Test(msg_ack, clone_ack)
{
AckRecord *t = ack_record_new();
t->init(t);
LogMessage *cloned = create_clone(t->original, &t->path_options);
log_msg_drop(cloned, &t->path_options, AT_PROCESSED);
cr_assert_not(t->acked);
t->deinit(t);
cr_assert(t->acked);
ack_record_free(t);
}
bool ProcessTwoBreakAndClone<graph_pack_t>::run(graph_pack_t & graph_pack) {
bool isChanged = false;
size_t number_rear = 0; // number of rearrangements
do {
number_rear = 0;
for (vertex_t const & x : graph_pack.graph) {
mularcs_t const & mularcs = graph_pack.get_all_adjacent_multiedges(x);
if (graph_pack.is_duplication_vertex(x) || (mularcs.begin()->second == graph_pack.multicolors.get_complete_color())) {
continue;
}
bool found = false;
for (auto im = mularcs.cbegin(); (im != mularcs.cend()) && !found; ++im) {
vertex_t const & y = im->first; // Q == im->second - color of central edge
if (y == Infty || graph_pack.is_duplication_vertex(y)) {
continue;
}
if (!graph_pack.is_mobility_edge(x, y)) {
mularcs_t mularcs_x = graph_pack.get_all_adjacent_multiedges_with_info(x);
mularcs_x.erase(y);
mularcs_t mularcs_y = graph_pack.get_all_adjacent_multiedges_with_info(y);
mularcs_y.erase(x);
/*SPLIT ALL EDGES ON MOBILE AND NON MOBILE*/
set_arc_t mobile_edges_x;
set_arc_t non_mobile_edges_x;
split_by_mobile_property(graph_pack, x, mularcs_x, mobile_edges_x, non_mobile_edges_x);
set_arc_t mobile_edges_y;
set_arc_t non_mobile_edges_y;
split_by_mobile_property(graph_pack, y, mularcs_y, mobile_edges_y, non_mobile_edges_y);
/*CREATE POSSIBLE MOBILE CLONES AND TWOBREAKS*/
std::map<ind_arcs_t, std::set<ind_arcs_t> > classes = split_by_colors(mularcs_x, mularcs_y);
std::vector<twobreak_t> possible_twobreaks;
std::vector<clone_t> possible_clones;
bool is_all_good = true;
for (auto const & color_set : classes) {
mularcs_t mularcs_left;
mularcs_t mularcs_right;
for (auto const & color : color_set.second) {
if (color.second == 0) {
mularcs_left.insert(color.first.first, color.first.second);
} else {
mularcs_right.insert(color.first.first, color.first.second);
}
}
if (mularcs_left.size() == 1 && mularcs_right.size() == 1 && mularcs_left.cbegin()->second == mularcs_right.cbegin()->second) {
mcolor_t const & color = mularcs_left.cbegin()->second;
if (mobile_edges_x.count(*mularcs_left.cbegin()) != 0
&& mobile_edges_y.count(*mularcs_right.cbegin()) != 0
&& graph_pack.multicolors.is_vec_T_consistent_color(color)) {
vertex_t const & u = mularcs_left.cbegin()->first;
vertex_t const & v = mularcs_right.cbegin()->first;
twobreak_t twobreak(x, u, y, v, color);
possible_twobreaks.push_back(twobreak);
} else {
is_all_good = false;
}
} else if (mularcs_left.size() == 1 && mularcs_left.cbegin()->second == mularcs_right.union_multicolors()) {
auto result = create_clone(graph_pack, mularcs_left, x, y, mularcs_right, mobile_edges_x, mobile_edges_y);
if (result.first) {
possible_clones.push_back(result.second);
} else {
is_all_good = false;
}
} else if (mularcs_right.size() == 1 && mularcs_right.cbegin()->second == mularcs_left.union_multicolors()) {
auto result = create_clone(graph_pack, mularcs_right, y, x, mularcs_left, mobile_edges_y, mobile_edges_x);
if (result.first) {
possible_clones.push_back(result.second);
} else {
is_all_good = false;
}
} else {
is_all_good = false;
}
}
/*START TO WORK WITH MAIN ALGORITHM*/
/*CASE 1: Create complete edge*/
if (is_all_good) {
std::set<mcolor_t> actions = get_worked_colors(possible_twobreaks);
std::set<mcolor_t> clone_action = get_worked_colors(possible_clones);
actions.insert(clone_action.begin(), clone_action.end());
if (is_good_actions(graph_pack, actions)) {
//std::cerr << "Do cloning and two-break in first case" << std::endl;
for (auto const & twobreak : possible_twobreaks) {
//std::cerr << twobreak.get_vertex(0) << " " << twobreak.get_vertex(1) << " " << twobreak.get_vertex(2) << " " << twobreak.get_vertex(3) << " " << genome_match::mcolor_to_name(twobreak.get_mcolor()) << std::endl;
graph_pack.apply(twobreak);
found = true;
++number_rear;
}
for (auto const & clone : possible_clones) {
graph_pack.apply(clone);
found = true;
++number_rear;
}
if (found) {
assert(graph_pack.get_all_multicolor_edge(x, y).empty() || graph_pack.get_all_multicolor_edge(x, y) == graph_pack.multicolors.get_complete_color());
}
}
}
/*CASE 2: Create min T-consistent color*/
if (!found) {
mcolor_t additional_color = graph_pack.multicolors.get_min_addit_color_for_tc(graph_pack.get_all_multicolor_edge(x, y));
if (!additional_color.empty() && additional_color != graph_pack.multicolors.get_complete_color()) {
std::vector<twobreak_t> included_twobreaks;
std::vector<clone_t> included_clones;
for (auto twobreak = possible_twobreaks.cbegin(); (twobreak != possible_twobreaks.cend()) && !additional_color.empty(); ++twobreak) {
mcolor_t action_color = twobreak->get_mcolor();
if (additional_color.includes(action_color) && graph_pack.multicolors.is_vec_T_consistent_color(action_color)) {
included_twobreaks.push_back(*twobreak);
additional_color = mcolor_t(additional_color, action_color, mcolor_t::Difference);
}
}
for (auto clone = possible_clones.cbegin(); (clone != possible_clones.cend()) && !additional_color.empty(); ++clone) {
mcolor_t action_color = clone->get_mcolor();
if (additional_color.includes(action_color) && graph_pack.multicolors.is_vec_T_consistent_color(action_color)) {
included_clones.push_back(*clone);
additional_color = mcolor_t(additional_color, action_color, mcolor_t::Difference);
}
}
if (additional_color.empty()) {
std::set<mcolor_t> actions = get_worked_colors(included_twobreaks);
std::set<mcolor_t> clone_action = get_worked_colors(included_clones);
actions.insert(clone_action.begin(), clone_action.end());
if (is_good_actions(graph_pack, actions)) {
for (auto const & twobreak : included_twobreaks) {
graph_pack.apply(twobreak);
found = true;
++number_rear;
}
for (auto const & clone : included_clones) {
graph_pack.apply(clone);
found = true;
++number_rear;
}
if (found) {
assert(graph_pack.get_all_multicolor_edge(x, y).empty() || graph_pack.multicolors.is_T_consistent_color(graph_pack.get_all_multicolor_edge(x, y)));
}
}
}
}
}
}
}
}
if (number_rear != 0) {
isChanged = true;
}
} while (number_rear > 0);
return isChanged;
}
void
APITests::testBasicOperations(int width, int height) {
const PixelFormat format = PF_R8G8B8A8;
const int bpp = 4;
auto_ptr<Image> image(CreateImage(width, height, format));
CPPUNIT_ASSERT(image->getWidth() == width);
CPPUNIT_ASSERT(image->getHeight() == height);
CPPUNIT_ASSERT(image->getFormat() == format);
// verify that the image is black
byte* pixels = (byte*)image->getPixels();
for (int i = 0; i < width * height * bpp; ++i) {
CPPUNIT_ASSERT(pixels[i] == 0);
}
// fill the image with random pixels
for (int i = 0; i < width * height * bpp; ++i) {
pixels[i] = rand() % 256;
}
auto_ptr<Image> create_clone(
CreateImage(image->getWidth(), image->getHeight(),
image->getFormat(), image->getPixels()));
CPPUNIT_ASSERT(create_clone.get() != 0);
CPPUNIT_ASSERT(image->getWidth() == create_clone->getWidth());
CPPUNIT_ASSERT(image->getHeight() == create_clone->getHeight());
CPPUNIT_ASSERT(image->getFormat() == create_clone->getFormat());
CPPUNIT_ASSERT(memcmp(image->getPixels(),
create_clone->getPixels(),
width * height * bpp) == 0);
// clone the image (use same pixel format)
auto_ptr<Image> identical_clone(CloneImage(image.get()));
CPPUNIT_ASSERT(image->getWidth() == identical_clone->getWidth());
CPPUNIT_ASSERT(image->getHeight() == identical_clone->getHeight());
CPPUNIT_ASSERT(image->getFormat() == identical_clone->getFormat());
CPPUNIT_ASSERT(memcmp(image->getPixels(),
identical_clone->getPixels(),
width * height * bpp) == 0);
// clone the image, removing the alpha channel
auto_ptr<Image> other_clone(CloneImage(identical_clone.get(), PF_R8G8B8));
CPPUNIT_ASSERT(image->getWidth() == other_clone->getWidth());
CPPUNIT_ASSERT(image->getHeight() == other_clone->getHeight());
CPPUNIT_ASSERT(other_clone->getFormat() == PF_R8G8B8);
byte* image_p = (byte*)image->getPixels();
byte* other_p = (byte*)other_clone->getPixels();
for (int i = 0; i < width * height; ++i) {
CPPUNIT_ASSERT(*image_p++ == *other_p++);
CPPUNIT_ASSERT(*image_p++ == *other_p++);
CPPUNIT_ASSERT(*image_p++ == *other_p++);
++image_p; // skip alpha
}
// flip the image
// clone source first, since flip frees the original
auto_ptr<Image> flip_none(FlipImage(CloneImage(image.get()), 0));
auto_ptr<Image> flip_x (FlipImage(CloneImage(image.get()), CA_X));
auto_ptr<Image> flip_y (FlipImage(CloneImage(image.get()), CA_Y));
auto_ptr<Image> flip_xy (FlipImage(CloneImage(image.get()), CA_X | CA_Y));
AssertImagesEqual("No flipping", flip_none.get(), image.get());
CPPUNIT_ASSERT(flip_x.get() != 0);
CPPUNIT_ASSERT(width == flip_x->getWidth());
CPPUNIT_ASSERT(height == flip_x->getHeight());
CPPUNIT_ASSERT(format == flip_x->getFormat());
CPPUNIT_ASSERT(flip_y.get() != 0);
CPPUNIT_ASSERT(width == flip_y->getWidth());
CPPUNIT_ASSERT(height == flip_y->getHeight());
CPPUNIT_ASSERT(format == flip_y->getFormat());
CPPUNIT_ASSERT(flip_xy.get() != 0);
CPPUNIT_ASSERT(width == flip_xy->getWidth());
CPPUNIT_ASSERT(height == flip_xy->getHeight());
CPPUNIT_ASSERT(format == flip_xy->getFormat());
const byte* flip_x_pixels = (const byte*)flip_x->getPixels();
const byte* flip_y_pixels = (const byte*)flip_y->getPixels();
const byte* flip_xy_pixels = (const byte*)flip_xy->getPixels();
for (int h = 0; h < height; h++) {
for (int w = 0; w < width; w++) {
const int image_index = (h * width + w) * bpp;
const int opp_w = width - 1 - w;
const int opp_h = height - 1 - h;
const int flip_x_index = (opp_h * width + w) * bpp;
const int flip_y_index = (h * width + opp_w) * bpp;
const int flip_xy_index = (opp_h * width + opp_w) * bpp;
for (int p = 0; p < bpp; p++) {
CPPUNIT_ASSERT(pixels[image_index] == flip_x_pixels [flip_x_index]);
CPPUNIT_ASSERT(pixels[image_index] == flip_y_pixels [flip_y_index]);
CPPUNIT_ASSERT(pixels[image_index] == flip_xy_pixels[flip_xy_index]);
}
}
}
}
