add search boxes

PretextView.cpp

@@ -1454,14 +1454,13 @@ FileBrowserRun(const char *name, struct file_browser *browser, struct nk_context
         {   
             /* define a string here for filtering */
             std::string searchbuf_str="";
-            if (!save){ // only need this while loading something
-                nk_layout_row_dynamic(NK_Context, Screen_Scale.y * 25.0f, 3);
-                nk_label(NK_Context, "Search: ", NK_TEXT_LEFT);
-                nk_edit_string_zero_terminated(NK_Context, NK_EDIT_FIELD, searchbuf, sizeof(searchbuf) - 1, nk_filter_default);
-                caseSensitive_search_sequences = nk_check_label(NK_Context, "Case Sensitive", caseSensitive_search_sequences) ? 1 : 0;
-                searchbuf_str = std::string(searchbuf);
-                if (!caseSensitive_search_sequences) std::transform(searchbuf_str.begin(), searchbuf_str.end(), searchbuf_str.begin(), ::tolower);
-            }
+            // Show search box for all file browser dialogs (load and save)
+            nk_layout_row_dynamic(NK_Context, Screen_Scale.y * 25.0f, 3);
+            nk_label(NK_Context, "Search: ", NK_TEXT_LEFT);
+            nk_edit_string_zero_terminated(NK_Context, NK_EDIT_FIELD, searchbuf, sizeof(searchbuf) - 1, nk_filter_default);
+            caseSensitive_search_sequences = nk_check_label(NK_Context, "Case Sensitive", caseSensitive_search_sequences) ? 1 : 0;
+            searchbuf_str = std::string(searchbuf);
+            if (!caseSensitive_search_sequences) std::transform(searchbuf_str.begin(), searchbuf_str.end(), searchbuf_str.begin(), ::tolower);
 
             s32 index = -1;
             size_t i = 0, j = 0;//, k = 0;
@@ -5790,7 +5789,7 @@ LoadFile(const char *filePath, memory_arena *arena, char **fileName, u64 *header
 {
     u64 fileSize = 0;
 
-    FILE *file = TestFile(filePath, &fileSize); //  检查前4个字节读取到的数据， 如果为 u08 Magic[] = {'p', 's', 't', 'm'} 则通过验证，否则将指针file设置为空指针
+    FILE *file = TestFile(filePath, &fileSize); //  Check the data read from the first 4 bytes. If it matches u08 Magic[] = {'p', 's', 't', 'm'}, the verification passes; otherwise, set the pointer file to a null pointer.
     if (!file)    // 如果为空指针， 返回读取错误fileErr
     {
         return(fileErr);
@@ -8867,7 +8866,7 @@ KeyBoard(GLFWwindow* window, s32 key, s32 scancode, s32 action, s32 mods)
                     break;
 
                 case GLFW_KEY_3:
-                    if (Extension_Mode && Extensions.head)
+                    if (Extensions.head)
                     {
                         TraverseLinkedList(Extensions.head, extension_node)
                         {
@@ -8884,7 +8883,6 @@ KeyBoard(GLFWwindow* window, s32 key, s32 scancode, s32 action, s32 mods)
                             }
                             }
                         }
-                        break;
                     }
                     else
                     {
@@ -8893,7 +8891,7 @@ KeyBoard(GLFWwindow* window, s32 key, s32 scancode, s32 action, s32 mods)
                     break;
 
                 case GLFW_KEY_5:
-                    if (Extension_Mode && Extensions.head)
+                    if (Extensions.head)
                     {
                         TraverseLinkedList(Extensions.head, extension_node)
                         {
@@ -8910,7 +8908,6 @@ KeyBoard(GLFWwindow* window, s32 key, s32 scancode, s32 action, s32 mods)
                             }
                             }
                         }
-                        break;
                     }
                     else
                     {

README.md

@@ -21,6 +21,8 @@ PretextView is a desktop application for viewing pretext contact maps.<br/>
 - `L`: toggle the Grid Line.
 - `T`: toggle the Tooltip.
 - `I`: toggle the ID bar.
+- `3`: toggle the 3p_telomere extension.
+- `5`: toggle the 5p_telomere extension.
 - `Up` / `Down`: change the color map.
 - `Left` / `Right`: decrease / increase the Gamma mid (default: 0.5).
 
@@ -50,15 +52,15 @@ Enter scaffolding mode with the 's' key.
 
 ## Extension edit mode (`X`)
 Enter extension mode with the `X` key to toggle various genomic feature overlays. Once in extension mode, press:
-- `3`: Toggle **3p_telomere** track on/off
-- `5`: Toggle **5p_telomere** track on/off
+- `3`: Toggle **3p_telomere** track on/off (also works at top level)
+- `5`: Toggle **5p_telomere** track on/off (also works at top level)
 - `T`: Toggle general **telomere** track on/off
 - `C`: Toggle **coverage** track on/off
 - `G`: Toggle **gap** track on/off
 - `R`: Toggle **repeat_density** track on/off
 - `X`: Exit extension mode
 
-**Note:** These shortcuts only work when in Extension Mode (after pressing `X`). Outside of this mode, some keys (like `T`) have different functions.
+**Note:** The `3` and `5` keys work both inside and outside Extension Mode. Other shortcuts (C, G, R, T) only work when in Extension Mode, as these keys have different functions outside of it.
 
 ## Select sort area mode (`F`)
 

python/frag_cluster/kmeans_utils.py

@@ -6,10 +6,13 @@
 import numpy as np 
 
 """
-    genome片段聚类分析:
-    1. 读取基因组片段数据
-    2. 计算拉普拉斯矩阵
-    3. 谱聚类
+    Genome Fragment Clustering Analysis:
+
+    Read genome fragment data
+
+    Compute Laplacian matrix
+
+    Spectral clustering
 
 """