/*
    This file is part of BioD.
    Copyright (C) 2012    Artem Tarasov <lomereiter@gmail.com>

    Permission is hereby granted, free of charge, to any person obtaining a
    copy of this software and associated documentation files (the "Software"),
    to deal in the Software without restriction, including without limitation
    the rights to use, copy, modify, merge, publish, distribute, sublicense,
    and/or sell copies of the Software, and to permit persons to whom the
    Software is furnished to do so, subject to the following conditions:
    
    The above copyright notice and this permission notice shall be included in
    all copies or substantial portions of the Software.
    
    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
    IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
    FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
    AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
    LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
    FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
    DEALINGS IN THE SOFTWARE.

*/
module bio.core.sequence;

import bio.core.base;

import std.algorithm;
import std.range;
import std.conv;
import std.traits;
public import std.array;

/// Identity function
T identity(T)(auto ref T t) { return t; }

/// Range that allows to unify operations in forward and reverse directions
/// without virtual function call overhead introduced by $(D inputRangeObject).
///
/// $(D reverseTransform) is a function that will be applied to elements
/// if range is iterated backwards.
struct ReversableRange(alias reverseTransform=identity, R)
    if(isBidirectionalRange!R)
{
    private 
    { 
        bool _rev = void;
        R _range = void;
    }

    /// Construct reversable range.
    ///
    /// Params:
    ///     range   =  bidirectional range
    ///     reverse =  if true, all operations on the range will be as if
    ///                $(D retro(range)) was used instead of $(D range).
    this(R range, bool reverse=false) 
    {
        _rev = reverse;
        _range = range;
    }

    /// Bidirectional range primitives
    bool empty() @property
    {
        return _range.empty;
    }

    /// ditto
    auto front() @property
    {
        return _rev ? reverseTransform(_range.back) : _range.front;
    }

    /// ditto
    auto back() @property
    {
        return _rev ? reverseTransform(_range.front) : _range.back;
    }

    /// ditto
    void popFront() 
    { 
        if (_rev) 
            _range.popBack(); 
        else 
            _range.popFront(); 
    }

    /// ditto
    void popBack()
    {
        if (_rev)
            _range.popFront();
        else
            _range.popBack();
    }

    /// ditto
    auto save() @property
    {
        return ReversableRange(_range.save, _rev);
    }

    /// Reverse of this range
    ReversableRange reverse() @property {
        return ReversableRange(_range.save, !_rev);
    }

    static if(hasLength!R) 
    {
        /// If source range has length, the result also has length
        size_t length() @property
        {
            return _range.length;
        }
    }

    static if(isRandomAccessRange!R)
    {
        /// If source range is a random access range, $(D opIndex) is defined
        auto opIndex(size_t index)
        {
            if (_rev)
                return reverseTransform(_range[_range.length - 1 - index]);
            else
                return _range[index];
        }
    }

    static if(hasSlicing!R)
    {
        /// Slicing is also propagated
        auto opSlice(size_t from, size_t to)
        {
            if (_rev)
            {
                auto len = _range.length;
                //
                //  [b, e) -> (len - 1 - e, len - 1 - b] ~ [len - e, len - b)
                //
                return ReversableRange(_range[len - to .. len - from], true);
            }
            else
                return ReversableRange(_range[from .. to], false);
        }
    }
}

/// Create reversable range from bidirectional one.
ReversableRange!(reverseTransform, R)
reversableRange(alias reverseTransform=identity, R)(R range, bool reverse=false)
{
    return typeof(return)(range, reverse);
}

unittest {
    import std.stdio;
    writeln("BioD: running unittests");
    auto bidir_range = [1, 2, 3, 4, 5];
    auto rev = reversableRange(bidir_range[], true);

    assert(rev.front == 5);
    assert(rev[2] == 3);
    rev.popFront();
    assert(rev.back == 1);
    assert(rev.front == 4);
    assert(equal(rev[1 .. 3], [3, 2]));

    // Here. That's the whole point.
    // One can't do the same with $(D retro)
    // without using $(D inputRangeObject),
    // but that kills performance because
    // virtual calls can not be inlined.
    rev = reversableRange(bidir_range[], false);

    assert(rev.front == 1);
    assert(equal(rev[1 .. 3], [2, 3]));
}


/// Sequence of bases. Element of reversed range will be complemented.
template Sequence(R)
{
    alias ReversableRange!(complementBase, R) Sequence;
}

/// Returns an object very similar to string, but sliceable.
/// Tricks std.traits.isNarrowString.
auto sliceableString(string s) {
    return map!"cast(char)a"(cast(ubyte[])s);
}

///
alias ReturnType!sliceableString SliceableString;

/// Create nucleotide sequence from bidirectional base range.
auto nucleotideSequence(R)(R bases, bool reverse=false)
    if(isBidirectionalRange!R)
{

    static if(isNarrowString!R)
    {
        return nucleotideSequence(sliceableString(bases), reverse);
    } 
    else static if(is(Unqual!(ElementType!R) == char) || 
              is(Unqual!(ElementType!R) == dchar))
    {
        return nucleotideSequence(map!(charToBase!Base16)(bases), reverse);
    }
    else
    {
        return Sequence!R(bases, reverse);
    }
}

///
alias ReturnType!(nucleotideSequence!SliceableString) NucleotideSequence;

unittest {
    auto seq0 = nucleotideSequence("ACGTACGT");

    // reverse-complement
    assert(equal(seq0.reverse[2 .. 6], "GTAC"));

    auto seq1 = nucleotideSequence(seq0, true);
    assert(equal(seq1[1 .. 5], "CGTA"));
    assert(equal(seq1, map!complementBase(retro(seq0))));

    seq1 = nucleotideSequence(seq0, false);
    assert(equal(seq1, seq0));
}