Massive refactoring, added SVG export, added names tracks, added converter batch mode, update README, updated years in license text.

Author: AxisAlexNT

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2021-2024 Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
+Copyright (c) 2021-2026 Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.adoc

@@ -4,14 +4,104 @@ image:https://github.com/AxisAlexNT/HiCT_JVM/actions/workflows/autobuild-release
 
 == Launching pre-built version
 
+
+== For users of `.jar` distribution
+
+This section is intended for bioinformatics users who download a ready-to-run fat JAR from GitHub Releases.
+You need to install Java 21+ (this project is built for Java 21 bytecode).
+Download the latest fat JAR from the https://github.com/ctlab/HiCT_JVM/releases[Releases page] (Assets section).
 **NOTE:** prebuilt native bundles are currently provided for *Windows* (tested on 10/11) and *Linux with glibc* (common Debian/Ubuntu-like distributions). Alpine/musl is not supported by these bundled binaries. Current prebuilt artifacts are AMD64-only. On Windows you might need to install https://learn.microsoft.com/en-us/cpp/windows/latest-supported-vc-redist?view=msvc-170[Microsoft Visual C++ Redistributable].
 
-1. Install Java 19+ (this project is built for Java 19 bytecode);
-1. Make sure `JAVA_HOME` points to that installation;
-1. Download the latest fat JAR from the https://github.com/ctlab/HiCT_JVM/releases[Releases page] (Assets section). The stable default is usually the latest autogenerated build from `master`;
-1. Open a terminal in the directory with your downloaded JAR;
-1. Run `java -jar hict.jar` and wait for startup logs;
-1. Open `http://localhost:8080` (or your configured WebUI port).
+=== Quick start
+
+1. Download the latest `-fat.jar` from the Releases page (Assets) and rename it to `hict-fat.jar`.
+2. Place your `.hict.hdf5`, `.mcool`, `.cool`, `.agp`, and `.fasta` files under a single directory.
+3. Run:
++
+```bash
+java -jar hict-fat.jar start-server
+```
++
+Directory with files is set using `DATA_DIR` environment variable, by default it scans subtree of the directory in which `hict-fat.jar` is launched from.
+In Linux you may set it as follows:
++
+```bash
+DATA_DIR=/path/to/data/ java -jar hict-fat.jar start-server
+```
++
+4. Open WebUI at `http://localhost:8080`.
+
+=== CLI commands (summary)
+
+```bash
+# API + WebUI (default mode, includes converters in WebUI as descibed below)
+java -jar hict-fat.jar start-server
+
+# API only (no WebUI)
+java -jar hict-fat.jar start-api-server
+
+# Convert .mcool -> .hict.hdf5 (CLI mode)
+java -jar hict-fat.jar convert mcool-to-hict \
+  --input /data/sample.mcool \
+  --output /data/sample.hict.hdf5
+
+# Convert .hict.hdf5 -> .mcool (CLI mode)
+java -jar hict-fat.jar convert hict-to-mcool \
+  --input /data/sample.hict.hdf5 \
+  --output /data/sample.mcool
+```
+
+Get full CLI help:
+
+```bash
+java -jar hict-fat.jar --help
+java -jar hict-fat.jar start-server --help
+java -jar hict-fat.jar start-api-server --help
+java -jar hict-fat.jar convert --help
+java -jar hict-fat.jar convert mcool-to-hict --help
+java -jar hict-fat.jar convert hict-to-mcool --help
+```
+
+=== WebUI conversion (Experimental / W.I.P.)
+
+WARNING: WebUI conversion is experimental and may be slower or less stable than the CLI.
+
+1. Open the WebUI.
+2. Use *File → Convert Coolers*.
+3. Track progress in the conversion window.
+
+=== API access (Experimental / W.I.P.)
+
+WARNING: The API is still evolving. Endpoints, parameters, and response formats may change.
+
+Example (Python) for fetching a submatrix tile as an image:
+
+```python
+import requests
+
+host = "http://localhost:5000"
+params = {
+    "version": 0,
+    "bpResolution": 10000,
+    "format": "PNG_BY_PIXELS",
+    "row": 0,
+    "col": 0,
+    "rows": 512,
+    "cols": 512,
+}
+
+r = requests.get(f"{host}/get_tile", params=params)
+r.raise_for_status()
+data = r.json()
+png_data_url = data["image"]
+print(png_data_url[:64])
+```
+
+To apply visualization/normalization settings before fetching tiles:
+
+* POST `/set_visualization_options` with visualization parameters.
+* POST `/set_normalization` with normalization settings.
+* Then call `/get_tile` as shown above.
 
 === Supported platforms / JDK details
 

build.gradle.kts

@@ -1,7 +1,7 @@
 /*
  * MIT License
  *
- * Copyright (c) 2021-2024. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
+ * Copyright (c) 2021-2026. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal
@@ -25,6 +25,8 @@ import com.github.jengelman.gradle.plugins.shadow.tasks.ShadowJar
 import org.gradle.api.tasks.testing.logging.TestLogEvent.*
 import java.io.ByteArrayOutputStream
 import java.nio.file.Files
+import java.nio.file.StandardCopyOption
+import java.nio.file.StandardCopyOption.REPLACE_EXISTING
 
 plugins {
   java
@@ -57,6 +59,7 @@ val watchForChange = "src/**/*"
 val doOnChange = "${projectDir}/gradlew classes"
 
 val versionFile = file("${project.projectDir}/version.txt")
+val webUiPackageJson = file("${project.projectDir}/../HiCT_WebUI/package.json")
 
 val webUICloneDirectory = layout.buildDirectory.dir("webui").get()
 val localWebUIRepositoryDirectory = layout.projectDirectory.dir("../HiCT_WebUI")
@@ -349,6 +352,20 @@ tasks.named("clean") {
 
 tasks.named("processResources") {
   dependsOn("copyWebUI")
+  doLast {
+    Files.copy(
+      versionFile.toPath(),
+      layout.buildDirectory.file("resources/main/version.txt").get().asFile.toPath(),
+      StandardCopyOption.REPLACE_EXISTING
+    )
+    if (webUiPackageJson.exists()) {
+      Files.copy(
+        webUiPackageJson.toPath(),
+        layout.buildDirectory.file("resources/main/webui-package.json").get().asFile.toPath(),
+        StandardCopyOption.REPLACE_EXISTING
+      )
+    }
+  }
 }
 
 tasks.named("build") {

settings.gradle.kts

@@ -1,7 +1,7 @@
 /*
  * MIT License
  *
- * Copyright (c) 2021-2024. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
+ * Copyright (c) 2021-2026. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal

src/main/java/ru/itmo/ctlab/hict/hict_library/assembly/AGPProcessor.java

@@ -1,7 +1,7 @@
 /*
  * MIT License
  *
- * Copyright (c) 2021-2024. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
+ * Copyright (c) 2021-2026. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal

src/main/java/ru/itmo/ctlab/hict/hict_library/assembly/FASTAProcessor.java

@@ -1,7 +1,7 @@
 /*
  * MIT License
  *
- * Copyright (c) 2021-2024. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
+ * Copyright (c) 2021-2026. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal

src/main/java/ru/itmo/ctlab/hict/hict_library/chunkedfile/ChunkedFile.java

@@ -1,7 +1,7 @@
 /*
  * MIT License
  *
- * Copyright (c) 2021-2024. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
+ * Copyright (c) 2021-2026. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal

src/main/java/ru/itmo/ctlab/hict/hict_library/chunkedfile/Initializers.java

@@ -1,7 +1,7 @@
 /*
  * MIT License
  *
- * Copyright (c) 2021-2024. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
+ * Copyright (c) 2021-2026. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal

src/main/java/ru/itmo/ctlab/hict/hict_library/chunkedfile/MatrixQueries.java

@@ -1,7 +1,7 @@
 /*
  * MIT License
  *
- * Copyright (c) 2021-2024. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
+ * Copyright (c) 2021-2026. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal

src/main/java/ru/itmo/ctlab/hict/hict_library/chunkedfile/ScaffoldingOperations.java

@@ -1,7 +1,7 @@
 /*
  * MIT License
  *
- * Copyright (c) 2021-2024. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
+ * Copyright (c) 2021-2026. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal