diff --git a/.gitignore b/.gitignore
index 5e25991..1570b61 100644
--- a/.gitignore
+++ b/.gitignore
@@ -3,9 +3,38 @@ app/
ascii.dSYM/
build_cmake/
builddir/
-.DS_Store
+*.DS_Store
+__pycache__/
+*.pyc
+.idea/ # JetBrains IDE
+.vscode/ # Visual Studio Code
+*.suo # VS Code user settings
+*.swp # Vim swap files
+*.log
+*.tmp
+*.bak # backup files
+venv/ #
+env/ #
+*.egg-info/ # Python egg files
+*.eggs/
-python/
+python/comparison_fig/
+python/test_data_from_openglbuffer/
+python/graphData_constructor.py
+python/open_plot_saved_compressed_extension.py
+python/open_plot_saved_compressed_hic.py
+python/open_plot_saved_textures.py
+python/test_cal_mass_center.py
+python/test_compresed_data.py
+python/test.py
+python/compressed_data_test/
+python/autoCut/models/cfgs/error_model.pth
+python/autoCut/models/cfgs/chr_model.pth
+python/autoCut/models/swin/mmdet.egg-info/*
+python/classic_cut/show_hic_density.py
+python/colormap_colorblind/*
+python/greedy_topo_sort_test/*
+python/linear_weight_test/*
subprojects/eigen
subprojects/glfw
@@ -36,6 +65,7 @@ logs/
.gitignore
ico_design/icon_design.ai
+ico_design/icon_v1.iconset/
include/GLFW/glfw3.h
include/GLFW/glfw3native.h
include/libdeflate.h
@@ -45,3 +75,10 @@ PretextViewAI.zip
test_data/
subprojects/libtorch(not needed in this version)/
+
+hic_figures/
+auto_cut_output/
+python/autoCut/models/swin/README.md
+python/autoCut/models/swin/mmcv_custom/
+
+yahs_archive/
\ No newline at end of file
diff --git a/.gitmodules b/.gitmodules
index 3e82001..cfbf012 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -14,3 +14,7 @@
[submodule "subprojects/pytorch_scatter"]
path = subprojects/pytorch_scatter
url = https://github.com/guanshaoheng/pytorch_scatter.git
+
+[submodule "subprojects/fmt"]
+ path = subprojects/fmt
+ url = https://github.com/fmtlib/fmt.git
diff --git a/CMakeLists.txt b/CMakeLists.txt
index f898a7c..e800b11 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,10 +1,12 @@
cmake_minimum_required(VERSION 3.17)
-project(PretextView VERSION "1.0.1")
+project(PretextView VERSION "1.0.3")
-option(FORCE_MAC_X86 "Force macOS x86_64 build" OFF)
+option(FORCE_MAC_X86 "Force macOS x86_64 build" OFF)
option(BUILD_UNIVERSAL "Build macOS universal binary" OFF)
option(WITH_TORCH "Find and link torch lib" OFF)
+option(DEBUG_OUTPUT_LIKELIHOOD_TABLE "Output likelihood table to file" OFF)
+option(DEBUG_OUTPUT_PIXEL_CUT_FILE "Output the pixel cut files" OFF)
set(CMAKE_C_STANDARD 17)
set(CMAKE_CXX_STANDARD 17)
@@ -14,7 +16,6 @@ set(CMAKE_CXX_STANDARD_REQUIRED ON)
set(target_name PretextViewAI)
if (APPLE)
-
if(FORCE_MAC_X86)
message(STATUS "Forcing x86_64 architecture build")
set(CMAKE_OSX_ARCHITECTURES "x86_64" CACHE STRING "Build architectures" FORCE)
@@ -55,6 +56,9 @@ else()
endif()
endif()
+if (MSVC)
+ add_compile_options(/utf-8) # force MSVC to use UTF-8
+endif()
message(STATUS "Install path: ${CMAKE_INSTALL_PREFIX}")
@@ -76,11 +80,26 @@ include_directories(
subprojects/glfw/include
subprojects/libdeflate
subprojects/glm
+ subprojects/fmt/include
)
add_subdirectory(subprojects/glfw)
add_subdirectory(subprojects/glm)
+find_library(
+ lib_fmt
+ NAMES fmt libfmt
+ PATHS
+ subprojects/fmt/build
+ subprojects/fmt/build/debug
+ subprojects/fmt/build/Release
+ subprojects/fmt/build/release)
+if(NOT lib_fmt)
+ message(FATAL_ERROR "lib_fmt not found")
+else()
+ message(STATUS "lib_fmt found: ${lib_fmt}")
+endif()
+
find_library(
lib_deflate_static
@@ -96,6 +115,9 @@ else()
message(STATUS "lib_deflate_static found: ${lib_deflate_static}")
endif()
+add_library(lib_yahs STATIC
+ src/yahs_sort.cpp
+)
# set(CMAKE_PREFIX_PATH "subprojects/libtorch/share/cmake/Torch")
if (WITH_TORCH)
@@ -111,14 +133,16 @@ if (WITH_TORCH)
target_link_libraries(
sortlib PUBLIC
${TORCH_LIBRARIES}
- ${torchscatter})
+ ${torchscatter}
+ lib_yahs)
else()
message(STATUS "Libtorch: Build without libtorch")
add_library(sortlib STATIC src/frag_sort.cpp )
+ target_link_libraries(sortlib PRIVATE lib_yahs)
endif()
-add_library(glad STATIC glad.c)
+add_library(glad STATIC src/glad.c)
add_library(utilsPretextView STATIC src/utilsPretextView.cpp)
add_library(copy_texture STATIC src/copy_texture.cpp)
# target_link_libraries(copy_texture PRIVATE Eigen3::Eigen)
@@ -141,6 +165,7 @@ else()
MACOSX_BUNDLE_INFO_PLIST "${CMAKE_SOURCE_DIR}/Info.plist"
)
endif()
+
target_compile_definitions(${target_name} PRIVATE PV=${PROJECT_VERSION})
if (CMAKE_BUILD_TYPE STREQUAL "Debug")
target_compile_definitions(${target_name} PRIVATE DEBUG)
@@ -149,9 +174,15 @@ if (CMAKE_BUILD_TYPE STREQUAL "Debug")
else()
message(STATUS "Release version: flag (${CMAKE_BUILD_TYPE}) without DEBUG")
endif()
+if (DEBUG_OUTPUT_LIKELIHOOD_TABLE)
+ message(STATUS "Debug version: flag (${CMAKE_BUILD_TYPE}) with DEBUG_OUTPUT_LIKELIHOOD_TABLE")
+ target_compile_definitions(${target_name} PRIVATE DEBUG_OUTPUT_LIKELIHOOD_TABLE)
+endif()
+
target_link_libraries(
${target_name} PRIVATE
${lib_deflate_static}
+ ${lib_fmt}
sortlib
glm
glad
@@ -159,6 +190,7 @@ target_link_libraries(
copy_texture
imgui
glfw
+ lib_yahs
)
if (APPLE)
diff --git a/Info.plist b/Info.plist
index 1d41b42..d9961f5 100644
--- a/Info.plist
+++ b/Info.plist
@@ -13,7 +13,7 @@
CFBundleIconFile
icon.icns
CFBundleShortVersionString
- 1.0.1
+ 1.0.3
CFBundleInfoDictionaryVersion
6.0
CFBundlePackageType
diff --git a/PretextView.cpp b/PretextView.cpp
index 440a1a5..ea20743 100644
--- a/PretextView.cpp
+++ b/PretextView.cpp
@@ -99,11 +99,15 @@ SOFTWARE.
#pragma clang diagnostic pop
-#include "Resources.cpp"
+#include "Resources.cpp" // defines icons, fonts
#include "genomeData.h"
#include "showWindowData.h"
-
+#include "hic_figure.h"
+#include "ai_cut_json_parse.h"
+#include "frag_cut_calculation.h"
+#include "grey_out_settings.h"
+#include "user_profile_settings.h"
#include "shaderSource.h"
/*
@@ -363,6 +367,16 @@ QuadTree_Data;
#endif
+global_variable
+Extension_Graph_Data * pixel_density_extension = nullptr;
+
+global_variable
+TexturesArray4AI* textures_array_ptr = nullptr;
+
+global_variable
+FragCutCal* frag_cut_cal_ptr = nullptr;
+
+
struct
CustomColorMapOrder
{
@@ -559,6 +573,10 @@ meta_mode_data *
Extension_Mode_Data;
+/*
+用于显示在input sequences中点击后选中的片段的名字，
+显示label持续 5 秒钟
+*/
struct selected_sequence_cover_countor
{
s32 original_contig_index;
@@ -657,10 +675,14 @@ Loading = 0;
global_variable
u32
-Yahs_sorting = 0;
+auto_sort_state = 0;
+
+global_variable
+u32
+auto_cut_state = 0;
-global_variable s32 ai_sort_button = 0;
-global_variable s32 yahs_sort_button = 0;
+global_variable s32 auto_cut_button = 0;
+global_variable s32 auto_sort_button = 0;
global_function
@@ -718,16 +740,14 @@ setContactMatrixVertexArray(contact_matrix* Contact_Matrix_, bool copy_flag=fals
global_function
void
-prepare_before_copy(f32 *original_control_points);
+prepare_before_copy(f32 *original_color_control_points);
global_function
void
-restore_settings_after_copy(const f32 *original_control_points);
+restore_settings_after_copy(const f32 *original_color_control_points);
-#define Max_Number_of_Contigs 4096
-
global_variable
meta_data *
@@ -777,7 +797,9 @@ Default_Tags[] =
"U",
"B1",
"B2",
- "B3"
+ "B3",
+ "FalseDuplicate",
+ "Primary"
};
@@ -788,13 +810,13 @@ Map_State;
#include "copy_texture.h"
// define the struct to store the ai model mask
-std::unique_ptr frag_sort_method = nullptr;
+FragSortTool* frag_sort_method = new FragSortTool();
global_variable auto auto_curation_state = AutoCurationState();
global_function
void
-UpdateContigsFromMapState() // todo reading 从map的状态更新contigs
+UpdateContigsFromMapState() // reading 从map的状态更新contigs
{
u32 lastScaffID = Map_State->scaffIds[0]; // 第一个scaff的编号
u32 scaffId = lastScaffID ? 1 : 0; //
@@ -816,13 +838,17 @@ UpdateContigsFromMapState() // todo reading 从map的状态更新contigs
++length; // current fragment length
pixelIdx = index + 1; // 像素点编号， 加一因为第一个已经用来初始化了
- u32 id = Map_State->originalContigIds[pixelIdx]; // 像素点的 contig id
+ u32 id = Map_State->originalContigIds[pixelIdx]; // 像素点的 original contig id, 这里 不使用 % Max_Number_of_Contigs的值是为了区分后面cut之后的片段
u32 coord = Map_State->contigRelCoords[pixelIdx]; // 像素点的局部坐标
- if (id != lastId || (inverted && coord != (lastCoord - 1)) || (!inverted && coord != (lastCoord + 1))) // 如果不是一个连续片段
+ if (
+ id != lastId ||
+ (inverted && coord != (lastCoord - 1)) ||
+ (!inverted && coord != (lastCoord + 1))
+ ) // 如果不是一个连续片段
{
- Original_Contigs[lastId].contigMapPixels[Original_Contigs[lastId].nContigs] = pixelIdx - 1 - (length >> 1); // update Original_Contigs: contigMapPixels
- Original_Contigs[lastId].nContigs++; // update Original_Contigs: nContigs, contigMapPixels
+ Original_Contigs[lastId % Max_Number_of_Contigs].contigMapPixels[Original_Contigs[lastId%Max_Number_of_Contigs].nContigs] = pixelIdx - 1 - (length >> 1); // update Original_Contigs: contigMapPixels
+ Original_Contigs[lastId % Max_Number_of_Contigs].nContigs++; // update Original_Contigs: nContigs, contigMapPixels
contig *last_cont = Contigs->contigs_arr + contigPtr; // 获取上一个contig的指针， 并且给contigPtr + 1
contigPtr++;
@@ -860,7 +886,7 @@ UpdateContigsFromMapState() // todo reading 从map的状态更新contigs
if (contigPtr < Max_Number_of_Contigs) // contigptr 小于 Number_of_Original_Contigs
// 更新最后一个contig的最后一个片段信息
{
- (Original_Contigs + lastId)->contigMapPixels[(Original_Contigs + lastId)->nContigs++] = pixelIdx - 1 - (length >> 1);
+ (Original_Contigs + lastId % Max_Number_of_Contigs)->contigMapPixels[(Original_Contigs + lastId % Max_Number_of_Contigs)->nContigs++] = pixelIdx - 1 - (length >> 1);
++length;
contig *cont = Contigs->contigs_arr + contigPtr++;
@@ -896,7 +922,7 @@ RebuildContig(u32 pixel)
for (;;)
{
u32 contigId = Map_State->contigIds[pixel];
- u32 origContigId = Map_State->originalContigIds[pixel];
+ u32 origContigId = Map_State->get_original_contig_id(pixel);
u32 top = (u32)pixel;
while (top && (Map_State->contigIds[top - 1] == contigId)) --top;
@@ -914,7 +940,7 @@ RebuildContig(u32 pixel)
u08 fragmented = 0;
ForLoop(Number_of_Pixels_1D)
{
- if ((Map_State->contigIds[index] != contigId) && (Map_State->originalContigIds[index] == origContigId))
+ if ((Map_State->contigIds[index] != contigId) && (Map_State->get_original_contig_id(index) == origContigId))
{
fragmented = 1;
break;
@@ -929,7 +955,7 @@ RebuildContig(u32 pixel)
u32 otherPixel = 0;
ForLoop(Number_of_Pixels_1D)
{
- if ((Map_State->originalContigIds[index] == origContigId) && (Map_State->contigRelCoords[index] == (contigTopCoord - 1)))
+ if ((Map_State->get_original_contig_id(index) == origContigId) && (Map_State->contigRelCoords[index] == (contigTopCoord - 1)))
{
otherPixel = index;
break;
@@ -963,7 +989,7 @@ RebuildContig(u32 pixel)
u32 otherPixel = 0;
ForLoop(Number_of_Pixels_1D)
{
- if ((Map_State->originalContigIds[index] == origContigId) && (Map_State->contigRelCoords[index] == (contigBottomCoord + 1)))
+ if ((Map_State->get_original_contig_id(index) == origContigId) && (Map_State->contigRelCoords[index] == (contigBottomCoord + 1)))
{
otherPixel = index;
break;
@@ -1627,7 +1653,7 @@ global_function
void
MouseMove(GLFWwindow* window, f64 x, f64 y)
{
- if (Loading || Yahs_sorting)
+ if (Loading || auto_sort_state || auto_cut_state)
{
return;
}
@@ -1639,7 +1665,7 @@ MouseMove(GLFWwindow* window, f64 x, f64 y)
if (UI_On)
{
}
- else
+ else // ui_on == false
{
if (Edit_Mode)
{
@@ -1664,24 +1690,51 @@ MouseMove(GLFWwindow* window, f64 x, f64 y)
u32 pixel1 = (u32)((f64)nPixels * (0.5 + (f64)wx));
u32 pixel2 = (u32)((f64)nPixels * (0.5 + (f64)wy));
+
+ // 防止在尾部溢出
+ pixel1 = my_Max(0, my_Min(nPixels - 1, pixel1));
+ pixel2 = my_Max(0, my_Min(nPixels - 1, pixel2));
- u32 contig = Map_State->contigIds[pixel1];
+ u32 contig = Map_State->contigIds[pixel1];
if (!Edit_Pixels.editing && !Edit_Pixels.selecting && Map_State->contigIds[pixel2] != contig)
{
u32 testPixel = pixel1;
u32 testContig = contig;
- while (testContig == contig)
+ while (testContig == contig) // move testContig to the 1 before the first or 1 after the last pixel of the contig
{
- testContig = pixel1 < pixel2 ? Map_State->contigIds[++testPixel] : Map_State->contigIds[--testPixel];
+
+ if (pixel1 < pixel2)
+ {
+ testPixel ++ ;
+ }
+ else
+ {
+ testPixel -- ;
+ }
+
+ testContig = Map_State->contigIds[testPixel];
+
if (testPixel == 0 || testPixel >= (nPixels - 1)) break;
+
+ // testContig = pixel1 < pixel2 ? Map_State->contigIds[++testPixel] : Map_State->contigIds[--testPixel];
+ // if (testPixel == 0 || testPixel >= (nPixels - 1)) break;
+ }
+ if (Map_State->contigIds[testPixel] == contig)
+ {
+ pixel2 = testPixel;
+ }
+ else
+ {
+ pixel2 = pixel1 < pixel2 ? testPixel - 1 : testPixel + 1;
}
- pixel2 = pixel1 < pixel2 ? testPixel - 1 : testPixel + 1;
}
+
- if (Edit_Pixels.selecting)
+ if (Edit_Pixels.selecting) // select the contig
{
- Edit_Pixels.selectPixels.x = my_Max(pixel1, my_Max(Edit_Pixels.selectPixels.x, Edit_Pixels.selectPixels.y));
+ Edit_Pixels.selectPixels.x = my_Max(pixel1, my_Max(Edit_Pixels.selectPixels.x, Edit_Pixels.selectPixels.y)); // used to select multiple contigs with pressing space and dragging the mouse
+ // Edit_Pixels.selectPixels.x = pixel1;
while( Edit_Pixels.selectPixels.x < (Number_of_Pixels_1D - 1) &&
((Edit_Pixels.scaffSelecting && Map_State->scaffIds[Edit_Pixels.selectPixels.x] && Map_State->scaffIds[Edit_Pixels.selectPixels.x] == Map_State->scaffIds[1 + Edit_Pixels.selectPixels.x] ) ||
Map_State->contigIds[Edit_Pixels.selectPixels.x] == Map_State->contigIds[1 + Edit_Pixels.selectPixels.x]))
@@ -1690,6 +1743,7 @@ MouseMove(GLFWwindow* window, f64 x, f64 y)
}
Edit_Pixels.selectPixels.y = my_Min(pixel1, my_Min(Edit_Pixels.selectPixels.x, Edit_Pixels.selectPixels.y));
+ // Edit_Pixels.selectPixels.y = pixel1;
while( Edit_Pixels.selectPixels.y > 0 &&
((Edit_Pixels.scaffSelecting && Map_State->scaffIds[Edit_Pixels.selectPixels.y] && Map_State->scaffIds[Edit_Pixels.selectPixels.y] == Map_State->scaffIds[Edit_Pixels.selectPixels.y - 1]) || Map_State->contigIds[Edit_Pixels.selectPixels.y] == Map_State->contigIds[Edit_Pixels.selectPixels.y - 1]))
{
@@ -1733,7 +1787,7 @@ MouseMove(GLFWwindow* window, f64 x, f64 y)
Edit_Pixels.worldCoords.x = (f32)(((f64)((2 * Edit_Pixels.pixels.x) + 1)) / ((f64)(2 * nPixels))) - 0.5f;
Edit_Pixels.worldCoords.y = (f32)(((f64)((2 * Edit_Pixels.pixels.y) + 1)) / ((f64)(2 * nPixels))) - 0.5f;
}
- else
+ else // edit_pixels.editing == 0
{
if (netDelta || Global_Edit_Invert_Flag)
{
@@ -1928,15 +1982,16 @@ MouseMove(GLFWwindow* window, f64 x, f64 y)
}
}
-global_variable
-u08
-Mouse_Invert = 0;
-
global_variable
u08
Grey_Haplotigs = 1;
+global_variable
+GreyOutSettings* Grey_Out_Settings = nullptr;
+
+global_variable
+UserProfileSettings* user_profile_settings_ptr = nullptr;
global_variable
u08
@@ -1946,10 +2001,10 @@ global_function
void
Mouse(GLFWwindow* window, s32 button, s32 action, s32 mods)
{
- s32 primaryMouse = Mouse_Invert ? GLFW_MOUSE_BUTTON_RIGHT : GLFW_MOUSE_BUTTON_LEFT;
- s32 secondaryMouse = Mouse_Invert ? GLFW_MOUSE_BUTTON_LEFT : GLFW_MOUSE_BUTTON_RIGHT;
+ s32 primaryMouse = user_profile_settings_ptr->invert_mouse ? GLFW_MOUSE_BUTTON_RIGHT : GLFW_MOUSE_BUTTON_LEFT;
+ s32 secondaryMouse = user_profile_settings_ptr->invert_mouse ? GLFW_MOUSE_BUTTON_LEFT : GLFW_MOUSE_BUTTON_RIGHT;
- if (Loading || Yahs_sorting)
+ if (Loading || auto_sort_state)
{
return;
}
@@ -2079,7 +2134,7 @@ global_function
void
Scroll(GLFWwindow* window, f64 x, f64 y)
{
- if (Loading || Yahs_sorting)
+ if (Loading || auto_sort_state)
{
return;
}
@@ -2733,7 +2788,7 @@ Render() {
}
// Text / UI Rendering
- if (Contig_Name_Labels->on || Scale_Bars->on || Tool_Tip->on || UI_On || Loading || Yahs_sorting || Edit_Mode || Waypoint_Edit_Mode || Waypoints_Always_Visible || Scaff_Edit_Mode || Scaffs_Always_Visible || MetaData_Edit_Mode || MetaData_Always_Visible || graphNamesOn)
+ if (Contig_Name_Labels->on || Scale_Bars->on || Tool_Tip->on || UI_On || Loading || auto_sort_state || Edit_Mode || Waypoint_Edit_Mode || Waypoints_Always_Visible || Scaff_Edit_Mode || Scaffs_Always_Visible || MetaData_Edit_Mode || MetaData_Always_Visible || graphNamesOn)
{
f32 textNormalMat[16];
f32 textRotMat[16];
@@ -2839,7 +2894,7 @@ Render() {
if (rightPixel > 0.0f && leftPixel < width)
{
- const char *name = (const char *)(Original_Contigs + cont->originalContigId)->name;
+ const char *name = (const char *)(Original_Contigs + cont->get_original_contig_id())->name;
f32 x = (rightPixel + leftPixel) * 0.5f;
f32 y = my_Max(wy0, 0.0f) + 10.0f;
f32 textWidth = fonsTextBounds(FontStash_Context, x, y, name, 0, NULL);
@@ -2888,7 +2943,7 @@ Render() {
if (topPixel < height && bottomPixel > 0.0f)
{
- const char *name = (const char *)(Original_Contigs + cont->originalContigId)->name;
+ const char *name = (const char *)(Original_Contigs + cont->get_original_contig_id())->name;
f32 y = (topPixel + bottomPixel) * 0.5f;
f32 x = my_Max(wx0, 0.0f) + 10.0f;
f32 textWidth = fonsTextBounds(FontStash_Context, x, y, name, 0, NULL);
@@ -3311,7 +3366,7 @@ Render() {
}
}
- // label to show the selected sequence
+ // label to show the selected sequence 从 input sequences 里面选中的片段
if (Selected_Sequence_Cover_Countor.end_time > 0.)
{
f64 crt_time = GetTime();
@@ -3496,13 +3551,8 @@ Render() {
f32 end_fraction = (f32)auto_curation_state.get_end() /(f32)Number_of_Pixels_1D;
// selected frags into a string
- std::vector selected_frag_ids;
- auto_curation_state.get_selected_fragments(selected_frag_ids, Map_State, Number_of_Pixels_1D);
- std::stringstream ss;
- if (selected_frag_ids.size() > 0) ss << selected_frag_ids[0];
- for (u32 i = 1; i < selected_frag_ids.size(); i++) ss <<", " << selected_frag_ids[i] ;
- std::string selectedFragmentsStr = "Selected fragments number: " + std::to_string(selected_frag_ids.size());
- std::string start_and_end_pixel_str = "Select range: " + std::to_string(auto_curation_state.get_start()) + " - " + std::to_string(auto_curation_state.get_end());
+ SelectArea select_area;
+ auto_curation_state.get_selected_fragments(select_area, Map_State, Number_of_Pixels_1D, Contigs);
{ // draw the help text in the bottom right corner
fonsSetFont(FontStash_Context, Font_Bold);
@@ -3510,23 +3560,26 @@ Render() {
fonsVertMetrics(FontStash_Context, 0, 0, &lh);
fonsSetColor(FontStash_Context, FourFloatColorToU32(Scaff_Mode_Data->text));
- std::vector helpTexts = {
- (char *)"Select/Exclude area for sorting",
- (char *)"K: exit",
- (char *)"S: clear select area",
- (char *)"Q/W: quit/redo edit",
- (char *)"Space: YaHS sort",
- (char *)"Left Click: select/unselect the fragment",
- (char *)selectedFragmentsStr.c_str(),
- (char *)start_and_end_pixel_str.c_str()
+ std::vector helpTexts = {
+ "Select/Exclude area for sorting",
+ "F: exit",
+ "S: clear select area",
+ "C/Z: cut / cancel cut",
+ "Q/W: quit / redo edit",
+ "Space: Pixel sort",
+ "Left Click: un/select the fragment",
+ fmt::format("Up/Down: inc/dec Cut threshold: {:.4f}", auto_curation_state.auto_cut_threshold).c_str(),
+ fmt::format("Left/Right: change Sort Mode ({})", auto_curation_state.sort_mode_names[auto_curation_state.sort_mode]),
+ // fmt::format("Selected fragments number: {}", select_area.selected_frag_ids.size()),
+ // fmt::format("Select pixel range: {} - {}", auto_curation_state.get_start(), auto_curation_state.get_end())
};
f32 textBoxHeight = (f32)helpTexts.size() * (lh + 1.0f) - 1.0f;
f32 spacing = 10.0f;
f32 textWidth = 0.f;
- for (auto* i :helpTexts){
- textWidth = my_Max(textWidth, fonsTextBounds(FontStash_Context, 0, 0, i, 0, NULL));
+ for (const auto& i :helpTexts){
+ textWidth = my_Max(textWidth, fonsTextBounds(FontStash_Context, 0, 0, i.c_str(), 0, NULL));
}
textWidth = my_Min(textWidth, width - 2 * spacing);
@@ -3552,7 +3605,7 @@ Render() {
FontStash_Context,
width - spacing - textWidth,
height - spacing - textBoxHeight + (i * (lh + 1.0f)),
- helpTexts[i],
+ helpTexts[i].c_str(),
0);
}
}
@@ -3566,7 +3619,7 @@ Render() {
// draw the start & end point
{
f32 line_width = 0.002f / Camera_Position.z;
- f32 mask_color[4] = {1.0f, 0.f, 0.f, 0.8f};
+ f32 mask_color[4] = {1.0f, 0.f, 0.f, 0.8f}; // red
glUseProgram(Flat_Shader->shaderProgram);
glUniform4fv(Flat_Shader->colorLocation, 1, (GLfloat *)&mask_color);
for (auto loc_fraction : {start_fraction, end_fraction})
@@ -3585,7 +3638,7 @@ Render() {
// draw the cover on selected area
{
- f32 mask_color[4] = {0.906f, 0.03921f, 0.949f, 0.5f};
+ // f32 mask_color[4] = {0.906f, 0.03921f, 0.949f, 0.5f};
vert[0].x = ModelXToScreen(start_fraction - 0.5f); vert[0].y = ModelYToScreen(0.5f - start_fraction);
vert[1].x = ModelXToScreen(start_fraction - 0.5f); vert[1].y = ModelYToScreen(0.5f - end_fraction);
vert[2].x = ModelXToScreen(end_fraction - 0.5f); vert[2].y = ModelYToScreen(0.5f - end_fraction);
@@ -3595,7 +3648,7 @@ Render() {
u32 colour = FourFloatColorToU32(*((nk_colorf *)font_color));
glUseProgram(Flat_Shader->shaderProgram);
- glUniform4fv(Flat_Shader->colorLocation, 1, (GLfloat *)&mask_color);
+ glUniform4fv(Flat_Shader->colorLocation, 1, (GLfloat *)&auto_curation_state.mask_color);
glBindBuffer(GL_ARRAY_BUFFER, Scaff_Bar_Data->vbos[ptr]);
glBufferSubData(GL_ARRAY_BUFFER, 0, 4 * sizeof(vertex), vert);
@@ -3604,15 +3657,19 @@ Render() {
glUseProgram(UI_Shader->shaderProgram);
fonsSetColor(FontStash_Context, colour);
+
+ std::string buff = fmt::format(
+ "{}: ({}) pixels, ({}) fragments",
+ auto_curation_state.selected_or_exclude==0?"Selected" :"Excluded",
+ std::abs(auto_curation_state.get_end() - auto_curation_state.get_start()),
+ select_area.selected_frag_ids.size());
- char buff[256];
f32 lh = 0.0f;
- stbsp_snprintf(buff, sizeof(buff), "%s (%d) Pixs: %s", auto_curation_state.selected_or_exclude==0?"Select" :"Exclude", std::abs(auto_curation_state.get_end() - auto_curation_state.get_start()), std::to_string(selected_frag_ids.size()).c_str());
- f32 textWidth = fonsTextBounds(FontStash_Context, 0, 0, buff, 0, NULL);
+ f32 textWidth = fonsTextBounds(FontStash_Context, 0, 0, buff.c_str(), 0, NULL);
fonsDrawText(
FontStash_Context,
ModelXToScreen( 0.5f * (end_fraction + start_fraction ) - 0.5f) - (0.5f * textWidth),
- ModelYToScreen(0.5f - 0.5f*(start_fraction + end_fraction)) - lh * 0.5f, buff, 0);
+ ModelYToScreen(0.5f - 0.5f*(start_fraction + end_fraction)) - lh * 0.5f, buff.c_str(), 0);
}
}
}
@@ -3649,7 +3706,7 @@ Render() {
end_contig += ((f32)cont->length / (f32)Number_of_Pixels_1D); // end of the contig
if (*cont->metaDataFlags)
{
- u32 tmp = 0;
+ u32 tmp = 0; // used to count the number of tags drawn
bool haplotigTagged = false;
ForLoop2(ArrayCount(Meta_Data->tags))
{
@@ -3686,7 +3743,9 @@ Render() {
}
}
- if (haplotigTagged && Grey_Haplotigs)
+ // draw the grey out mask
+ std::string grey_out_tag = Grey_Out_Settings->is_grey_out(cont->metaDataFlags, Meta_Data);
+ if (!grey_out_tag.empty())
{
vert[0].x = ModelXToScreen(start_contig - 0.5f); vert[0].y = ModelYToScreen(0.5f - start_contig);
vert[1].x = ModelXToScreen(start_contig - 0.5f); vert[1].y = ModelYToScreen(0.5f - end_contig);
@@ -3829,8 +3888,8 @@ Render() {
textBoxHeight *= (3.0f + (f32)nExtra);
textBoxHeight += (2.0f + (f32)nExtra);
- u32 id1 = Map_State->originalContigIds[Tool_Tip_Move.pixels.x];
- u32 id2 = Map_State->originalContigIds[Tool_Tip_Move.pixels.y];
+ u32 id1 = Map_State->get_original_contig_id(Tool_Tip_Move.pixels.x);
+ u32 id2 = Map_State->get_original_contig_id(Tool_Tip_Move.pixels.y);
u32 coord1 = Map_State->contigRelCoords[Tool_Tip_Move.pixels.x];
u32 coord2 = Map_State->contigRelCoords[Tool_Tip_Move.pixels.y];
@@ -4092,7 +4151,7 @@ Render() {
pix1 = pix1 ? pix1 - 1 : (pix2 < (Number_of_Pixels_1D - 1) ? pix2 + 1 : pix2);
}
- original_contig *cont = Original_Contigs + Map_State->originalContigIds[pix1];
+ original_contig *cont = Original_Contigs + Map_State->get_original_contig_id(pix1);
u32 nPixels = Number_of_Pixels_1D;
f64 bpPerPixel = (f64)Total_Genome_Length / (f64)nPixels;
@@ -4111,7 +4170,7 @@ Render() {
if (!line1Done)
{
f64 bpEnd = bpPerPixel * (f64)Map_State->contigRelCoords[pix2];
- original_contig *cont2 = Original_Contigs + Map_State->originalContigIds[pix2];
+ original_contig *cont2 = Original_Contigs + Map_State->get_original_contig_id(pix2);
stbsp_snprintf(line1, 64, "%s[%$.2fbp] to %s[%$.2fbp]", cont->name, bpStart, cont2->name, bpEnd);
if (Edit_Pixels.editing)
{
@@ -4318,7 +4377,7 @@ Render() {
}
- if (Yahs_sorting)
+ if (auto_sort_state)
{
u32 colour = glfonsRGBA(Theme_Colour.r, Theme_Colour.g, Theme_Colour.b, Theme_Colour.a);
@@ -4331,7 +4390,25 @@ Render() {
glUseProgram(UI_Shader->shaderProgram);
glUniformMatrix4fv(Flat_Shader->matLocation, 1, GL_FALSE, textNormalMat);
glViewport(0, 0, (s32)width, (s32)height);
- fonsDrawText(FontStash_Context, width * 0.5f, height * 0.5f, "YaHS Sorting...", 0);
+ fonsDrawText(FontStash_Context, width * 0.5f, height * 0.5f, "Pixel Sorting...", 0);
+
+ ChangeSize((s32)width, (s32)height);
+ }
+
+ if (auto_cut_state)
+ {
+ u32 colour = glfonsRGBA(Theme_Colour.r, Theme_Colour.g, Theme_Colour.b, Theme_Colour.a);
+
+ fonsClearState(FontStash_Context);
+ fonsSetSize(FontStash_Context, 64.0f * Screen_Scale.x);
+ fonsSetAlign(FontStash_Context, FONS_ALIGN_CENTER | FONS_ALIGN_MIDDLE);
+ fonsSetFont(FontStash_Context, Font_Bold);
+ fonsSetColor(FontStash_Context, colour);
+
+ glUseProgram(UI_Shader->shaderProgram);
+ glUniformMatrix4fv(Flat_Shader->matLocation, 1, GL_FALSE, textNormalMat);
+ glViewport(0, 0, (s32)width, (s32)height);
+ fonsDrawText(FontStash_Context, width * 0.5f, height * 0.5f, "Pixel cut...", 0);
ChangeSize((s32)width, (s32)height);
}
@@ -4565,6 +4642,142 @@ TestFile(const char *fileName, u64 *fileSize = 0)
return(file); // 仅仅返回正确的file指针，否则返回空指针
}
+
+
+global_function
+void
+add_graph_to_extensions(
+ memory_arena *arena,
+ const u32* graph_name,
+ const u32* graph_data)
+{
+
+ graph *gph = PushStructP(arena, graph); // create the size to store the extension data
+ extension_node *node = PushStructP(arena, extension_node);
+ u08 *dataPlusName = PushArrayP(arena, u08, ((sizeof(u32) * Number_of_Pixels_1D) + sizeof(gph->name) ));
+ gph->data = (u32 *)(dataPlusName + sizeof(gph->name));
+ u32 *namePtr = (u32 *)graph_name;
+ for (u32 i = 0; i < ArrayCount(gph->name); i++ ) // get the graph name
+ {
+ gph->name[i] = *(namePtr + i);
+ }
+ for (u32 i = 0; i < Number_of_Pixels_1D; i++) // get the graph data
+ {
+ gph->data[i] = *(graph_data + i);
+ }
+ node->type = extension_graph; // assign the gph to node
+ node->extension = gph;
+ AddExtension(node); // add node to extension
+
+ return ;
+}
+
+
+
+global_function
+void
+push_extensions_to_opengl(memory_arena *arena, u32 added_index = 0, f32 scale=-1.f)
+{
+ u32 exIndex = 0;
+ // TraverseLinkedList(Extensions.head, extension_node)
+
+ extension_node* node = Extensions.head ;
+ while (added_index--)
+ {
+ node = node->next; // 移动到最后一个节点
+ exIndex ++ ;
+ }
+ for ( ; node; node = node->next) {
+
+ switch (node->type)
+ {
+ case extension_graph:
+ {
+ graph *gph = (graph *)node->extension; // get the graph ptr and assigned to gph
+#define DefaultGraphScale 0.2f
+#define DefaultGraphBase 32.0f
+#define DefaultGraphLineSize 1.0f
+#define DefaultGraphColour {0.1f, 0.8f, 0.7f, 1.0f}
+ gph->scale = scale>0.f? scale : DefaultGraphScale;
+ gph->base = DefaultGraphBase;
+ gph->lineSize = DefaultGraphLineSize;
+ gph->colour = DefaultGraphColour;
+ gph->on = 0;
+
+ gph->shader = PushStructP(arena, editable_plot_shader);
+ gph->shader->shaderProgram = CreateShader(FragmentSource_EditablePlot.c_str(), VertexSource_EditablePlot.c_str(), GeometrySource_EditablePlot.c_str());
+
+ glUseProgram(gph->shader->shaderProgram);
+ glBindFragDataLocation(gph->shader->shaderProgram, 0, "outColor");
+ gph->shader->matLocation = glGetUniformLocation(gph->shader->shaderProgram, "matrix");
+ gph->shader->colorLocation = glGetUniformLocation(gph->shader->shaderProgram, "color");
+ gph->shader->yScaleLocation = glGetUniformLocation(gph->shader->shaderProgram, "yscale");
+ gph->shader->yTopLocation = glGetUniformLocation(gph->shader->shaderProgram, "ytop");
+ gph->shader->lineSizeLocation = glGetUniformLocation(gph->shader->shaderProgram, "linewidth");
+
+ glUniform1i(glGetUniformLocation(gph->shader->shaderProgram, "pixrearrangelookup"), 3);
+ glUniform1i(glGetUniformLocation(gph->shader->shaderProgram, "yvalues"), 4 + (s32)exIndex);
+
+ u32 nValues = Number_of_Pixels_1D;
+ auto* xValues = new f32[nValues]; // allocate memory for xValues, actually, x is the coordinate of the pixel
+ auto* yValues = new f32[nValues];
+
+ u32 max = 0;
+ ForLoop(Number_of_Pixels_1D)
+ {
+ max = my_Max(max, gph->data[index]);
+ }
+
+ ForLoop(Number_of_Pixels_1D)
+ {
+ xValues[index] = (f32)index;
+ yValues[index] = (f32)gph->data[index] / (f32)max ; // normalise the data
+ }
+
+ glActiveTexture(GL_TEXTURE4 + exIndex++);
+
+ GLuint yVal, yValTex;
+
+ // generate a buffer object named yVal and save data to yVal
+ glGenBuffers(1, &yVal);
+ glBindBuffer(GL_TEXTURE_BUFFER, yVal);
+ glBufferData(GL_TEXTURE_BUFFER, sizeof(f32) * nValues, yValues, GL_STATIC_DRAW);
+
+ // add texture and link to the buffer object
+ glGenTextures(1, &yValTex);
+ glBindTexture(GL_TEXTURE_BUFFER, yValTex);
+ glTexBuffer(GL_TEXTURE_BUFFER, GL_R32F, yVal);
+
+ gph->shader->yValuesBuffer = yVal;
+ gph->shader->yValuesBufferTex = yValTex;
+
+ // add the vertext data into buffer
+ glGenBuffers(1, &gph->vbo);
+ glBindBuffer(GL_ARRAY_BUFFER, gph->vbo);
+ glBufferData(GL_ARRAY_BUFFER, sizeof(f32) * nValues, xValues, GL_STATIC_DRAW);
+
+ // gen the vertex array object
+ glGenVertexArrays(1, &gph->vao);
+ glBindVertexArray(gph->vao);
+
+ GLuint posAttrib = (GLuint)glGetAttribLocation(gph->shader->shaderProgram, "position");
+ glEnableVertexAttribArray(posAttrib);
+ glVertexAttribPointer(posAttrib, 1, GL_FLOAT, GL_FALSE, 0, 0);
+
+ delete[] xValues;
+ delete[] yValues;
+
+ glActiveTexture(GL_TEXTURE0);
+ }
+ break;
+ }
+ }
+
+ return ;
+}
+
+
+
global_function
u08
LoadState(u64 headerHash, char *path = 0);
@@ -4659,6 +4872,16 @@ LoadFile(const char *filePath, memory_arena *arena, char **fileName, u64 *header
delete[] Contact_Matrix->vbos;
Contact_Matrix->vbos = nullptr;
}
+ if (pixel_density_extension)
+ {
+ delete pixel_density_extension;
+ pixel_density_extension = nullptr;
+ }
+ if (frag_cut_cal_ptr)
+ {
+ delete frag_cut_cal_ptr;
+ frag_cut_cal_ptr = nullptr;
+ }
ResetMemoryArenaP(arena); // release all the memory allocated, avoid memory leak
auto_curation_state.clear();
}
@@ -5202,93 +5425,7 @@ LoadFile(const char *filePath, memory_arena *arena, char **fileName, u64 *header
// Extensions
{
- u32 exIndex = 0;
- // TraverseLinkedList(Extensions.head, extension_node)
- for (extension_node* node = Extensions.head; node; node = node->next) {
-
- switch (node->type)
- {
- case extension_graph:
- {
- graph *gph = (graph *)node->extension; // get the graph ptr and assigned to gph
-#define DefaultGraphScale 0.2f
-#define DefaultGraphBase 32.0f
-#define DefaultGraphLineSize 1.0f
-#define DefaultGraphColour {0.1f, 0.8f, 0.7f, 1.0f}
- gph->scale = DefaultGraphScale;
- gph->base = DefaultGraphBase;
- gph->lineSize = DefaultGraphLineSize;
- gph->colour = DefaultGraphColour;
- gph->on = 0;
-
- gph->shader = PushStructP(arena, editable_plot_shader);
- gph->shader->shaderProgram = CreateShader(FragmentSource_EditablePlot.c_str(), VertexSource_EditablePlot.c_str(), GeometrySource_EditablePlot.c_str());
-
- glUseProgram(gph->shader->shaderProgram);
- glBindFragDataLocation(gph->shader->shaderProgram, 0, "outColor");
- gph->shader->matLocation = glGetUniformLocation(gph->shader->shaderProgram, "matrix");
- gph->shader->colorLocation = glGetUniformLocation(gph->shader->shaderProgram, "color");
- gph->shader->yScaleLocation = glGetUniformLocation(gph->shader->shaderProgram, "yscale");
- gph->shader->yTopLocation = glGetUniformLocation(gph->shader->shaderProgram, "ytop");
- gph->shader->lineSizeLocation = glGetUniformLocation(gph->shader->shaderProgram, "linewidth");
-
- glUniform1i(glGetUniformLocation(gph->shader->shaderProgram, "pixrearrangelookup"), 3);
- glUniform1i(glGetUniformLocation(gph->shader->shaderProgram, "yvalues"), 4 + (s32)exIndex);
-
- u32 nValues = Number_of_Pixels_1D;
- auto* xValues = new f32[nValues]; // allocate memory for xValues, actually, x is the coordinate of the pixel
- auto* yValues = new f32[nValues];
-
- u32 max = 0;
- ForLoop(Number_of_Pixels_1D)
- {
- max = my_Max(max, gph->data[index]);
- }
-
- ForLoop(Number_of_Pixels_1D)
- {
- xValues[index] = (f32)index;
- yValues[index] = (f32)gph->data[index] / (f32)max ; // normalise the data
- }
-
- glActiveTexture(GL_TEXTURE4 + exIndex++);
-
- GLuint yVal, yValTex;
-
- // generate a buffer object named yVal and save data to yVal
- glGenBuffers(1, &yVal);
- glBindBuffer(GL_TEXTURE_BUFFER, yVal);
- glBufferData(GL_TEXTURE_BUFFER, sizeof(f32) * nValues, yValues, GL_STATIC_DRAW);
-
- // add texture and link to the buffer object
- glGenTextures(1, &yValTex);
- glBindTexture(GL_TEXTURE_BUFFER, yValTex);
- glTexBuffer(GL_TEXTURE_BUFFER, GL_R32F, yVal);
-
- gph->shader->yValuesBuffer = yVal;
- gph->shader->yValuesBufferTex = yValTex;
-
- // add the vertext data into buffer
- glGenBuffers(1, &gph->vbo);
- glBindBuffer(GL_ARRAY_BUFFER, gph->vbo);
- glBufferData(GL_ARRAY_BUFFER, sizeof(f32) * nValues, xValues, GL_STATIC_DRAW);
-
- // gen the vertex array object
- glGenVertexArrays(1, &gph->vao);
- glBindVertexArray(gph->vao);
-
- GLuint posAttrib = (GLuint)glGetAttribLocation(gph->shader->shaderProgram, "position");
- glEnableVertexAttribArray(posAttrib);
- glVertexAttribPointer(posAttrib, 1, GL_FLOAT, GL_FALSE, 0, 0);
-
- delete[] xValues;
- delete[] yValues;
-
- glActiveTexture(GL_TEXTURE0);
- }
- break;
- }
- }
+ push_extensions_to_opengl(arena, 0);
}
#ifdef Internal
@@ -5335,6 +5472,63 @@ LoadFile(const char *filePath, memory_arena *arena, char **fileName, u64 *header
}
}
+ // 为添加的功能初始化指针
+ {
+ // 给pixel_density_extension分配内存
+ // pixel_density_extension = new Extension_Graph_Data(Number_of_Pixels_1D);
+
+ // 为 copy textures to cpu 分配内存
+ if (textures_array_ptr) delete textures_array_ptr;
+ textures_array_ptr = new TexturesArray4AI(
+ Number_of_Textures_1D,
+ Texture_Resolution,
+ *fileName,
+ Contigs
+ );
+ // prepare before reading textures
+ f32 original_color_control_points[3];
+ prepare_before_copy(original_color_control_points);
+ textures_array_ptr->copy_buffer_to_textures(
+ Contact_Matrix,
+ false
+ );
+ restore_settings_after_copy(original_color_control_points);
+
+ // 为 Pixel Cut 存储的数据分配空间，初始化，并且将数据push到extension中
+ if (frag_cut_cal_ptr) delete frag_cut_cal_ptr;
+ frag_cut_cal_ptr = new FragCutCal(
+ textures_array_ptr,
+ Number_of_Pixels_1D,
+ auto_curation_state.auto_cut_diag_window_for_pixel_mean);
+
+ // clear mem for textures
+ textures_array_ptr->clear_textures();
+
+ // 添加数据到extensions
+ std::string graph_name = "pixel_discontinuity";
+ bool is_pix_density_added = Extensions.is_graph_name_exist(graph_name);
+ if (!is_pix_density_added) // 未添加pixel density
+ {
+ u32 added_num = Extensions.get_num_extensions();
+ u32* graph_data = new u32[Number_of_Pixels_1D];
+ f32 max_desity = 0.f;
+ for (auto& i : frag_cut_cal_ptr->hic_pixel_density_origin) max_desity = std::max(max_desity, i);
+ for (u32 i=0; i < Number_of_Pixels_1D; i ++)
+ {
+ graph_data[i] = (u32)(255 * (1.001f- frag_cut_cal_ptr->hic_pixel_density_origin[i] / max_desity));
+ }
+ add_graph_to_extensions(arena, (u32*)graph_name.c_str(), graph_data);
+ delete[] graph_data;
+
+ push_extensions_to_opengl(arena, added_num, 0.05f); // push hic_pixel_density to opengl buffer
+ }
+ else
+ {
+ fmt::print("hic_pixel_density extension already exists\n");
+ assert(false);
+ }
+ }
+
FenceIn(File_Loaded = 1);
if (LoadState(*headerHash)) LoadState(*headerHash + 1);
@@ -5527,6 +5721,18 @@ Setup()
memset(Meta_Data, 0, sizeof(meta_data));
MetaData_Active_Tag = 0;
ForLoop(ArrayCount(Default_Tags)) strcpy((char *)Meta_Data->tags[MetaData_Active_Tag + index], Default_Tags[index]);
+ if (Grey_Out_Settings)
+ {
+ delete Grey_Out_Settings;
+ Grey_Out_Settings = nullptr;
+ }
+ Grey_Out_Settings = new GreyOutSettings(Meta_Data);
+ if (user_profile_settings_ptr)
+ {
+ delete user_profile_settings_ptr;
+ user_profile_settings_ptr = nullptr;
+ }
+ user_profile_settings_ptr = new UserProfileSettings();
// Contig Name Label UI
{
@@ -5983,20 +6189,26 @@ RearrangeMap( // NOTE: VERY IMPORTANT
bool update_contigs_flag // if true, update the contigs from the map state
)
{
- if (pixelFrom > pixelTo) // Swap, make sure pixelFrom is less than pixelTo
- {
- u32 tmp = pixelFrom;
- pixelFrom = pixelTo;
- pixelTo = tmp;
- }
u32 nPixels = Number_of_Pixels_1D;
- Assert((delta > 0 ? (u32)delta : (u32)(-delta)) < nPixels);
-
- Assert(pixelFrom < nPixels);
- Assert(pixelTo < nPixels);
+ if (std::abs(delta) >= nPixels ||
+ pixelFrom >= nPixels ||
+ pixelTo >= nPixels)
+ {
+ fmt::print(
+ stderr,
+ "RearrangeMap: Invalid parameters: delta = {}, pixelFrom = {}, pixelTo = {}, nPixels = {}, file: {}, line: {}\n",
+ delta, pixelFrom, pixelTo, nPixels,
+ __FILE__, __LINE__
+ );
+ assert(0);
+ }
+ if (pixelFrom > pixelTo) // Swap, make sure pixelFrom is less than pixelTo
+ {
+ std::swap(pixelFrom, pixelTo);
+ }
u32 nPixelsInRange = pixelTo - pixelFrom + 1;
pixelFrom += nPixels;
@@ -6172,6 +6384,82 @@ RearrangeMap( // NOTE: VERY IMPORTANT
}
+
+global_function
+void
+BreakMap(
+ const u32& loc,
+ const u32 ignore_len // cut点到开头或者结尾的长度不足ignore_len的contig不会被切断
+)
+{
+ if (loc >= Number_of_Pixels_1D)
+ {
+ char buff[512];
+ snprintf(buff, sizeof(buff), "[Pixel Cut] Error: loc (%d) should be smaller than number of pixels (%d)", loc, Number_of_Pixels_1D);
+ MY_CHECK(buff);
+ assert(0);
+ }
+ u32 original_contig_id = Map_State->originalContigIds[loc];
+ u32 contig_id = Map_State->contigIds[loc];
+ u32 contig_rel_coord = Map_State->contigRelCoords[loc];
+
+ s32 ptr_left = (s32)loc, ptr_right = (s32)loc;
+ u08 inversed = IsContigInverted(contig_id);
+ while ( // 从loc向左遍历，找到第一个不满足条件的像素点索引
+ --ptr_left >= 0 &&
+ Map_State->contigIds[ptr_left] == contig_id &&
+ (Map_State->contigRelCoords[ptr_left] == Map_State->contigRelCoords[ptr_left+1]+ (inversed ? +1 : -1)) ) {};
+ while ( // 从loc向右遍历，找到第一个不满足条件的像素点索引
+ ++ptr_right < Number_of_Pixels_1D &&
+ Map_State->contigIds[ptr_right] == contig_id &&
+ (Map_State->contigRelCoords[ptr_right - 1] == Map_State->contigRelCoords[ptr_right]+ (inversed ? +1 : -1)) ) {};
+
+ if ((loc - ptr_left) < ignore_len || (ptr_right - loc) < ignore_len )
+ {
+ fmt::print(
+ "[Pixel Cut] Warning: original_contig_id {} current_contig_id {}, pixel range: [{}, cut({}), {}], left({}), right({}), smaller than ignore_len ({}), cut at loc: ({}) is ignored\n",
+ original_contig_id%Max_Number_of_Contigs,
+ contig_id,
+ ptr_left,
+ loc,
+ ptr_right,
+ loc - ptr_left,
+ ptr_right - loc,
+ ignore_len, loc);
+ return;
+ }
+
+ ptr_left++; ptr_right--;
+
+ // cut the contig by amending the original Contig Ids.
+ for (u32 tmp = loc; tmp <= ptr_right; tmp++) // left side
+ {
+ if (Map_State->originalContigIds[tmp] > (std::numeric_limits::max() - Max_Number_of_Contigs))
+ {
+ fmt::print("[Pixel Cut] originalContigIds[{}] + {} = {} is greater than the max number of contigs ({}), file: {}, line: {}\n", tmp,
+ Max_Number_of_Contigs,
+ (u64)Map_State->originalContigIds[tmp] + Max_Number_of_Contigs,
+ std::numeric_limits::max(),
+ __FILE__, __LINE__);
+ assert(0);
+ }
+ Map_State->originalContigIds[tmp] += Max_Number_of_Contigs; // NOTE: the number can not exceed the max number 2**32 - 1 = 4294967295. However, it is not easy to exceed the max number of contigs, as 4294967295 / 4096 = 1048575.9997
+ }
+
+ fmt::print(
+ "[Pixel Cut] Original contig_id ({}), current_id ({}), pixel range: [{}, {}] {} inversed, cut at {}\n",
+ original_contig_id%Max_Number_of_Contigs,
+ contig_id,
+ ptr_left,
+ ptr_right,
+ inversed ? "(is)" : "(isn\'t)",
+ loc );
+
+ return ;
+
+}
+
+
global_function
std::vector
get_exclude_metaData_idx(const std::vector& exclude_tags)
@@ -6213,6 +6501,30 @@ void EraseAllEdits(map_editor* map_editor_, u32 max_edit_recorded=Edits_Stack_Si
}
+void run_ai_detection()
+{
+ std::cout << "Running AI detection..." << std::endl;
+ int status = std::system("/Users/sg35/miniconda3/envs/auto_cut/bin/python /Users/sg35/PretextView/python/autoCut/auto_cut.py");
+
+ // 检查命令执行状态
+ if (status == 0) {
+ std::cout << "Command successful!" << std::endl;
+ } else {
+ std::cerr << "Command failed, code: " << status << std::endl;
+ }
+}
+
+void cut_frags(const std::vector& problem_locs)
+{
+ for (auto & i : problem_locs)
+ {
+ // cut the fragment
+ BreakMap(i, auto_curation_state.auto_cut_smallest_frag_size_in_pixel);
+ UpdateContigsFromMapState();
+ }
+ Redisplay = 1;
+}
+
void AutoCurationFromFragsOrder(
const FragsOrder* frags_order_,
@@ -6222,24 +6534,40 @@ void AutoCurationFromFragsOrder(
{
u08 using_select_area = (select_area && select_area->select_flag)? 1 : 0;
u32 num_frags = contigs_->numberOfContigs;
- if (!using_select_area && num_frags != frags_order_->get_num_frags())
+ if (!using_select_area )
+ {
+ if ( num_frags != frags_order_->get_num_frags())
+ {
+ fprintf(stderr, "Number of contigs(%d) and fragsOrder.num_frags(%d) do not match.\n", num_frags, frags_order_->get_num_frags());
+ assert(0);
+ }
+ }
+ else
{
- fprintf(stderr, "Number of contigs(%d) and fragsOrder.num_frags(%d) do not match.\n", num_frags, frags_order_->get_num_frags());
- return;
+ if (select_area->get_to_sort_frags_num() != frags_order_->get_num_frags())
+ {
+ fmt::print(
+ stderr,
+ "num_to_sort_contigs({}) != fragsOrder.num_frags({}), file:{}, line:{}\n", select_area->get_to_sort_frags_num(),
+ frags_order_->get_num_frags(),
+ __FILE__, __LINE__);
+ assert(0);
+ }
}
u32 num_autoCurated_edits=0;
// check the difference between the contigs, order and the new frags order
u32 start_loc = 0;
- std::vector> current_order(num_frags);
+ std::vector> current_order(num_frags); // [contig_id, contig_length]
std::vector predicted_order = frags_order_->get_order_without_chromosomeInfor(); // start from 1
if (using_select_area)
{
std::vector full_predicted_order(num_frags);
std::iota(full_predicted_order.begin(), full_predicted_order.end(), 1);
- for (u32 i=0; i< select_area->selected_frag_ids.size(); i++)
- full_predicted_order[select_area->selected_frag_ids[i]] = (predicted_order[i]>0?1:-1) * (select_area->selected_frag_ids[0] + std::abs(predicted_order[i]));
+ auto frags_id_to_sort = select_area->get_to_sort_frags_id(Contigs);
+ for (u32 i=0; i< select_area->get_to_sort_frags_num(); i++)
+ full_predicted_order[frags_id_to_sort[i]] = (predicted_order[i]>0?1:-1) * (select_area->get_first_frag_id() + std::abs(predicted_order[i]));
predicted_order = full_predicted_order;
}
for (s32 i = 0; i < num_frags; ++i) current_order[i] = {i+1, contigs_->contigs_arr[i].length}; // start from 1
@@ -6280,7 +6608,7 @@ void AutoCurationFromFragsOrder(
AddMapEdit(0, {start_loc, start_loc + current_order[i].second - 1}, true);
current_order[i].first = -current_order[i].first;
start_loc += current_order[i].second;
- printf("[Auto curation] (#%d) Invert contig %d.\n", ++num_autoCurated_edits, predicted_order[i]);
+ printf("[Pixel Sort] (#%d) Invert contig %d.\n", ++num_autoCurated_edits, predicted_order[i]);
continue;
}
else if (
@@ -6295,15 +6623,19 @@ void AutoCurationFromFragsOrder(
while (std::abs(predicted_order[i])!=std::abs(current_order[tmp_i].first))
{
if (tmp_i >= num_frags)
- {
- fprintf(stderr, "Error: contig %d not found in the current order.\n", current_order[i].first);
- MY_CHECK(0);
+ {
+ char buff[256];
+ snprintf(buff, sizeof(buff), "Error: contig %d not found in the current order.\n", current_order[i].first);
+ MY_CHECK(buff);
+ assert(0);
}
pixelFrom += current_order[tmp_i].second; // length updated based on the current order
if (pixelFrom>=Number_of_Pixels_1D)
- {
- fprintf(stderr, "Error: pixelFrom(%d) >= Number_of_Pixels_1D(%d).\n", pixelFrom, Number_of_Pixels_1D);
- MY_CHECK(0);
+ {
+ char buff[256];
+ snprintf(buff, sizeof(buff), "Error: pixelFrom(%d) >= Number_of_Pixels_1D(%d).\n", pixelFrom, Number_of_Pixels_1D);
+ MY_CHECK(buff);
+ assert(0);
}
++tmp_i;
}
@@ -6322,9 +6654,9 @@ void AutoCurationFromFragsOrder(
start_loc += current_order[i].second; // update start_loc after move fragments
if (is_curated_inverted)
{
- printf("[Auto curation] (#%d) Invert and Move contig %d to %d, start_loc:%d.\n", ++num_autoCurated_edits, predicted_order[i], i, start_loc);
+ printf("[Pixel Sort] (#%d) Invert and Move contig %d to %d, start_loc:%d.\n", ++num_autoCurated_edits, predicted_order[i], i, start_loc);
}
- else printf("[Auto curation] (#%d) Move contig %d to %d, start_loc:%d.\n", ++num_autoCurated_edits, predicted_order[i], i, start_loc);
+ else printf("[Pixel Sort] (#%d) Move contig %d to %d, start_loc:%d.\n", ++num_autoCurated_edits, predicted_order[i], i, start_loc);
continue;
}
else
@@ -6333,7 +6665,88 @@ void AutoCurationFromFragsOrder(
continue;
}
}
- printf("[Auto curatioin] finished with %d edits\n", num_autoCurated_edits);
+ printf("[Pixel Sort] finished with %d edits\n", num_autoCurated_edits);
+
+ return ;
+}
+
+
+global_function
+void
+auto_cut_func(
+ char * currFileName,
+ memory_arena* arena = nullptr,
+ std::string file_save_name = std::string("/auto_curation_tmp")
+)
+{
+ if (!currFileName || !auto_cut_state) return;
+
+ if (auto_cut_state == 2) // restore the cutted frags within the selected area
+ {
+ u32 start = auto_curation_state.get_start();
+ u32 end = auto_curation_state.get_end();
+ if (start < 0 || end < 0)
+ {
+ fmt::print(
+ stdout,
+ "Error: no area selected. start({}) or end({}) is less than 0\n",
+ start, end);
+ return ;
+ }
+ fmt::print(stdout, "[Pixel cut] restoring the cutted frags within the selected area: [{}, {}]\n", start, end);
+ Map_State->restore_cutted_contigs( start, end );
+ UpdateContigsFromMapState();
+ Redisplay = 1;
+ return ;
+ }
+
+ // classic cut
+ {
+ SelectArea selected_area;
+ auto_curation_state.get_selected_fragments(
+ selected_area,
+ Map_State,
+ Number_of_Pixels_1D,
+ Contigs);
+ glBindBuffer(GL_TEXTURE_BUFFER, Contact_Matrix->pixelRearrangmentLookupBuffer);
+ const u32 *pixel_rearrange_index = (const u32 *)glMapBufferRange(GL_TEXTURE_BUFFER, 0, Number_of_Pixels_1D * sizeof(u32), GL_MAP_READ_BIT);
+ std::vector cut_locs_pixel = frag_cut_cal_ptr->get_cut_locs_pixel(
+ auto_curation_state,
+ pixel_rearrange_index, // pixel_rearrangement_buffer
+ Contigs,
+ &selected_area
+ );
+ glUnmapBuffer(GL_TEXTURE_BUFFER);
+
+ fmt::print(stdout, "[Pixel cut] cut locs in pixel: [");
+ for (auto & i : cut_locs_pixel) fmt::print(stdout, "{} ", i);
+ fmt::print(stdout, "]\n");
+
+ // cut the contigs
+ cut_frags(cut_locs_pixel);
+ }
+
+ // generate figures
+ if (0)
+ {
+ fprintf(stdout, "[Pixel cut] generating hic figures...\n");
+ Hic_Figure hic_figure(
+ Total_Genome_Length,
+ file_save_name,
+ textures_array_ptr );
+ hic_figure.generate_hic_figures();
+
+ // run ai model with python script
+ run_ai_detection();
+
+ // restore the error info via reading the error json
+ HIC_Problems hic_problems("/auto_curation_tmp/auto_cut_output/infer_result/infer_result.json", (f32) Total_Genome_Length / (f32)Number_of_Pixels_1D );
+ std::vector> problem_loc = hic_problems.get_problem_loci();
+ }
+
+
+ // cut the contigs
+ // cut_frags();
return ;
}
@@ -6341,85 +6754,110 @@ void AutoCurationFromFragsOrder(
global_function
void
-Sort_yahs(char* currFileName)
+auto_sort_func(char* currFileName)
{
- if (!currFileName || !Yahs_sorting) return;
+ if (!currFileName || !auto_sort_state) return;
fprintf(stdout, "========================\n");
- fprintf(stdout, "[YaHS Sort] start...\n");
- fprintf(stdout, "[YaHS Sort] smallest_frag_size_in_pixel: %d\n", auto_curation_state.smallest_frag_size_in_pixel);
- fprintf(stdout, "[YaHS Sort] link_score_threshold: %.3f\n", auto_curation_state.link_score_threshold);
- fprintf(stdout, "[YaHS Sort] Sort mode: %s\n", auto_curation_state.get_sort_mode_name().c_str());
- // compress the HiC data
- auto texture_array_4_ai = TexturesArray4AI(Number_of_Textures_1D, Texture_Resolution, (char*)currFileName, Contigs);
+ fprintf(stdout, "[Pixel Sort] start...\n");
+ fprintf(stdout, "[Pixel Sort] smallest_frag_size_in_pixel: %d\n", auto_curation_state.smallest_frag_size_in_pixel);
+ fprintf(stdout, "[Pixel Sort] link_score_threshold: %.3f\n", auto_curation_state.link_score_threshold);
+ fprintf(stdout, "[Pixel Sort] Sort mode: %s\n", auto_curation_state.get_sort_mode_name().c_str());
+ // compress the HiC data
// prepare before reading textures
- f32 original_control_points[3];
- prepare_before_copy(original_control_points);
- texture_array_4_ai.copy_buffer_to_textures_dynamic(Contact_Matrix, false); // copy the remapped data which is reordered according to the Map_State
- restore_settings_after_copy(original_control_points);
-
+ f32 original_color_control_points[3];
+ prepare_before_copy(original_color_control_points);
+ textures_array_ptr->copy_buffer_to_textures_dynamic(Contact_Matrix, false);
+ restore_settings_after_copy(original_color_control_points);
// check if select the area for sorting
SelectArea selected_area;
- auto_curation_state.get_selected_fragments(selected_area.selected_frag_ids, Map_State, Number_of_Pixels_1D);
+ auto_curation_state.get_selected_fragments(
+ selected_area,
+ Map_State,
+ Number_of_Pixels_1D,
+ Contigs
+ );
if (auto_curation_state.get_start() >=0 && auto_curation_state.get_end() >= 0 && selected_area.selected_frag_ids.size() > 0)
{
- fprintf(stdout, "Using selected area for sorting:\n");
- fprintf(stdout, "Selected pixel range: %d ~ %d\n", auto_curation_state.get_start(), auto_curation_state.get_end());
+ fprintf(stdout, "[Pixel Sort] Using selected area for sorting:\n");
+ fprintf(stdout, "[Pixel Sort] Selected pixel range: %d ~ %d\n", auto_curation_state.get_start(), auto_curation_state.get_end());
std::stringstream ss;
ss << selected_area.selected_frag_ids[0];
for (u32 i = 1; i < selected_area.selected_frag_ids.size(); ++i) ss << ", " << selected_area.selected_frag_ids[i];
- fprintf(stdout, "Selected fragments: %s\n\n", ss.str().c_str());
+ fmt::print(stdout, "[Pixel Sort] Selected fragments ({}): {}\n\n", selected_area.selected_frag_ids.size(), ss.str().c_str());
selected_area.select_flag = true;
selected_area.start_pixel = auto_curation_state.get_start();
selected_area.end_pixel = auto_curation_state.get_end();
}
- texture_array_4_ai.cal_compressed_hic(
+ textures_array_ptr->cal_compressed_hic(
Contigs,
Extensions,
false,
false,
&selected_area
);
- FragsOrder frags_order(texture_array_4_ai.get_num_frags()); // intilize the frags_order with the number of fragments including the filtered out ones
- // exclude the fragments with first two tags during the auto curationme
+ FragsOrder frags_order(textures_array_ptr->get_num_frags()); // intilize the frags_order with the number of fragments including the filtered out ones
+ // exclude the fragments with first two tags during the auto curation
std::vector exclude_tags = {"haplotig", "unloc"};
std::vector exclude_meta_tag_idx = get_exclude_metaData_idx(exclude_tags);
LikelihoodTable likelihood_table(
- texture_array_4_ai.get_frags(),
- texture_array_4_ai.get_compressed_hic(),
+ textures_array_ptr->get_frags(),
+ textures_array_ptr->get_compressed_hic(),
(f32)auto_curation_state.smallest_frag_size_in_pixel / ((f32)Number_of_Pixels_1D + 1.f),
exclude_meta_tag_idx,
Number_of_Pixels_1D);
+
+ #ifdef DEBUG_OUTPUT_LIKELIHOOD_TABLE
+ likelihood_table.output_fragsInfo_likelihoodTable("frags_info_likelihood_table.txt", textures_array_ptr->get_compressed_hic());
+ #endif // DEBUG_OUTPUT_LIKELIHOOD_TABLE
+
+ // clear mem for textures and compressed hic
+ textures_array_ptr->clear_textures();
+ textures_array_ptr->clear_compressed_hic();
+
// use the compressed_hic to calculate the frags_order directly
- if (auto_curation_state.sort_mode == 0)
+ if (auto_curation_state.sort_mode == 0 || !selected_area.select_flag) // sort with union find if sorting the whole genome
{
frag_sort_method->sort_according_likelihood_unionFind(
likelihood_table,
frags_order,
+ selected_area,
auto_curation_state.link_score_threshold,
- texture_array_4_ai.get_frags());
+ textures_array_ptr->get_frags());
}
else if (auto_curation_state.sort_mode == 1)
{
frag_sort_method->sort_according_likelihood_unionFind_doFuse(
likelihood_table,
frags_order,
+ selected_area,
auto_curation_state.link_score_threshold,
- texture_array_4_ai.get_frags(), true, true);
+ textures_array_ptr->get_frags(), true, true);
}
else if (auto_curation_state.sort_mode == 2)
{
frag_sort_method->sort_according_likelihood_unionFind_doFuse(
likelihood_table,
frags_order,
+ selected_area,
auto_curation_state.link_score_threshold,
- texture_array_4_ai.get_frags(), false, true);
+ textures_array_ptr->get_frags(), false, true);
+ }
+ else if (auto_curation_state.sort_mode == 3) // not finished yet
+ {
+ frag_sort_method->sort_according_yahs(
+ likelihood_table,
+ frags_order,
+ selected_area,
+ auto_curation_state.link_score_threshold,
+ textures_array_ptr->get_frags()
+ );
}
else
{
- fprintf(stderr, "[YaHS Sort] Error: Unknown sort mode (%d)\n", auto_curation_state.sort_mode);
+ fprintf(stderr, "[Pixel Sort] Error: Unknown sort mode (%d)\n", auto_curation_state.sort_mode);
assert(0);
}
AutoCurationFromFragsOrder(
@@ -6428,16 +6866,19 @@ Sort_yahs(char* currFileName)
Map_State,
&selected_area);
std::cout << std::endl;
- Yahs_sorting = 0;
+ auto_sort_state = 0;
return;
}
// set the vertex array for the contact matrix
-// copy_flag: if true, show full texture for copy the texture to array on cpu
+// copy_flag: if true, set vaos to [-1, 1, -1, 1] for copying tiles from opengl buffer to cpu memory
global_function
-void setContactMatrixVertexArray(contact_matrix* Contact_Matrix_, bool copy_flag, bool regenerate_flag)
+void setContactMatrixVertexArray(
+ contact_matrix* Contact_Matrix_,
+ bool copy_flag,
+ bool regenerate_flag)
{
glUseProgram(Contact_Matrix_->shaderProgram);
GLuint posAttrib = (GLuint)glGetAttribLocation(Contact_Matrix_->shaderProgram, "position");
@@ -6494,26 +6935,27 @@ void setContactMatrixVertexArray(contact_matrix* Contact_Matrix_, bool copy_flag
3 2
0 1
*/
- textureVertices[0].x = !copy_flag? x : -1.f; // x -> [-0.5, 0.5]
- textureVertices[0].y = !copy_flag? y - quadSize : -1.f; // y -> [-0.5, 0.5]
+ f32 half_len = 1.0f;
+ textureVertices[0].x = !copy_flag? x : -half_len; // x -> [-0.5, 0.5]
+ textureVertices[0].y = !copy_flag? y - quadSize : -half_len; // y -> [-0.5, 0.5]
textureVertices[0].s = !copy_flag? cornerCoords[0] : 0.f; // s表示texture的水平分量
textureVertices[0].t = !copy_flag? cornerCoords[1] : 0.f; // t表示texture的垂直分量
textureVertices[0].u = texture_index_symmetric;
- textureVertices[1].x = !copy_flag? x + quadSize : 1.f;
- textureVertices[1].y = !copy_flag? y - quadSize : -1.f;
+ textureVertices[1].x = !copy_flag? x + quadSize : half_len;
+ textureVertices[1].y = !copy_flag? y - quadSize : -half_len;
textureVertices[1].s = !copy_flag? 1.0f : 1.f;
textureVertices[1].t = !copy_flag? 1.0f : 0.f;
textureVertices[1].u = texture_index_symmetric;
- textureVertices[2].x = !copy_flag? x + quadSize : 1.f;
- textureVertices[2].y = !copy_flag? y : 1.f;
+ textureVertices[2].x = !copy_flag? x + quadSize : half_len;
+ textureVertices[2].y = !copy_flag? y : half_len;
textureVertices[2].s = !copy_flag? cornerCoords[1] : 1.f;
textureVertices[2].t = !copy_flag? cornerCoords[0] : 1.f;
textureVertices[2].u = texture_index_symmetric;
- textureVertices[3].x = !copy_flag? x : -1.f;
- textureVertices[3].y = !copy_flag? y : 1.f;
+ textureVertices[3].x = !copy_flag? x : -half_len;
+ textureVertices[3].y = !copy_flag? y : half_len;
textureVertices[3].s = !copy_flag? 0.0f : 0.f;
textureVertices[3].t = !copy_flag? 0.0f : 1.f;
textureVertices[3].u = texture_index_symmetric;
@@ -6562,14 +7004,15 @@ void setContactMatrixVertexArray(contact_matrix* Contact_Matrix_, bool copy_flag
global_function
void
-prepare_before_copy(f32 *original_control_points)
+prepare_before_copy(f32 *original_color_control_points)
{
// prepare before reading textures
glActiveTexture(GL_TEXTURE1);
- glBindTexture(GL_TEXTURE_BUFFER, Color_Maps->maps[Color_Maps->nMaps-1]);
+
+ glBindTexture(GL_TEXTURE_BUFFER, Color_Maps->maps[Color_Maps->nMaps-1]); // 绑定到颜色映射的最后一个颜色
glActiveTexture(GL_TEXTURE0);
for (u32 i = 0; i < 3 ; i ++ )
- original_control_points[i] = Color_Maps->controlPoints[i];
+ original_color_control_points[i] = Color_Maps->controlPoints[i];
Color_Maps->controlPoints[0] = 0.0f;
Color_Maps->controlPoints[1] = 0.5f;
Color_Maps->controlPoints[2] = 1.0f;
@@ -6582,12 +7025,12 @@ prepare_before_copy(f32 *original_control_points)
global_function
void
-restore_settings_after_copy(const f32 *original_control_points)
+restore_settings_after_copy(const f32 *original_color_control_points)
{
// restore settings
setContactMatrixVertexArray(Contact_Matrix, false, true); // restore the vertex array for rendering
for (u32 i = 0 ; i < 3 ; i ++ )
- Color_Maps->controlPoints[i] = original_control_points[i];
+ Color_Maps->controlPoints[i] = original_color_control_points[i];
glUseProgram(Contact_Matrix->shaderProgram);
glUniform3fv( Color_Maps->cpLocation, 1, Color_Maps->controlPoints);
glActiveTexture(GL_TEXTURE1);
@@ -6858,7 +7301,7 @@ global_function
void
KeyBoard(GLFWwindow* window, s32 key, s32 scancode, s32 action, s32 mods)
{
- if (!Loading && !Yahs_sorting && (action != GLFW_RELEASE || key == GLFW_KEY_SPACE || key == GLFW_KEY_A || key == GLFW_KEY_LEFT_SHIFT))
+ if (!Loading && !auto_sort_state && !auto_cut_state && (action != GLFW_RELEASE || key == GLFW_KEY_SPACE || key == GLFW_KEY_A || key == GLFW_KEY_LEFT_SHIFT))
{
if (UI_On)
{
@@ -6991,23 +7434,31 @@ KeyBoard(GLFWwindow* window, s32 key, s32 scancode, s32 action, s32 mods)
break;
case GLFW_KEY_C:
- if (!Extensions.head) break;
- TraverseLinkedList(Extensions.head, extension_node)
+ if (Select_Sort_Area_Mode && auto_curation_state.get_selected_fragments_num(Map_State, Number_of_Pixels_1D) > 0) // local area break
{
- switch (node->type)
- {
- case extension_graph:
+ auto_cut_state = 1;
+ }
+ else // open "coverage" extension
+ {
+ if (!Extensions.head) break;
+ TraverseLinkedList(Extensions.head, extension_node)
{
-
- graph *gph = (graph *)node->extension;
- if (strcmp((char *)gph->name, "coverage") == 0)
+ switch (node->type)
{
- gph->on = !gph->on;
- break;
+ case extension_graph:
+ {
+
+ graph *gph = (graph *)node->extension;
+ if (strcmp((char *)gph->name, "coverage") == 0)
+ {
+ gph->on = !gph->on;
+ break;
+ }
+ }
}
- }
}
}
+
break;
case GLFW_KEY_D:
@@ -7025,6 +7476,7 @@ KeyBoard(GLFWwindow* window, s32 key, s32 scancode, s32 action, s32 mods)
break;
case GLFW_KEY_F:
+ keyPressed = ToggleSelectSortAreaMode(window);
break;
case GLFW_KEY_G:
@@ -7059,7 +7511,6 @@ KeyBoard(GLFWwindow* window, s32 key, s32 scancode, s32 action, s32 mods)
break;
case GLFW_KEY_K:
- keyPressed = ToggleSelectSortAreaMode(window);
break;
case GLFW_KEY_L:
@@ -7139,7 +7590,7 @@ KeyBoard(GLFWwindow* window, s32 key, s32 scancode, s32 action, s32 mods)
}
else if (Select_Sort_Area_Mode)
{
- auto_curation_state.clear();
+ auto_curation_state.clear(); // clear the selected area
}
else
{
@@ -7202,6 +7653,10 @@ KeyBoard(GLFWwindow* window, s32 key, s32 scancode, s32 action, s32 mods)
break;
case GLFW_KEY_Z:
+ if (Select_Sort_Area_Mode)
+ {
+ auto_cut_state = 2; // restore the cutted frags within the selected area
+ }
break;
case GLFW_KEY_SPACE:
@@ -7250,11 +7705,10 @@ KeyBoard(GLFWwindow* window, s32 key, s32 scancode, s32 action, s32 mods)
}
else if (Select_Sort_Area_Mode && action == GLFW_PRESS)
{
- std::vector frags_id;
- auto_curation_state.get_selected_fragments(frags_id, Map_State, Number_of_Pixels_1D);
- if (frags_id.size() >= 2)
+ u32 selected_frag_num = auto_curation_state.get_selected_fragments_num(Map_State, Number_of_Pixels_1D);
+ if (selected_frag_num >= 2)
{
- Yahs_sorting = 1;
+ auto_sort_state = 1;
}
}
else
@@ -7288,6 +7742,10 @@ KeyBoard(GLFWwindow* window, s32 key, s32 scancode, s32 action, s32 mods)
}
}
+ else if (Select_Sort_Area_Mode)
+ {
+ auto_curation_state.change_sort_mode(-1);
+ }
else AdjustColorMap(-1);
break;
@@ -7305,15 +7763,28 @@ KeyBoard(GLFWwindow* window, s32 key, s32 scancode, s32 action, s32 mods)
}
}
}
+ else if (Select_Sort_Area_Mode)
+ {
+ auto_curation_state.change_sort_mode(1);
+ }
else AdjustColorMap(1);
break;
case GLFW_KEY_UP:
- NextColorMap(1);
+ if (Select_Sort_Area_Mode)
+ {
+ auto_curation_state.adjust_cut_threshold(1);
+ }
+ else NextColorMap(1);
break;
case GLFW_KEY_DOWN:
- NextColorMap(-1);
+ if (Select_Sort_Area_Mode)
+ {
+ auto_curation_state.adjust_cut_threshold(-1);
+ }
+ else
+ NextColorMap(-1);
break;
#ifdef Internal
case GLFW_KEY_ESCAPE:
@@ -8141,24 +8612,28 @@ resources, click each entry to view its licence.)text";
global_function void
UserSaveState(const char *, u08, char *);
+global_function
+void
+default_user_profile_settings () ;
+
global_variable char
- profile_savebuff[1024] = {0};
+profile_savebuff[1024] = {0};
global_function
- u08
- UserProfileEditorRun(const char *name, struct file_browser *browser, struct nk_context *ctx, u32 show, u08 save = 0)
+u08
+UserProfileEditorRun(const char *name, struct file_browser *browser, struct nk_context *ctx, u32 show, u08 save = 0)
{
struct nk_window *window = nk_window_find(ctx, name);
u32 doesExist = window != 0;
- if (!show && !doesExist)
+ if (!show && !doesExist) // 不显示 且 不存在
{
return (0);
}
- if (show && doesExist && (window->flags & NK_WINDOW_HIDDEN))
+ if (show && doesExist && (window->flags & NK_WINDOW_HIDDEN)) // 显示 且 存在 且 隐藏
{
- window->flags &= ~(nk_flags)NK_WINDOW_HIDDEN;
+ window->flags &= ~(nk_flags)NK_WINDOW_HIDDEN; // 取消隐藏
FileBrowserReloadDirectoryContent(browser, browser->directory);
}
@@ -8172,11 +8647,28 @@ global_function
nk_layout_row_dynamic(ctx, Screen_Scale.y * 30.0f, 1);
- if (nk_button_label(ctx, "Save"))
+ if (nk_button_label(ctx, "Save") && window && !(window->flags & NK_WINDOW_HIDDEN))
+ {
+ ret = 2;
+ }
+
+ if (nk_button_label(ctx, "Default") && window && !(window->flags & NK_WINDOW_HIDDEN))
{
- UserSaveState("userprofile", 1, 0);
+ default_user_profile_settings();
+ ret = 2;
}
+ // invert mouse setting
+ nk_layout_row_dynamic(ctx, Screen_Scale.y * 30.0f, 4);
+ bool original_value = user_profile_settings_ptr->invert_mouse;
+ nk_checkbox_label(NK_Context, "Invert Mouse Buttons", (int*)&user_profile_settings_ptr->invert_mouse);
+ if (original_value != user_profile_settings_ptr->invert_mouse)
+ {
+ fmt::print("[UserPofile]: Mouse_invert settings changed ({}) -> ({})\n", original_value, user_profile_settings_ptr->invert_mouse);
+ ret = 2;
+ }
+
+ // extensions
nk_layout_row_dynamic(NK_Context, Screen_Scale.y * 30.0f, 4);
if (Extensions.head)
@@ -8365,13 +8857,35 @@ global_function
nk_tree_pop(NK_Context);
}
+
+ // select the color for the selected area
+ if (nk_tree_push(NK_Context, NK_TREE_TAB, "Colour Selected Area", NK_MINIMIZED))
+ {
+ struct nk_colorf colour_bg = {
+ auto_curation_state.mask_color[0],
+ auto_curation_state.mask_color[1],
+ auto_curation_state.mask_color[2],
+ auto_curation_state.mask_color[3]};
+ nk_layout_row_dynamic(NK_Context, Screen_Scale.y * 200.0f, 4);
+ colour_bg = nk_color_picker(NK_Context, colour_bg, NK_RGBA);
+ auto_curation_state.mask_color[0] = colour_bg.r;
+ auto_curation_state.mask_color[1] = colour_bg.g;
+ auto_curation_state.mask_color[2] = colour_bg.b;
+ auto_curation_state.mask_color[3] = colour_bg.a;
+ nk_layout_row_dynamic(NK_Context, Screen_Scale.y * 30, 4);
+ if (nk_button_label(NK_Context, "Default"))
+ {
+ auto_curation_state.set_mask_color(auto_curation_state.mask_color_default);
+ }
+ nk_tree_pop(NK_Context);
+ }
// nk_tree_pop(NK_Context); // used to have this here, but it was causing a crash
nk_style_set_font(ctx, &NK_Font->handle);
}
nk_end(ctx);
- return (ret);
+ return ret;
}
@@ -8565,9 +9079,19 @@ global_variable
u08
SaveState_Magic_Tail_Manual = 3;
+/*
+保存当前状态，
+ headerHash: 用于生成文件名的哈希值
+ path: 保存路径
+ overwrite: 是否覆盖
+ version: 版本号，用于控制生成文件的版本，兼容上一个版本
+*/
global_function
u08
-SaveState(u64 headerHash, char *path = 0, u08 overwrite = 0)
+SaveState(
+ u64 headerHash, char *path = 0, u08 overwrite = 0,
+ u32 version = 0
+)
{
if (!path)
{
@@ -8608,7 +9132,8 @@ SaveState(u64 headerHash, char *path = 0, u08 overwrite = 0)
break;
}
}
-
+
+ // number of scaffs and metaFlags
u32 nScaffs = 0;
u32 nMetaFlags = 0;
ForLoop(Contigs->numberOfContigs)
@@ -8616,7 +9141,7 @@ SaveState(u64 headerHash, char *path = 0, u08 overwrite = 0)
if ((Contigs->contigs_arr + index)->scaffId) ++nScaffs;
if (*(Contigs->contigs_arr + index)->metaDataFlags) ++nMetaFlags;
}
-
+ // number of meta tags
u08 nMetaTags = 0;
u32 totalMetaTagSpace = 0;
ForLoop(ArrayCount(Meta_Data->tags))
@@ -8645,7 +9170,7 @@ SaveState(u64 headerHash, char *path = 0, u08 overwrite = 0)
settings |= Grid->on ? (1 << 3) : 0;
settings |= Contig_Ids->on ? (1 << 4) : 0;
settings |= Tool_Tip->on ? (1 << 5) : 0;
- settings |= Mouse_Invert ? (1 << 6) : 0;
+ settings |= user_profile_settings_ptr->invert_mouse ? (1 << 6) : 0;
settings |= Scaffs_Always_Visible ? (1 << 7) : 0;
*fileWriter++ = settings;
@@ -8970,8 +9495,10 @@ SaveState(u64 headerHash, char *path = 0, u08 overwrite = 0)
if (!path) // save the name SaveState_Name to file named as ptlsn
{
- u08 nameCache[17];
- CopyNullTerminatedString((u08 *)SaveState_Name, (u08 *)nameCache);
+ // u08 nameCache[17];
+ // CopyNullTerminatedString((u08 *)SaveState_Name, (u08 *)nameCache);
+
+ std::string nameCache_string = std::string((char *)SaveState_Name);
*(SaveState_Name + 0) = 'p';
*(SaveState_Name + 1) = 't';
@@ -8981,7 +9508,8 @@ SaveState(u64 headerHash, char *path = 0, u08 overwrite = 0)
*(SaveState_Name + 5) = '\0';
file = fopen((const char *)SaveState_Path, "wb");
- fwrite((u08 *)nameCache, 1, sizeof(nameCache), file);
+ // fwrite((u08 *)nameCache, 1, sizeof(nameCache), file);
+ fwrite((u08 *)nameCache_string.c_str(), 1, nameCache_string.size(), file);
fclose(file);
}
}
@@ -9187,7 +9715,7 @@ LoadState(u64 headerHash, char *path)
Grid->on = settings & (1 << 3);
Contig_Ids->on = settings & (1 << 4);
Tool_Tip->on = settings & (1 << 5);
- Mouse_Invert = settings & (1 << 6);
+ // user_profile_settings_ptr->invert_mouse = settings & (1 << 6); // this is moved to the user settings, then this setting will not be influnced by clearcache
Scaffs_Always_Visible = settings & (1 << 7);
nBytesRead += 2;
@@ -9545,7 +10073,7 @@ restore_initial_state()
Grid->on = 1;
Contig_Ids->on = 1;
Tool_Tip->on = 1;
- Mouse_Invert = 0;
+ // user_profile_settings_ptr = 0;
Scaffs_Always_Visible = 1;
MetaData_Always_Visible = 1;
@@ -9638,6 +10166,12 @@ restore_initial_state()
u32 nEdits = my_Min(Edits_Stack_Size, Map_Editor->nEdits);
ForLoop(nEdits) UndoMapEdit();
}
+
+ // restore all the splited contigs
+ {
+ Map_State->restore_cutted_contigs_all(Number_of_Pixels_1D);
+ }
+
// waypoints
{
@@ -9806,6 +10340,47 @@ UserSetSaveStatePaths()
}
}
+
+
+
+// default user profile settings
+global_function
+void
+default_user_profile_settings()
+{
+ // metadata tags color profile
+ meta_outline->on = 1;
+
+ // background color
+ active_bgcolor = 0;
+
+ // color map order
+ useCustomOrder = 1;
+ userColourMapOrder.nMaps = Color_Maps->nMaps;
+ for (u32 i = 0; i < Color_Maps->nMaps; i++)
+ {
+ userColourMapOrder.order[i] = i;
+ }
+
+ // select area color
+ auto_curation_state.set_default_mask_color();
+
+ // invert mouse
+ if (user_profile_settings_ptr)
+ {
+ user_profile_settings_ptr->invert_mouse = false;
+ }
+
+ // Grey out settings
+ if (Grey_Out_Settings)
+ {
+ delete Grey_Out_Settings;
+ Grey_Out_Settings = new GreyOutSettings(Meta_Data);
+ }
+ return ;
+}
+
+
global_function void
UserSaveState(const char *headerHash = "userprofile", u08 overwrite = 1, char *path = 0)
{
@@ -9889,6 +10464,33 @@ UserSaveState(const char *headerHash = "userprofile", u08 overwrite = 1, char *p
fwrite(&userColourMapOrder.nMaps, sizeof(userColourMapOrder.nMaps), 1, file);
fwrite(userColourMapOrder.order, sizeof(u32), userColourMapOrder.nMaps, file);
+ // save selected area color
+ fwrite(&auto_curation_state.mask_color, sizeof(auto_curation_state.mask_color), 1, file);
+
+ // save grey out flags
+ if (Grey_Out_Settings)
+ {
+ fwrite(Grey_Out_Settings->grey_out_flags, sizeof(int32_t), 64, file);
+ }
+ else
+ {
+ int32_t grey_out_flags[64] = {0};
+ fwrite(grey_out_flags, sizeof(int32_t), 64, file);
+ }
+
+ // save user profile settings
+ if (user_profile_settings_ptr)
+ {
+ fwrite(&user_profile_settings_ptr->invert_mouse, sizeof(bool), 1, file);
+ }
+ else
+ {
+ bool invert_mouse_tmp = false;
+ fwrite(&invert_mouse_tmp, sizeof(bool), 1, file);
+ }
+
+ // END of SAVE user profile settings
+
fclose(file);
printf("[UserProfile]: Saved to: %s\n", path);
@@ -10000,6 +10602,39 @@ global_function
fread(&userColourMapOrder.nMaps, sizeof(userColourMapOrder.nMaps), 1, file);
fread(userColourMapOrder.order, sizeof(u32), userColourMapOrder.nMaps, file);
+ // load selected area color
+ f32 tmp_mask_color[4];
+ if (fread(tmp_mask_color, sizeof(tmp_mask_color), 1, file) == 1)
+ {
+ auto_curation_state.set_mask_color(tmp_mask_color);
+ }
+ else
+ {
+ auto_curation_state.set_mask_color(auto_curation_state.mask_color_default);
+ }
+
+ // load grey out flags
+ int32_t grey_out_flags[64];
+ if (fread(grey_out_flags, sizeof(int32_t), 64, file) == 64)
+ {
+ if (Grey_Out_Settings)
+ {
+ memcpy(Grey_Out_Settings->grey_out_flags, grey_out_flags, 64 * sizeof(int32_t));
+ }
+ }
+
+ // load user profile settings
+ bool invert_mouse_tmp;
+ if (fread(&invert_mouse_tmp, sizeof(bool), 1, file) == 1)
+ {
+ if (user_profile_settings_ptr)
+ {
+ user_profile_settings_ptr->invert_mouse = invert_mouse_tmp;
+ }
+ }
+
+
+
fclose(file);
return 0; // Success
}
@@ -10060,9 +10695,9 @@ CopyEditsToClipBoard(GLFWwindow *window)
u32 oldFrom = Map_State->contigRelCoords[start];
u32 oldTo = Map_State->contigRelCoords[end];
- u32 *name1 = (Original_Contigs + Map_State->originalContigIds[start])->name;
- u32 *name2 = (Original_Contigs + Map_State->originalContigIds[end])->name;
- u32 *newName = (Original_Contigs + Map_State->originalContigIds[to])->name;
+ u32 *name1 = (Original_Contigs + Map_State->get_original_contig_id(start))->name;
+ u32 *name2 = (Original_Contigs + Map_State->get_original_contig_id(end))->name;
+ u32 *newName = (Original_Contigs + Map_State->get_original_contig_id(to))->name;
bufferPtr += (u32)stbsp_snprintf((char *)buffer + bufferPtr, (s32)(bufferSize - bufferPtr), "Edit %d:\n %s[%$.2fbp] to %s[%$.2fbp]\n%s\n %s[%$.2fbp]\n",
index + 1, (char *)name1, (f64)oldFrom * bpPerPixel, (char *)name2, (f64)oldTo * bpPerPixel,
@@ -10080,7 +10715,14 @@ CopyEditsToClipBoard(GLFWwindow *window)
global_function
void
GenerateAGP(char *path, u08 overwrite, u08 formatSingletons, u08 preserveOrder)
-{
+{
+
+ // 这里粘贴所有的original contigs
+ u32* tmp_orignal_contig_ids = new u32[Number_of_Pixels_1D];
+ for (u32 i = 0 ; i< Number_of_Pixels_1D; i++ )tmp_orignal_contig_ids[i] = Map_State->originalContigIds[i];
+ Map_State->restore_cutted_contigs_all(Number_of_Pixels_1D);
+ UpdateContigsFromMapState(); // todo 检查粘贴后会不会影响 painted 的 scaffolds
+
FILE *file;
if (!overwrite && (file = fopen((const char *)path, "rb")))
{
@@ -10124,7 +10766,7 @@ GenerateAGP(char *path, u08 overwrite, u08 formatSingletons, u08 preserveOrder)
u64 contRealEndCoord = (u64)((f64)(startCoord + cont->length) / (f64)Number_of_Pixels_1D * (f64)Total_Genome_Length);
u64 contRealSize = contRealEndCoord - contRealStartCoord + 1;
- char *contName = (char *)((Original_Contigs + cont->originalContigId)->name);
+ char *contName = (char *)((Original_Contigs + cont->get_original_contig_id())->name);
if (cont->scaffId && !type)
{
@@ -10185,6 +10827,12 @@ GenerateAGP(char *path, u08 overwrite, u08 formatSingletons, u08 preserveOrder)
fclose(file);
}
+
+ // 把临时切开的再粘贴上
+ for (u32 i = 0; i < Number_of_Pixels_1D; i++) Map_State->originalContigIds[i] = tmp_orignal_contig_ids[i];
+ UpdateContigsFromMapState();
+ delete[] tmp_orignal_contig_ids;
+ return;
}
@@ -10266,7 +10914,8 @@ void SortMapByMetaTags(u64 tagMask)
}
-MainArgs {
+MainArgs
+{
u32 initWithFile = 0; // initialization with .map file or not
u08 currFile[256]; // save the name of file inputed
u08 *currFileName = 0;
@@ -10456,11 +11105,19 @@ MainArgs {
Redisplay = 1;
}
- if (Yahs_sorting)
+ if (auto_sort_state)
{
if (currFileName) SaveState(headerHash);
- Sort_yahs((char*)currFileName);
- Yahs_sorting = 0;
+ auto_sort_func((char*)currFileName);
+ auto_sort_state = 0;
+ Redisplay = 1;
+ }
+
+ if (auto_cut_state)
+ {
+ if (currFileName) SaveState(headerHash);
+ auto_cut_func((char*)currFileName, Loading_Arena);
+ auto_cut_state = 0;
Redisplay = 1;
}
@@ -10533,7 +11190,7 @@ MainArgs {
{
static nk_flags flags = NK_WINDOW_BORDER | NK_WINDOW_SCALABLE | NK_WINDOW_MOVABLE | NK_WINDOW_SCROLL_AUTO_HIDE | NK_WINDOW_TITLE;
- if (nk_begin_titled(NK_Context, "Options", currFileName ? (const char *)currFileName : "", nk_rect(Screen_Scale.x * 10, Screen_Scale.y * 10, Screen_Scale.x * 800, Screen_Scale.y * 350), flags))
+ if (nk_begin_titled(NK_Context, "Options", currFileName ? (const char *)currFileName : "", nk_rect(Screen_Scale.x * 10, Screen_Scale.y * 10, Screen_Scale.x * 800, Screen_Scale.y * 600), flags))
{
struct nk_rect bounds = nk_window_get_bounds(NK_Context);
bounds.w /= 8;
@@ -10566,15 +11223,13 @@ MainArgs {
showUserProfileScreen = nk_button_label(NK_Context, "User Profile");
showAboutScreen = nk_button_label(NK_Context, "About");
- // AI & YaHS sort button
+ // AI & Pixel Sort button
struct nk_color sort_button_normal = nk_rgb(153, 50, 204);
struct nk_color sort_button_hover = nk_rgb(186, 85, 211);
struct nk_color sort_button_active = nk_rgb(128, 0, 128);
push_nk_style(NK_Context, sort_button_normal, sort_button_hover, sort_button_active);
nk_layout_row_dynamic(NK_Context, Screen_Scale.y * 30.0f, 3);
- // ai_sort_button = nk_button_label(NK_Context, "AI Sort");
- bounds = nk_widget_bounds(NK_Context);
- yahs_sort_button = nk_button_label(NK_Context, "YaHS Sort");
+
// AI sort button
/*
{
@@ -10617,18 +11272,86 @@ MainArgs {
}
}
*/
- // YaHS sort button
+ // Pixel Cut
+ {
+ bounds = nk_widget_bounds(NK_Context);
+ auto_cut_button = nk_button_label(NK_Context, "Pixel Cut");
+
+ if (auto_cut_button && currFileName)
+ {
+ auto_cut_state = 1;
+ auto_curation_state.clear(); // if click the button, the sort/cut will be applied globally
+ }
+ // window to set the parameters for cut
+ if (nk_contextual_begin(NK_Context, 0, nk_vec2(Screen_Scale.x * 480, Screen_Scale.y * 800), bounds))
+ {
+ nk_layout_row_dynamic(NK_Context, Screen_Scale.y * 30.0f, 1);
+
+ nk_label(NK_Context, "Cut threshold (default: 0.05)", NK_TEXT_LEFT);
+ nk_edit_string_zero_terminated(
+ NK_Context,
+ NK_EDIT_FIELD,
+ (char*)auto_curation_state.auto_cut_threshold_buf,
+ sizeof(auto_curation_state.auto_cut_threshold_buf),
+ nk_filter_float);
+
+ nk_label(NK_Context, "Pixel_mean window size (default: 8)", NK_TEXT_LEFT); // 见鬼了，见鬼了，这个地方，如果我使用 "Pixel_mean windows (default: 8)" 点击弹出的窗口外面程序就会卡死，但是使用"Pixel_mean window size (default: 8)" 就不会卡死
+ nk_edit_string_zero_terminated(
+ NK_Context,
+ NK_EDIT_FIELD,
+ (char*)auto_curation_state.auto_cut_diag_window_for_pixel_mean_buf,
+ sizeof(auto_curation_state.auto_cut_diag_window_for_pixel_mean_buf),
+ nk_filter_decimal);
+
+ nk_label(NK_Context, "Smallest frag size (default: 8)", NK_TEXT_LEFT);
+ nk_edit_string_zero_terminated(
+ NK_Context,
+ NK_EDIT_FIELD,
+ (char*)auto_curation_state.auto_cut_smallest_frag_size_in_pixel_buf,
+ sizeof(auto_curation_state.auto_cut_smallest_frag_size_in_pixel_buf),
+ nk_filter_decimal);
+
+ nk_layout_row_dynamic(NK_Context, Screen_Scale.y * 30.0f, 2);
+ if (nk_button_label(NK_Context, "Cancel"))
+ {
+ printf("[Pixel Cut] Cancel button clicked\n");
+ auto_curation_state.set_buf();
+ nk_contextual_close(NK_Context);
+ }
+ if (nk_button_label(NK_Context, "Apply"))
+ {
+ // Apply changes
+ // Convert text to integer and float
+ auto_curation_state.update_value_from_buf(); // todo 这里还有问题，因为设置了pixel_mean之后 并没有重新计算 pixel_density...
+
+ nk_contextual_close(NK_Context);
+
+ auto_curation_state.set_buf();
+ fmt::print("[Pixel Cut] cut_threshold: {:.3f}\n", auto_curation_state.auto_cut_threshold);
+ fmt::print("[Pixel Cut] pixel mean window size: {}\n", auto_curation_state.auto_cut_diag_window_for_pixel_mean);
+ fmt::print("[Pixel Cut] smallest_frag_size_in_pixel: {}\n", auto_curation_state.auto_cut_smallest_frag_size_in_pixel);
+ }
+
+ nk_contextual_end(NK_Context);
+
+
+ }
+ }
+
+ // Pixel Sort button
+ bounds = nk_widget_bounds(NK_Context);
+ auto_sort_button = nk_button_label(NK_Context, "Pixel Sort");
{
- if (yahs_sort_button)
+ if (auto_sort_button && currFileName)
{
- Yahs_sorting = 1;
- auto_curation_state.clear();
+ auto_sort_state = 1;
+ auto_curation_state.clear(); // if click the button, the sort/cut will be applied globally
}
// window to set the parameters for sort
if (nk_contextual_begin(NK_Context, 0, nk_vec2(Screen_Scale.x * 480, Screen_Scale.y * 400), bounds))
{
nk_layout_row_dynamic(NK_Context, Screen_Scale.y * 30.0f, 1);
- nk_label(NK_Context, "Smallest Frag Size (pixels):", NK_TEXT_LEFT);
+ nk_label(NK_Context, "Smallest Frag Size (default: 2)", NK_TEXT_LEFT);
nk_edit_string_zero_terminated(
NK_Context,
NK_EDIT_FIELD,
@@ -10636,7 +11359,7 @@ MainArgs {
sizeof(auto_curation_state.frag_size_buf),
nk_filter_decimal);
- nk_label(NK_Context, "Link Score Threshold:", NK_TEXT_LEFT);
+ nk_label(NK_Context, "Link threshold (default: 0.4)", NK_TEXT_LEFT);
nk_edit_string_zero_terminated(
NK_Context,
NK_EDIT_FIELD,
@@ -10660,36 +11383,38 @@ MainArgs {
auto_curation_state.sort_mode = 2;
}
+ // if (nk_option_label(NK_Context, "YaHS", auto_curation_state.sort_mode == 3))
+ // {
+ // auto_curation_state.sort_mode = 3;
+ // }
+
nk_layout_row_dynamic(NK_Context, Screen_Scale.y * 30.0f, 2);
if (nk_button_label(NK_Context, "Cancel"))
{
- printf("[YaHS Sort] Cancel button clicked\n");
+ printf("[Pixel Sort] Cancel button clicked\n");
+ auto_curation_state.set_buf();
nk_contextual_close(NK_Context);
}
if (nk_button_label(NK_Context, "Apply"))
{
// Apply changes
// Convert text to integer and float
- auto_curation_state.smallest_frag_size_in_pixel = (u32)atoi((char*)auto_curation_state.frag_size_buf);
- auto_curation_state.link_score_threshold = (float)atof((char*)auto_curation_state.score_threshold_buf);
+ auto_curation_state.update_value_from_buf();
+
nk_contextual_close(NK_Context);
- if (auto_curation_state.link_score_threshold > 1.0f || auto_curation_state.link_score_threshold < 0.0f)
- {
- printf("[YaHS Sort] Warning: link Score Threshold should be in the range of [0, 1]\n");
- auto_curation_state.link_score_threshold = std::max(0.0f, std::min(1.0f, auto_curation_state.link_score_threshold));
- }
+
auto_curation_state.set_buf();
- printf("[YaHS Sort] smallest_frag_size_in_pixel: %d\n", auto_curation_state.smallest_frag_size_in_pixel);
- printf("[YaHS Sort] link_score_threshold: %.3f\n", auto_curation_state.link_score_threshold);
- printf("[YaHS Sort] Sort mode: %s\n", auto_curation_state.get_sort_mode_name().c_str());
+ fmt::print("[Pixel Sort] smallest_frag_size_in_pixel: {}\n", auto_curation_state.smallest_frag_size_in_pixel);
+ fmt::print("[Pixel Sort] link_score_threshold: {:.3f}\n", auto_curation_state.link_score_threshold);
+ fmt::print("[Pixel Sort] Sort mode: {}\n", auto_curation_state.get_sort_mode_name());
}
// redo all the changes
- if (!auto_curation_state.show_yahs_redo_confirm_popup)
+ if (!auto_curation_state.show_autoSort_redo_confirm_popup)
{
nk_layout_row_dynamic(NK_Context, Screen_Scale.y * 30.0f, 1);
if (nk_button_label(NK_Context, "Redo All (Careful!)"))
{
- auto_curation_state.show_yahs_redo_confirm_popup=true;
+ auto_curation_state.show_autoSort_redo_confirm_popup=true;
}
} else
{
@@ -10698,22 +11423,22 @@ MainArgs {
nk_layout_row_dynamic(NK_Context, Screen_Scale.y * 30.0f, 2);
if (nk_button_label(NK_Context, "Yes"))
{
- auto_curation_state.show_yahs_redo_confirm_popup=false;
- printf("[YaHS Sort] Redo all edits.\n");
+ auto_curation_state.show_autoSort_redo_confirm_popup=false;
+ printf("[Pixel Sort] Redo all edits.\n");
RedoAllEdits(Map_Editor);
}
if (nk_button_label(NK_Context, "No"))
{
- auto_curation_state.show_yahs_redo_confirm_popup=false;
+ auto_curation_state.show_autoSort_redo_confirm_popup=false;
}
}
// reject all the edits
- if (!auto_curation_state.show_yahs_erase_confirm_popup)
+ if (!auto_curation_state.show_autoSort_erase_confirm_popup)
{
nk_layout_row_dynamic(NK_Context, Screen_Scale.y * 30.0f, 1);
if (nk_button_label(NK_Context, "Erase All (Careful!)"))
{
- auto_curation_state.show_yahs_erase_confirm_popup=true;
+ auto_curation_state.show_autoSort_erase_confirm_popup=true;
}
} else
{
@@ -10722,19 +11447,19 @@ MainArgs {
nk_layout_row_dynamic(NK_Context, Screen_Scale.y * 30.0f, 2);
if (nk_button_label(NK_Context, "Yes"))
{
- auto_curation_state.show_yahs_erase_confirm_popup=false;
- printf("[YaHS Sort] Erase all edits.\n");
+ auto_curation_state.show_autoSort_erase_confirm_popup=false;
+ printf("[Pixel Sort] Erase all edits.\n");
EraseAllEdits(Map_Editor);
}
if (nk_button_label(NK_Context, "No"))
{
- auto_curation_state.show_yahs_erase_confirm_popup=false;
+ auto_curation_state.show_autoSort_erase_confirm_popup=false;
}
}
nk_contextual_end(NK_Context);
}
}
- pop_nk_style(NK_Context, 3);
+ pop_nk_style(NK_Context, 3); // pop the style for Pixel Cut and Pixel Sort button
// waypoint edit mode
nk_layout_row_dynamic(NK_Context, Screen_Scale.y * 30.0f, 3);
@@ -11024,11 +11749,49 @@ MainArgs {
nk_contextual_end(NK_Context);
}
+
+ bool original_value = user_profile_settings_ptr->invert_mouse;
+ nk_checkbox_label(NK_Context, "Invert Mouse Buttons", (int*)&user_profile_settings_ptr->invert_mouse);
+ if (original_value != user_profile_settings_ptr->invert_mouse)
+ {
+ fmt::print("[UserPofile]: Mouse_invert settings changed ({}) -> ({})\n", original_value, user_profile_settings_ptr->invert_mouse);
+ UserSaveState();
+ }
+
+
+ // select current active tag
+ if (nk_tree_push(NK_Context, NK_TREE_TAB, "Select Active Tag", NK_MINIMIZED))
+ {
+ nk_layout_row_dynamic(NK_Context, Screen_Scale.y * 20.0f, 4);
+ for (u32 i = 0; i < ArrayCount(Meta_Data->tags); i ++ )
+ {
+ if (*Meta_Data->tags[i] == 0) break;
+ int tmp = ( MetaData_Active_Tag == i) ;
+ tmp = nk_check_label(NK_Context, (char*)Meta_Data->tags[i], tmp);
+ if (tmp) MetaData_Active_Tag = i;
+ }
+ nk_tree_pop(NK_Context);
+ }
+
+ // grey out settings
+ if (nk_tree_push(NK_Context, NK_TREE_TAB, "Grey Out Tags", NK_MINIMIZED))
+ {
+ nk_layout_row_dynamic(NK_Context, Screen_Scale.y * 20.0f, 4);
+ for (u32 i = 0; i < ArrayCount(Meta_Data->tags); i ++ )
+ {
+ if (*Meta_Data->tags[i] == 0) break;
+ s32 tmp = Grey_Out_Settings->grey_out_flags[i];
+ nk_checkbox_label(NK_Context, (char*)Meta_Data->tags[i], Grey_Out_Settings->grey_out_flags+i);
+ if (tmp!=Grey_Out_Settings->grey_out_flags[i])
+ {
+ fmt::print("[UserPofile]: Grey out tags changed\n");
+ UserSaveState();
+ }
+ }
+ nk_tree_pop(NK_Context);
+ }
- Mouse_Invert = nk_check_label(NK_Context, "Invert Mouse Buttons", (s32)Mouse_Invert) ? 1 : 0;
- nk_layout_row_dynamic(NK_Context, Screen_Scale.y * 30.0f, 2);
- Grey_Haplotigs = nk_check_label(NK_Context, "Grey out 'Haplotig'", (s32)Grey_Haplotigs) ? 1 : 0;
nk_layout_row_dynamic(NK_Context, Screen_Scale.y * 30.0f, 2);
nk_label(NK_Context, "Gamma Min", NK_TEXT_LEFT);
@@ -11115,7 +11878,7 @@ MainArgs {
static int tree_state = 0;
// Tree tab for checkboxes
- if (nk_tree_push(NK_Context, NK_TREE_TAB, "Select Tags", NK_MINIMIZED))
+ if (nk_tree_push(NK_Context, NK_TREE_TAB, "Select Tags Move to End", NK_MINIMIZED))
{
nk_layout_row_dynamic(NK_Context, Screen_Scale.y * 20.0f, 4); // Adjust layout for checkboxes
for (int i = 0; i < NUM_TAGS; i++)
@@ -11128,7 +11891,7 @@ MainArgs {
}
nk_layout_row_dynamic(NK_Context, Screen_Scale.y * 30.0f, 3); // Layout for buttons
- if (nk_button_label(NK_Context, "Sort Selected"))
+ if (nk_button_label(NK_Context, "Move Selected"))
{
if (!sortMetaEdits)
{
@@ -11143,7 +11906,7 @@ MainArgs {
SortMapByMetaTags(tag_mask); // Pass the tag mask to the sorting function
}
}
- if (nk_button_label(NK_Context, "Sort All Tags"))
+ if (nk_button_label(NK_Context, "Move All Tags"))
{
if (!sortMetaEdits)
{
@@ -11151,7 +11914,7 @@ MainArgs {
SortMapByMetaTags(all_tags_mask);
}
}
- if (nk_button_label(NK_Context, "Undo Sort"))
+ if (nk_button_label(NK_Context, "Undo Move"))
{
while (sortMetaEdits)
{
@@ -11220,9 +11983,9 @@ MainArgs {
u32 oldFrom = Map_State->contigRelCoords[start];
u32 oldTo = Map_State->contigRelCoords[end];
- u32 *name1 = (Original_Contigs + Map_State->originalContigIds[start])->name;
- u32 *name2 = (Original_Contigs + Map_State->originalContigIds[end])->name;
- u32 *newName = (Original_Contigs + Map_State->originalContigIds[to])->name;
+ u32 *name1 = (Original_Contigs + Map_State->get_original_contig_id(start))->name;
+ u32 *name2 = (Original_Contigs + Map_State->get_original_contig_id(end))->name;
+ u32 *newName = (Original_Contigs + Map_State->get_original_contig_id(to))->name;
stbsp_snprintf((char *)buff, sizeof(buff), "Edit %d:", index + 1);
nk_label(NK_Context, (const char *)buff, NK_TEXT_LEFT);
@@ -11334,9 +12097,10 @@ MainArgs {
}
// Input Sequences
- {
+ {
+ std::string input_sequence_name = fmt::format("Input Sequences ({})", Number_of_Original_Contigs);
nk_layout_row_dynamic(NK_Context, Screen_Scale.y * 30.0f, 1);
- if (nk_tree_push(NK_Context, NK_TREE_TAB, "Input Sequences", NK_MINIMIZED))
+ if (nk_tree_push(NK_Context, NK_TREE_TAB, input_sequence_name.c_str(), NK_MINIMIZED))
{
nk_layout_row_dynamic(NK_Context, Screen_Scale.y * 30.0f, 3);
nk_label(NK_Context, "Search: ", NK_TEXT_LEFT);
@@ -11431,7 +12195,7 @@ MainArgs {
u32 startCoord = cont->startCoord;
u32 endCoord = IsContigInverted(index2) ? (startCoord - cont->length + 1) : (startCoord + cont->length);
- stbsp_snprintf((char *)buff, sizeof(buff), "%s [%$" PRIu64 "bp to %$" PRIu64 "bp]", (char *)((Original_Contigs + cont->originalContigId)->name), (u64)((f64)startCoord / (f64)Number_of_Pixels_1D * (f64)Total_Genome_Length), (u64)((f64)(endCoord) / (f64)Number_of_Pixels_1D * (f64)Total_Genome_Length));
+ stbsp_snprintf((char *)buff, sizeof(buff), "%s [%$" PRIu64 "bp to %$" PRIu64 "bp]", (char *)((Original_Contigs + cont->get_original_contig_id())->name), (u64)((f64)startCoord / (f64)Number_of_Pixels_1D * (f64)Total_Genome_Length), (u64)((f64)(endCoord) / (f64)Number_of_Pixels_1D * (f64)Total_Genome_Length));
if (nk_button_label(NK_Context, (char *)buff))
{
f32 p = pos + (0.5f * contLen);
@@ -11600,7 +12364,9 @@ MainArgs {
u08 state;
if ((state = UserProfileEditorRun("User profile editor", &saveBrowser, NK_Context, (u32)showUserProfileScreen, 1)))
{
- UserSaveState("trial", state & 2, saveBrowser.file);
+ if (showUserProfileScreen)
+ fmt::print("[UserPofile]: showUserProfileScreen = {} \n", showUserProfileScreen);
+ UserSaveState("userprofile", state & 2, 0); // save the user profile settings
FileBrowserReloadDirectoryContent(&saveBrowser, saveBrowser.directory);
}
@@ -11651,6 +12417,35 @@ MainArgs {
// and memory allocated by new or malloc
delete[] Contact_Matrix->vaos;
delete[] Contact_Matrix->vbos;
+ if (Grey_Out_Settings)
+ {
+ delete Grey_Out_Settings; Grey_Out_Settings = nullptr;
+ }
+ if (user_profile_settings_ptr)
+ {
+ delete user_profile_settings_ptr; user_profile_settings_ptr = nullptr;
+ }
+
+ if (pixel_density_extension)
+ {
+ delete pixel_density_extension; pixel_density_extension = nullptr;
+ }
+
+ if (textures_array_ptr)
+ {
+ delete textures_array_ptr; textures_array_ptr = nullptr;
+ }
+
+ if (frag_cut_cal_ptr)
+ {
+ delete frag_cut_cal_ptr; frag_cut_cal_ptr = nullptr;
+ }
+
+ if (frag_sort_method)
+ {
+ delete frag_sort_method; frag_sort_method = nullptr;
+ }
+
ResetMemoryArenaP(Loading_Arena);
fprintf(stdout, "Memory freed for the arena.\n");
diff --git a/README.md b/README.md
index baa86b3..c69cf85 100644
--- a/README.md
+++ b/README.md
@@ -12,7 +12,7 @@ PretextView is a desktop application for viewing pretext contact maps.
- `right mouse button`: holding down and move to drag the Hi-C figure move within the window.
- `Mouse scroll` to zoom. A three button mouse is recomended.
- `E`: enter the Edit mode.
-- `K`: enter the Select sort area mode.
+- `F`: enter the Select sort area mode.
- `M`: enter the Meta Tag edit mode.
- `S`: enter the Scaffold painting mode.
- `X`: enter the extension edit mode.
@@ -48,36 +48,50 @@ PretextView is a desktop application for viewing pretext contact maps.
Enter scaffolding mode with the 's' key.
- Use the GUI to see a list of scaffolds.
-## Select sort area model (`K`)
+## Select sort area mode (`F`)
-After click `YaHS sort` button in the main UI, it will defaultly run sort globally. If enter the the `select sort area mode`(by pressing `K`), it can sort only the selected area with pressing `Space` after selecting at least 3 contigs.
+After click `Pixel Sort` button in the main UI, it will defaultly run sort globally. If enter the the `select sort area mode`(by pressing `F`), it can sort only the selected area with pressing `Space` after selecting at least 2 contigs.
-Enter the select sort area mode by pressing `K`.
+Enter the select sort area mode by pressing `F`.
- `Left mouse click`: select / un-select area for sorting.
- `S`: clear all the select area.
-- `Space`: call `YaHS sort` to sort the select area **(NOTE: only work if select at least 3 fragments)**.
+- `Space`: call `Pixel Sort` to sort the select area **(NOTE: only work if select at least 3 fragments)**.
- `Q/W`: quit/redo edit (currently will change the edit made globally not only the edit made within the selected area, so use this with caution as it can change also other parts)
+- `C`: cut the scaffolds/contigs within the selected area.
+- `Z`: glue the splitted fragments within the selected area. (NOTE: only link the continuous fragments.)
## Sort fragments according to link score
Usage, first endter the main GUI:
-- **Right click** the `YaHS Sort` button to open sort settings,
+- **Right click** the `Pixel Sort` button to open sort settings,
- `Smallest Frag Size (pixels)` (defaul: 2) which represents the smallest fragment size in unit of pixels to consider during the sorting
- `Link Score Threshold`: $S_{thresh}$ (defaul: 0.4).
- Select the sort mode:
- `UnionFind`: sort all links higher than $S_{thresh}$ and then traverse all the links by from high to low.
- `Fuse`: traverse all links and fuse two chains.
-- **Left click** the `YaHS Sort` button: run.
+- **Left click** the `Pixel Sort` button: run.
- **Redo all edits**
- **Erase all edits**
+## `Pixel Cut` according to the continuity of HiC density
+Usage:
+In the main GUI:
+ - **Right click** the `Pixel Cut` button to open cut settings,
+ - `Cut threshold`: the smaller, the more likely to break one contig at the discontinuous locations.
+ - `Pixel_mean window size`: length of range from diagonl line, which is considered to calculate the HiC density.
+ - `Smallest frag size`: the smallest fragment length that can be generated.
+ - **Left click** the `Pixel Cut` button: cut all the scaffolds/contigs globally.
+
+
+
+
## User Profile
Click the `User Profile` button in main GUI.
-
+
-Set the `Meta tags`, `Background Color`, `Color Map`(HiC figure), `Extension settings`.
+Set the `Meta tags`, `Background Color`, `Color Map`(HiC figure), `Extension settings` and the `Colour Selected Area`.
# Saving
@@ -120,6 +134,7 @@ PretextView uses the following third-party libraries:
* [stb_sprintf](https://github.com/nothings/stb/blob/master/stb_sprintf.h)
* Fonts from the 'Droid Serif' font set
* [Icons from open-iconic](https://github.com/iconic/open-iconic)
+* [fmt](https://github.com/fmtlib/fmt)
# Installation
@@ -151,7 +166,7 @@ to remove the **quarantine** and then unmount and re-mount the dmg file. And the
The score between two fragments represents the level of continuity. The higher score the better continuity.
-The link score calculation method refers to [YaHS](https://github.com/c-zhou/yahs). Thus, we call this function as **YaHS Sort**.
+The link score calculation method refers to [YaHS](https://github.com/c-zhou/yahs).
Reference: Chenxi Zhou, Shane A McCarthy, Richard Durbin, YaHS: yet another Hi-C scaffolding tool,
Bioinformatics, Volume 39, Issue 1, January 2023, btac808, https://doi.org/10.1093/bioinformatics/btac808
diff --git a/doc/image.png b/doc/image.png
deleted file mode 100644
index a6c47f7..0000000
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diff --git a/doc/image_mainGUI.png b/doc/image_mainGUI.png
index 3cdb4d7..badd407 100644
Binary files a/doc/image_mainGUI.png and b/doc/image_mainGUI.png differ
diff --git a/doc/image_user_profile.png b/doc/image_user_profile.png
new file mode 100644
index 0000000..3e4ec70
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diff --git a/ico_design/icon_v2.iconset/icon_128x128.png b/ico_design/icon_v2.iconset/icon_128x128.png
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diff --git a/ico_design/icon_v2.iconset/icon_32x32.png b/ico_design/icon_v2.iconset/icon_32x32.png
new file mode 100644
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diff --git a/ico_design/icon_v2.iconset/icon_512x512.png b/ico_design/icon_v2.iconset/icon_512x512.png
new file mode 100644
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diff --git a/ico_design/icon_v2.iconset/icon_64x64.png b/ico_design/icon_v2.iconset/icon_64x64.png
new file mode 100644
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diff --git a/include/nlohmann/json.hpp b/include/nlohmann/json.hpp
new file mode 100644
index 0000000..07dea3c
--- /dev/null
+++ b/include/nlohmann/json.hpp
@@ -0,0 +1,25510 @@
+// __ _____ _____ _____
+// __| | __| | | | JSON for Modern C++
+// | | |__ | | | | | | version 3.11.3
+// |_____|_____|_____|_|___| https://github.com/nlohmann/json
+//
+// SPDX-FileCopyrightText: 2013 - 2025 Niels Lohmann
+// SPDX-License-Identifier: MIT
+
+/****************************************************************************\
+ * Note on documentation: The source files contain links to the online *
+ * documentation of the public API at https://json.nlohmann.me. This URL *
+ * contains the most recent documentation and should also be applicable to *
+ * previous versions; documentation for deprecated functions is not *
+ * removed, but marked deprecated. See "Generate documentation" section in *
+ * file docs/README.md. *
+\****************************************************************************/
+
+#ifndef INCLUDE_NLOHMANN_JSON_HPP_
+#define INCLUDE_NLOHMANN_JSON_HPP_
+
+#include // all_of, find, for_each
+#include // nullptr_t, ptrdiff_t, size_t
+#include // hash, less
+#include // initializer_list
+#ifndef JSON_NO_IO
+ #include // istream, ostream
+#endif // JSON_NO_IO
+#include // random_access_iterator_tag
+#include // unique_ptr
+#include // string, stoi, to_string
+#include // declval, forward, move, pair, swap
+#include // vector
+
+// #include
+// __ _____ _____ _____
+// __| | __| | | | JSON for Modern C++
+// | | |__ | | | | | | version 3.11.3
+// |_____|_____|_____|_|___| https://github.com/nlohmann/json
+//
+// SPDX-FileCopyrightText: 2013 - 2025 Niels Lohmann
+// SPDX-License-Identifier: MIT
+
+
+
+#include
+
+// #include
+// __ _____ _____ _____
+// __| | __| | | | JSON for Modern C++
+// | | |__ | | | | | | version 3.11.3
+// |_____|_____|_____|_|___| https://github.com/nlohmann/json
+//
+// SPDX-FileCopyrightText: 2013 - 2025 Niels Lohmann
+// SPDX-License-Identifier: MIT
+
+
+
+// This file contains all macro definitions affecting or depending on the ABI
+
+#ifndef JSON_SKIP_LIBRARY_VERSION_CHECK
+ #if defined(NLOHMANN_JSON_VERSION_MAJOR) && defined(NLOHMANN_JSON_VERSION_MINOR) && defined(NLOHMANN_JSON_VERSION_PATCH)
+ #if NLOHMANN_JSON_VERSION_MAJOR != 3 || NLOHMANN_JSON_VERSION_MINOR != 11 || NLOHMANN_JSON_VERSION_PATCH != 3
+ #warning "Already included a different version of the library!"
+ #endif
+ #endif
+#endif
+
+#define NLOHMANN_JSON_VERSION_MAJOR 3 // NOLINT(modernize-macro-to-enum)
+#define NLOHMANN_JSON_VERSION_MINOR 11 // NOLINT(modernize-macro-to-enum)
+#define NLOHMANN_JSON_VERSION_PATCH 3 // NOLINT(modernize-macro-to-enum)
+
+#ifndef JSON_DIAGNOSTICS
+ #define JSON_DIAGNOSTICS 0
+#endif
+
+#ifndef JSON_DIAGNOSTIC_POSITIONS
+ #define JSON_DIAGNOSTIC_POSITIONS 0
+#endif
+
+#ifndef JSON_USE_LEGACY_DISCARDED_VALUE_COMPARISON
+ #define JSON_USE_LEGACY_DISCARDED_VALUE_COMPARISON 0
+#endif
+
+#if JSON_DIAGNOSTICS
+ #define NLOHMANN_JSON_ABI_TAG_DIAGNOSTICS _diag
+#else
+ #define NLOHMANN_JSON_ABI_TAG_DIAGNOSTICS
+#endif
+
+#if JSON_DIAGNOSTIC_POSITIONS
+ #define NLOHMANN_JSON_ABI_TAG_DIAGNOSTIC_POSITIONS _dp
+#else
+ #define NLOHMANN_JSON_ABI_TAG_DIAGNOSTIC_POSITIONS
+#endif
+
+#if JSON_USE_LEGACY_DISCARDED_VALUE_COMPARISON
+ #define NLOHMANN_JSON_ABI_TAG_LEGACY_DISCARDED_VALUE_COMPARISON _ldvcmp
+#else
+ #define NLOHMANN_JSON_ABI_TAG_LEGACY_DISCARDED_VALUE_COMPARISON
+#endif
+
+#ifndef NLOHMANN_JSON_NAMESPACE_NO_VERSION
+ #define NLOHMANN_JSON_NAMESPACE_NO_VERSION 0
+#endif
+
+// Construct the namespace ABI tags component
+#define NLOHMANN_JSON_ABI_TAGS_CONCAT_EX(a, b, c) json_abi ## a ## b ## c
+#define NLOHMANN_JSON_ABI_TAGS_CONCAT(a, b, c) \
+ NLOHMANN_JSON_ABI_TAGS_CONCAT_EX(a, b, c)
+
+#define NLOHMANN_JSON_ABI_TAGS \
+ NLOHMANN_JSON_ABI_TAGS_CONCAT( \
+ NLOHMANN_JSON_ABI_TAG_DIAGNOSTICS, \
+ NLOHMANN_JSON_ABI_TAG_LEGACY_DISCARDED_VALUE_COMPARISON, \
+ NLOHMANN_JSON_ABI_TAG_DIAGNOSTIC_POSITIONS)
+
+// Construct the namespace version component
+#define NLOHMANN_JSON_NAMESPACE_VERSION_CONCAT_EX(major, minor, patch) \
+ _v ## major ## _ ## minor ## _ ## patch
+#define NLOHMANN_JSON_NAMESPACE_VERSION_CONCAT(major, minor, patch) \
+ NLOHMANN_JSON_NAMESPACE_VERSION_CONCAT_EX(major, minor, patch)
+
+#if NLOHMANN_JSON_NAMESPACE_NO_VERSION
+#define NLOHMANN_JSON_NAMESPACE_VERSION
+#else
+#define NLOHMANN_JSON_NAMESPACE_VERSION \
+ NLOHMANN_JSON_NAMESPACE_VERSION_CONCAT(NLOHMANN_JSON_VERSION_MAJOR, \
+ NLOHMANN_JSON_VERSION_MINOR, \
+ NLOHMANN_JSON_VERSION_PATCH)
+#endif
+
+// Combine namespace components
+#define NLOHMANN_JSON_NAMESPACE_CONCAT_EX(a, b) a ## b
+#define NLOHMANN_JSON_NAMESPACE_CONCAT(a, b) \
+ NLOHMANN_JSON_NAMESPACE_CONCAT_EX(a, b)
+
+#ifndef NLOHMANN_JSON_NAMESPACE
+#define NLOHMANN_JSON_NAMESPACE \
+ nlohmann::NLOHMANN_JSON_NAMESPACE_CONCAT( \
+ NLOHMANN_JSON_ABI_TAGS, \
+ NLOHMANN_JSON_NAMESPACE_VERSION)
+#endif
+
+#ifndef NLOHMANN_JSON_NAMESPACE_BEGIN
+#define NLOHMANN_JSON_NAMESPACE_BEGIN \
+ namespace nlohmann \
+ { \
+ inline namespace NLOHMANN_JSON_NAMESPACE_CONCAT( \
+ NLOHMANN_JSON_ABI_TAGS, \
+ NLOHMANN_JSON_NAMESPACE_VERSION) \
+ {
+#endif
+
+#ifndef NLOHMANN_JSON_NAMESPACE_END
+#define NLOHMANN_JSON_NAMESPACE_END \
+ } /* namespace (inline namespace) NOLINT(readability/namespace) */ \
+ } // namespace nlohmann
+#endif
+
+// #include
+// __ _____ _____ _____
+// __| | __| | | | JSON for Modern C++
+// | | |__ | | | | | | version 3.11.3
+// |_____|_____|_____|_|___| https://github.com/nlohmann/json
+//
+// SPDX-FileCopyrightText: 2013 - 2025 Niels Lohmann
+// SPDX-License-Identifier: MIT
+
+
+
+#include // transform
+#include // array
+#include // forward_list
+#include // inserter, front_inserter, end
+#include