor with 4 constructor elements

later access and set

global.free_end_gaps_sequence1_leading = true/ false;
global.free_end_gaps_sequence2_leading = true/ false;
global.free_end_gaps_sequence1_trailing = true/ false;
global.free_end_gaps_sequence2_trailing = true/ false;

or by seqan::get

auto && global = seqan3::get<seqan3::align_cfg::method_global>(config);

global.free_end_gaps_sequence1_leading = true/ false;
global.free_end_gaps_sequence2_leading = true/ false;
global.free_end_gaps_sequence1_trailing = true/ false;
global.free_end_gaps_sequence2_trailing = true/ false;

query if configuration was piped

Acceptance Criteria

• gap configuration can be set over method_global liek described above

Tasks

• Introduce strong types free_end_gaps_sequence[1/2]_[leading/trailing]
• Make seqan3::method_global a pipeable ocnfig element (not a tag), that is constructible from the 4 strong_types
• Make alignment algorithm use the method_global end gap configuration instead of using the aligned_ends configuration
• Remove the seqan3::align_cfg::aligned_ends configuration

Definition of Done

• Implementation and design approved
• Unit tests pass
• Test coverage = 100%
• Microbenchmarks added and/or affected microbenchmarks < 5% performance drop
• API documentation added
• Tutorial/teaching material added
• Test suite compiles in less than 30 seconds (on travis)
• Changelog entry added

[smehringer]

We decided to introduce shortcuts:

// gap short cuts
struct free_end_gaps_sequence1;
struct free_end_gaps_sequence2;
struct free_end_gaps_all;

// ... extra constructor in method_global that sets the four members for each short cut
    constexpr method_global(seqan3::align_cfg::free_end_gaps_sequence1) noexcept :
        free_end_gaps_sequence1_leading{seqan3::align_cfg::free_end_gaps_sequence1_leading{true}},
        free_end_gaps_sequence2_leading{seqan3::align_cfg::free_end_gaps_sequence2_leading{false}},
        free_end_gaps_sequence1_trailing{seqan3::align_cfg::free_end_gaps_sequence1_trailing{true}},
        free_end_gaps_sequence2_trailing{seqan3::align_cfg::free_end_gaps_sequence2_trailing{false}}
    {}
     constexpr method_global(seqan3::align_cfg::free_end_gaps_sequence2) noexcept {}// ...
     constexpr method_global(seqan3::align_cfg::free_end_gaps_all) noexcept {}// ...

// usage:
auto cfg = seqan3::align_cfg::method_global{seqan3::align_cfg::free_end_gaps_sequence1};

Why not directly introducing method_global short cuts:

// gap short cuts
inline constexpr method_global_free_end_gaps_sequence1 = method_global
{
    free_end_gaps_sequence1_leading{true},
    free_end_gaps_sequence2_leading{false},
    free_end_gaps_sequence1_trailing{true},
    free_end_gaps_sequence2_trailing{false}
};

inline constexpr method_global_free_end_gaps_sequence2 = method_global{...};
inline constexpr method_global_free_end_gaps_all = method_global{...};

// usage
auto cfg = seqan3::align_cfg::method_global_free_end_gaps_sequence1;


auto cfg = seqan3::align_cfg::method_global_overlap;

Names may have to be discussed

[marehr]

Short note, we don't necessarily need an extra method_global_ prefix name, because

inline constexpr method_global free_end_gaps_sequence1
{
    free_end_gaps_sequence1_leading{true},
    free_end_gaps_sequence2_leading{false},
    free_end_gaps_sequence1_trailing{true},
    free_end_gaps_sequence2_trailing{false}
};

seqan3::align_cfg::method_global{free_end_gaps_sequence1}; // is still valid

but I see you point that

auto cfg = free_end_gaps_sequence1 | ...

Could be piped directly which would be bad. I'm a bit against all those method_global_ prefixes.

We could also do a construct like this:

struct free_end_gaps
{
seqan3::align_cfg::free_end_gaps_sequence1_leading free_end_gaps_sequence1_leading{};
seqan3::align_cfg::free_end_gaps_sequence2_leading free_end_gaps_sequence2_leading{};
seqan3::align_cfg::free_end_gaps_sequence1_trailing free_end_gaps_sequence1_trailing{};
seqan3::align_cfg::free_end_gaps_sequence2_trailing free_end_gaps_sequence2_trailing{};
};

inline constexpr free_end_gaps free_end_gaps_sequence1
{
    free_end_gaps_sequence1_leading{true},
    free_end_gaps_sequence2_leading{false},
    free_end_gaps_sequence1_trailing{true},
    free_end_gaps_sequence2_trailing{false}
};

struct method_global : free_end_gaps
{
//..
};

// you need to use method_global as data-holder which is different from method_global

method_global{free_end_gaps{...}};
method_global{{...}};
method_global{...};

seqan3::align_cfg::method_global{seqan3::align_cfg::free_end_gaps{seqan3::align_cfg::free_end_gaps....}}