/*
 * Copyright (C) 2021  Christopher J. Howard
 *
 * This file is part of Antkeeper source code.
 *
 * Antkeeper source code is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * Antkeeper source code is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with Antkeeper source code.  If not, see <http://www.gnu.org/licenses/>.
 */

#include "animation/ease.hpp"
#include "animation/screen-transition.hpp"
#include "configuration.hpp"
#include "debug/logger.hpp"
#include "ecs/archetype.hpp"
#include "ecs/components/cavity-component.hpp"
#include "ecs/components/copy-transform-component.hpp"
#include "ecs/components/copy-translation-component.hpp"
#include "ecs/components/model-component.hpp"
#include "ecs/components/snap-component.hpp"
#include "ecs/components/terrain-component.hpp"
#include "ecs/components/tool-component.hpp"
#include "ecs/components/transform-component.hpp"
#include "ecs/components/camera-follow-component.hpp"
#include "ecs/components/orbit-component.hpp"
#include "ecs/components/blackbody-component.hpp"
#include "ecs/components/light-component.hpp"
#include "ecs/commands.hpp"
#include "game/game-context.hpp"
#include "game/states/game-states.hpp"
#include "math/math.hpp"
#include "nest.hpp"
#include "renderer/material.hpp"
#include "gl/texture-2d.hpp"
#include "gl/texture-filter.hpp"
#include "gl/texture-wrapping.hpp"
#include "renderer/model.hpp"
#include "renderer/passes/sky-pass.hpp"
#include "renderer/passes/shadow-map-pass.hpp"
#include "resources/resource-manager.hpp"
#include "scene/model-instance.hpp"
#include "scene/collection.hpp"
#include "scene/camera.hpp"
#include "scene/ambient-light.hpp"
#include "scene/directional-light.hpp"
#include "ecs/systems/control-system.hpp"
#include "ecs/systems/camera-system.hpp"
#include "ecs/systems/render-system.hpp"
#include "ecs/systems/tool-system.hpp"
#include "ecs/systems/orbit-system.hpp"
#include "ecs/systems/astronomy-system.hpp"
#include "game/biome.hpp"
#include "utility/fundamental-types.hpp"

#include "utility/bit-math.hpp"
#include "genetics/genetics.hpp"
#include <iostream>
#include <bitset>
#include <ctime>


void play_state_enter(game_context* ctx)
{
	debug::logger* logger = ctx->logger;
	logger->push_task("Entering play state");
	
	resource_manager* resource_manager = ctx->resource_manager;
	entt::registry& ecs_registry = *ctx->ecs_registry;
	
	// Load biome
	if (ctx->option_biome.has_value())
	{
		ctx->biome = resource_manager->load<biome>(ctx->option_biome.value() + ".bio");
	}
	else
	{
		ctx->biome = resource_manager->load<biome>("forest.bio");
	}
	
	// Apply biome parameters to scene
	sky_pass* sky_pass = ctx->overworld_sky_pass;
	sky_pass->set_enabled(true);
	sky_pass->set_sky_model(ctx->resource_manager->load<model>("sky-dome.mdl"));
	sky_pass->set_moon_model(ctx->resource_manager->load<model>("moon.mdl"));
	
	sky_pass->set_horizon_color({1.1f, 1.1f, 1.1f});
	sky_pass->set_zenith_color({0.0f, 0.0f, 0.0f});
	sky_pass->set_time_of_day(0.0f);
	sky_pass->set_julian_day(0.0f);
	sky_pass->set_observer_location(4.26352e-5, ctx->biome->location[0], ctx->biome->location[1]);
	sky_pass->set_moon_angular_radius(math::radians(1.0f));
	sky_pass->set_sun_angular_radius(math::radians(1.0f));
	sky_pass->set_sky_gradient(resource_manager->load<gl::texture_2d>("sky-gradient.tex"), resource_manager->load<gl::texture_2d>("sky-gradient2.tex"));
	
	// Create sun
	auto sun_entity = ecs_registry.create();
	{
		ecs::orbit_component orbit;
		orbit.elements.a = 0.0;
		orbit.elements.e = 0.0;
		orbit.elements.i = math::radians(0.0);
		orbit.elements.raan = math::radians(0.0);
		orbit.elements.w = math::radians(0.0);
		orbit.elements.ta = math::radians(0.0);
		
		ecs::blackbody_component blackbody;
		blackbody.temperature = 5772.0;
		
		ecs::transform_component transform;
		transform.local = math::identity_transform<float>;
		transform.warp = true;
		
		ecs_registry.assign<ecs::orbit_component>(sun_entity, orbit);
		ecs_registry.assign<ecs::blackbody_component>(sun_entity, blackbody);
		ecs_registry.assign<ecs::transform_component>(sun_entity, transform);
	}
	
	// Create Earth
	auto earth_entity = ecs_registry.create();
	{
		ecs::orbit_component orbit;
		orbit.elements.a = 1.00000261;
		orbit.elements.e = 0.01671123;
		orbit.elements.i = math::radians(-0.00001531);
		orbit.elements.raan = math::radians(0.0);
		const double longitude_periapsis = math::radians(102.93768193);
		orbit.elements.w = longitude_periapsis - orbit.elements.raan;
		orbit.elements.ta = math::radians(100.46457166) - longitude_periapsis;
		
		ecs::transform_component transform;
		transform.local = math::identity_transform<float>;
		transform.warp = true;
		
		ecs_registry.assign<ecs::orbit_component>(earth_entity, orbit);
		ecs_registry.assign<ecs::transform_component>(earth_entity, transform);
	}
	
	scene::ambient_light* ambient = new scene::ambient_light();
	ambient->set_color({1, 1, 1});
	ambient->set_intensity(0.0f);
	ambient->update_tweens();
	ctx->overworld_scene->add_object(ambient);
	
	scene::directional_light* sun = new scene::directional_light();
	sun->set_intensity(1000.0f);
	sun->set_light_texture(resource_manager->load<gl::texture_2d>("forest-gobo.tex"));
	sun->set_light_texture_scale({2000, 2000});
	sun->set_light_texture_opacity(0.925f);
	sun->look_at({2, 1, 0}, {0, 0, 0}, {0, 0, 1});
	sun->update_tweens();
	ctx->overworld_scene->add_object(sun);
	ctx->overworld_shadow_map_pass->set_light(sun);
	
	// Set universal time
	const double universal_time = 0.0;
	ctx->astronomy_system->set_universal_time(universal_time);
	ctx->orbit_system->set_universal_time(universal_time);
	
	// Set astronomy system observation parameters
	const double earth_radius_au = 4.2635e-5;
	ctx->astronomy_system->set_reference_body(earth_entity);
	ctx->astronomy_system->set_reference_body_axial_tilt(math::radians(23.4393));
	ctx->astronomy_system->set_observer_location(double3{4.26352e-5, math::radians(0.0f), math::radians(0.0f)});
	ctx->astronomy_system->set_sun_light(sun);
	ctx->astronomy_system->set_sky_pass(ctx->overworld_sky_pass);

	// Load entity archetypes
	ecs::archetype* ant_hill_archetype = resource_manager->load<ecs::archetype>("ant-hill.ent");
	ecs::archetype* nest_archetype = resource_manager->load<ecs::archetype>("harvester-nest.ent");
	ecs::archetype* redwood_archetype = resource_manager->load<ecs::archetype>("redwood.ent");
	ecs::archetype* forceps_archetype = resource_manager->load<ecs::archetype>("forceps.ent");
	ecs::archetype* lens_archetype = resource_manager->load<ecs::archetype>("lens.ent");
	ecs::archetype* brush_archetype = resource_manager->load<ecs::archetype>("brush.ent");
	ecs::archetype* marker_archetype = resource_manager->load<ecs::archetype>("marker.ent");
	ecs::archetype* container_archetype = resource_manager->load<ecs::archetype>("container.ent");
	ecs::archetype* twig_archetype = resource_manager->load<ecs::archetype>("twig.ent");
	ecs::archetype* larva_archetype = resource_manager->load<ecs::archetype>("ant-larva.ent");
	ecs::archetype* flashlight_archetype = resource_manager->load<ecs::archetype>("flashlight.ent");
	ecs::archetype* flashlight_light_cone_archetype = resource_manager->load<ecs::archetype>("flashlight-light-cone.ent");
	ecs::archetype* lens_light_cone_archetype = resource_manager->load<ecs::archetype>("lens-light-cone.ent");
	ecs::archetype* cube_archetype = resource_manager->load<ecs::archetype>("unit-cube.ent");
	ecs::archetype* color_checker_archetype = resource_manager->load<ecs::archetype>("color-checker.ent");
	
	// Create tools
	forceps_archetype->assign(ecs_registry, ctx->forceps_entity);
	lens_archetype->assign(ecs_registry, ctx->lens_entity);
	brush_archetype->assign(ecs_registry, ctx->brush_entity);
	marker_archetype->assign(ecs_registry, ctx->marker_entity);
	container_archetype->assign(ecs_registry, ctx->container_entity);
	twig_archetype->assign(ecs_registry, ctx->twig_entity);
	
	// Create flashlight and light cone, set light cone parent to flashlight, and move both to underworld scene
	flashlight_archetype->assign(ecs_registry, ctx->flashlight_entity);
	auto flashlight_light_cone = flashlight_light_cone_archetype->create(ecs_registry);
	ecs::command::parent(ecs_registry, flashlight_light_cone, ctx->flashlight_entity);
	ecs::command::assign_render_layers(ecs_registry, ctx->flashlight_entity, 2);
	ecs::command::assign_render_layers(ecs_registry, flashlight_light_cone, 2);
	
	// Make lens tool's model instance unculled, so its shadow is always visible.
	scene::model_instance* lens_model_instance = ctx->render_system->get_model_instance(ctx->lens_entity);
	if (lens_model_instance)
	{
		//lens_model_instance->set_culling_mask(&ctx->no_cull);
	}
	
	// Create lens light cone and set its parent to lens
	auto lens_light_cone = lens_light_cone_archetype->create(ecs_registry);
	ecs::command::bind_transform(ecs_registry, lens_light_cone, ctx->lens_entity);
	ecs::command::parent(ecs_registry, lens_light_cone, ctx->lens_entity);
	
	// Hide inactive tools
	ecs::command::assign_render_layers(ecs_registry, ctx->forceps_entity, 0);
	ecs::command::assign_render_layers(ecs_registry, ctx->brush_entity, 0);
	ecs::command::assign_render_layers(ecs_registry, ctx->lens_entity, 0);
	ecs::command::assign_render_layers(ecs_registry, ctx->marker_entity, 0);
	ecs::command::assign_render_layers(ecs_registry, ctx->container_entity, 0);
	ecs::command::assign_render_layers(ecs_registry, ctx->twig_entity, 0);
	
	// Activate brush tool
	ctx->tool_system->set_active_tool(ctx->brush_entity);

	// Create ant-hill
	auto ant_hill_entity = ant_hill_archetype->create(ecs_registry);
	ecs::command::place(ecs_registry, ant_hill_entity, {0, -40});

	// Creat nest
	auto nest_entity = nest_archetype->create(ecs_registry);
	
	// Create terrain
	int terrain_radius = 0;//6;
	for (int x = -terrain_radius; x <= terrain_radius; ++x)
	{
		for (int z = -terrain_radius; z <= terrain_radius; ++z)
		{
			ecs::terrain_component terrain_component;
			terrain_component.subdivisions = TERRAIN_PATCH_RESOLUTION;
			terrain_component.x = x;
			terrain_component.z = z;
			auto terrain_entity = ecs_registry.create();
			ecs_registry.assign<ecs::terrain_component>(terrain_entity, terrain_component);
		}
	}

	// Create trees
	for (int i = 0; i < 0; ++i)
	{
		auto redwood = redwood_archetype->create(ecs_registry);

		auto& transform = ecs_registry.get<ecs::transform_component>(redwood);
		float zone = 500.0f;
		ecs::command::place(ecs_registry, redwood, {math::random(-zone, zone), math::random(-zone, zone)});
	}
	
	// Create unit cube
	auto cube = cube_archetype->create(ecs_registry);
	ecs::command::place(ecs_registry, cube, {10, 10});
	
	// Create color checker
	auto color_checker = color_checker_archetype->create(ecs_registry);
	ecs::command::place(ecs_registry, color_checker, {-10, -10});
	auto& cc_transform = ecs_registry.get<ecs::transform_component>(color_checker);
	cc_transform.local.scale *= 10.0f;
	cc_transform.local.rotation = math::angle_axis(math::radians(-90.0f), {1, 0, 0});
	
	// Setup camera focal point
	ecs::transform_component focal_point_transform;
	focal_point_transform.local = math::identity_transform<float>;
	focal_point_transform.warp = true;
	ecs::camera_follow_component focal_point_follow;
	ecs::snap_component focal_point_snap;
	focal_point_snap.ray = {float3{0, 10000, 0}, float3{0, -1, 0}};
	focal_point_snap.warp = false;
	focal_point_snap.relative = true;
	focal_point_snap.autoremove = false;
	ecs_registry.assign_or_replace<ecs::transform_component>(ctx->focal_point_entity, focal_point_transform);
	ecs_registry.assign_or_replace<ecs::camera_follow_component>(ctx->focal_point_entity, focal_point_follow);
	ecs_registry.assign_or_replace<ecs::snap_component>(ctx->focal_point_entity, focal_point_snap);
	
	// Setup camera
	ctx->overworld_camera->look_at({0, 0, 1}, {0, 0, 0}, {0, 1, 0});
	ctx->camera_system->set_camera(ctx->overworld_camera);
	
	ctx->overworld_scene->update_tweens();
	
	// Allocate a nest
	nest* nest = new ::nest();
	
	// Setup initial nest parameters
	float tunnel_radius = 1.15f;
	nest->set_tunnel_radius(tunnel_radius);
	nest::shaft* central_shaft = nest->get_central_shaft();
	central_shaft->chirality = 1.0f;
	central_shaft->rotation = math::radians(0.0f);
	central_shaft->depth = {0.0f, 200.0f};
	central_shaft->radius = {15.0f, 15.0f};
	central_shaft->pitch = {40.0f, 40.0f};
	central_shaft->translation = {{{0.0f, 0.0f}, {0.0f, 0.0f}}};
	central_shaft->current_depth = 0.0f;
	for (std::size_t i = 0; i < 4; ++i)
	{
		nest::chamber chamber;
		chamber.shaft = central_shaft;
		chamber.depth = (i + 1) * 50.0f;
		chamber.rotation = math::radians(0.0f);
		chamber.inner_radius = 4.0f;
		chamber.outer_radius = 10.0f;
		central_shaft->chambers.push_back(chamber);
	}
	
	// Dig nest shafts
	float shift = 0.1f;
	for (int i = 0; i < 800; ++i)
	{
		ecs::cavity_component cavity;
		cavity.position = nest->extend_shaft(*nest->get_central_shaft());
		cavity.position += float3{math::random(-shift, shift), math::random(-shift, shift), math::random(-shift, shift)};
		cavity.radius = tunnel_radius * math::random(1.0f, 1.1f);

		ecs_registry.assign<ecs::cavity_component>(ecs_registry.create(), cavity);
	}

	// Dig nest chambers
	/*
	for (int i = 0; i < central_shaft->chambers.size(); ++i)
	{
		for (int j = 0; j < 150; ++j)
		{
			ecs::cavity_component cavity;
			cavity.position = nest->expand_chamber(central_shaft->chambers[i]);
			cavity.position += float3{math::random(-shift, shift), math::random(-shift, shift), math::random(-shift, shift)};
			cavity.radius = tunnel_radius * math::random(1.0f, 1.1f);

			ecs_registry.assign<ecs::cavity_component>(ecs_registry.create(), cavity);
		}
	}
	*/
	
	// Place larva in chamber
	{
		auto larva = larva_archetype->create(ecs_registry);
		ecs::command::assign_render_layers(ecs_registry, larva, 1);
		ecs::command::warp_to(ecs_registry, larva, {50, 0.1935f, 0});
		//auto& transform = ecs_registry.get<ecs::transform_component>(larva_entity);
		//transform.transform = math::identity_transform<float>;
		//transform.transform.translation = nest->get_shaft_position(*central_shaft, central_shaft->depth[1]);
		//transform.transform.translation.y -= 1.0f;
	}
	
	ecs::control_system* control_system = ctx->control_system;
	control_system->update(0.0, 0.0);
	control_system->set_nest(nest);
	
	// Start fade in
	ctx->fade_transition->transition(1.0f, true, ease<float>::in_quad);

	logger->pop_task(EXIT_SUCCESS);
	
	std::string biome_name = (*ctx->strings)[ctx->biome->name];
	logger->log("Entered biome \"" + biome_name + "\"");
	
	
	std::srand(std::time(nullptr));
	//auto rng = [](){ return std::rand(); };
	
	std::random_device rd;
	std::mt19937 rng(rd());
	
	
	std::string sequence_a = "CCTTGCCCTTTGGGTCGCCCCCCTAG";
	std::string sequence_b = "ATGTTTCCCGAAGGGTAG";
	std::string sequence_c = "AAATGCCCCCCCCCCCCCCCCCCCCCCCCCCCTAGAAAAAAAAA";
	std::string orf_a;
	std::string protein_a;
	std::string protein_b;
	std::string protein_c;
	
	
	std::cout << "sequence a: " << sequence_a << std::endl;
	genetics::sequence::transcribe(sequence_a.begin(), sequence_a.end(), sequence_a.begin());
	std::cout << "sequence a: " << sequence_a << std::endl;
	
	std::string complement;
	genetics::sequence::rna::complement(sequence_a.begin(), sequence_a.end(), std::back_inserter(complement));
	std::cout << "complement: "  << complement << std::endl;
	
	auto orf = genetics::sequence::find_orf(sequence_a.begin(), sequence_a.end(), genetics::standard_code);
	if (orf.start != sequence_a.end())
	{
		std::copy(orf.start, orf.stop, std::back_inserter(orf_a));
		std::cout << "orf      a: " << orf_a << std::endl;
		
		genetics::sequence::translate(orf.start, orf.stop, std::back_inserter(protein_a), genetics::standard_code);
		std::cout << "protein  a: " << protein_a << std::endl;
	}
	
	protein_b = "MFFFFP";
	protein_c = "MFFFYP";
	int score;

	std::cout << std::endl;
	std::cout << "protein_b: " << protein_b << std::endl;
	std::cout << "protein_c: " << protein_c << std::endl;
	
	score = genetics::protein::score(protein_b.begin(), protein_b.end(), protein_c.begin(), genetics::matrix::blosum62<int>);
	std::cout << "score blosum62: " << score << std::endl;
	
	score = genetics::protein::score(protein_b.begin(), protein_b.end(), protein_c.begin(), genetics::matrix::blosum80<int>);
	std::cout << "score blosum80: " << score << std::endl;
	
	
	std::cout << "identity  : " << genetics::protein::identity<float>(protein_b.begin(), protein_b.end(), protein_c.begin()) << std::endl;
	std::cout << "similarity62: " << genetics::protein::similarity<float>(protein_b.begin(), protein_b.end(), protein_c.begin(), genetics::matrix::blosum62<int>) << std::endl;
	std::cout << "similarity80: " << genetics::protein::similarity<float>(protein_b.begin(), protein_b.end(), protein_c.begin(), genetics::matrix::blosum80<int>) << std::endl;
	
	
}

void play_state_exit(game_context* ctx)
{
	debug::logger* logger = ctx->logger;
	logger->push_task("Exiting play state");
	
	logger->pop_task(EXIT_SUCCESS);
}