Review pull request

.gitignore

@@ -1,6 +1,7 @@
 .DS_Store
 .gradle
-#build/
+build
+*.pages
 
 # Ignore Gradle GUI config
 gradle-app.setting
@@ -15,5 +16,5 @@ gradle-app.setting
 # gradle/wrapper/gradle-wrapper.properties
 
 # IDE
-.idea/
+.idea
 *.iml

README.md

@@ -0,0 +1,6 @@
+GFE Search Generator
+====================
+
+There are currently tens of thousands of known variants of the Human Leukocyte Antigen (HLA) genes, the genes most responsible for transplant success or failure, with new variants (known as “alleles”) being discovered and “named” every day. The current names give very little information about the structure of the proteins encoded by these genes, and in 2015, Dr. Steven Mack proposed a new naming convention called Gene Feature Enumeration (GFE). New tools are required to use the new GFE naming convention, including (1) the ability to switch between the HLA allele names and the GFE names, (2) search through the GFE names, and (3) assign GFE names to new alleles. 
+
+The project is built using Kotlin 1.4.0, JVM 11, OpenJavaFX 0.0.9, and TornadoFX 1.7.20, bundled together with Gradle 6.7.1.

build.gradle.kts

@@ -1,33 +1,71 @@
 plugins {
-    id 'org.jetbrains.kotlin.jvm' version "1.4.0"
-    id 'application'
+    kotlin("jvm") version "1.5.30"
+    application
+    id("org.openjfx.javafxplugin") version "0.0.9"
+    kotlin("plugin.serialization") version "1.5.0"
 }
-group = 'com.test'
-version = '1.0-SNAPSHOT'
+
+application { mainClassName = "org.b12x.gfe.MainKt" }
 
 repositories {
     mavenCentral()
     jcenter()
+    maven("https://plugins.gradle.org/m2/")
+    maven("https://dl.bintray.com/kotlin/kotlin-eap")
 }
 
-javafx {
-    version = "11.0.2"
-    modules = ['javafx.controls', 'javafx.fxml']
-}
+dependencies {
+    // Kotlin standard library
+    implementation(kotlin("stdlib-jdk8"))
+    implementation( "org.jetbrains.kotlin:kotlin-reflect:1.5.0")
+    implementation("org.jetbrains.kotlinx:kotlinx-serialization-json:1.2.2")
+    implementation("org.jetbrains.kotlinx:kotlinx-coroutines-core:1.5.2")
+    implementation("io.ktor:ktor-client-core:1.6.7")
+    implementation("io.ktor:ktor-client-cio:1.6.7")
+
+    // TornadoFX dependency
+    implementation("no.tornado:tornadofx:1.7.20")
+
+    // API tools
+    implementation("com.squareup.okhttp3:okhttp:4.9.1")
+    implementation("com.squareup.okio:okio:2.10.0")
+
+    // JSON parsing
+    implementation("com.fasterxml.jackson.module:jackson-module-kotlin:2.12.3")
+    implementation("com.beust:klaxon:5.5")
+
+    //Text comparison
+    // https://mvnrepository.com/artifact/io.github.java-diff-utils/java-diff-utils
+    implementation("io.github.java-diff-utils:java-diff-utils:4.11")
+
+
+    // RxJava for Kotlin
+    implementation("io.reactivex.rxjava3:rxkotlin:3.0.1")
+
+    // JUnit 5 for testing
+    testImplementation("org.junit.jupiter:junit-jupiter:5.7.0")
+    testImplementation("org.junit.jupiter:junit-jupiter-engine:5.7.0")
+    testImplementation("org.junit.jupiter:junit-jupiter-params:5.7.0")
+
+    // Mockito
+    testImplementation("org.mockito:mockito-core:3.8.0")
+    testImplementation("com.nhaarman.mockitokotlin2:mockito-kotlin:2.2.0")
 
-application {
-    mainClassName = "edu.ucsf.MainKt"
-}
 
-dependencies {
-    implementation "org.jetbrains.kotlin:kotlin-stdlib-jdk8"
-    implementation "no.tornado:tornadofx:$tornadofx_version"
-    testImplementation "org.jetbrains.kotlin:kotlin-test-junit"
 }
 
-compileKotlin {
+// JavaFX module to include
+javafx { modules("javafx.controls", "javafx.fxml", "javafx.graphics") }
+
+// Set Kotlin/JVM target versions
+tasks.withType<org.jetbrains.kotlin.gradle.tasks.KotlinCompile> {
     kotlinOptions.jvmTarget = "11"
+    kotlinOptions.languageVersion = "1.5"
 }
-compileTestKotlin {
-    kotlinOptions.jvmTarget = "11"
-}
+
+// Use JUnit
+tasks.test { useJUnitPlatform() }
+
+// Be sure to use latest Gradle version
+tasks.named<Wrapper>("wrapper") { gradleVersion = "6.7.1" }
+

local.properties

@@ -0,0 +1,8 @@
+## This file must *NOT* be checked into Version Control Systems,
+# as it contains information specific to your local configuration.
+#
+# Location of the SDK. This is only used by Gradle.
+# For customization when using a Version Control System, please read the
+# header note.
+#Sun Jan 02 09:33:44 PST 2022
+sdk.dir=/Users/EatonK/Library/Android/sdk

settings.gradle.kts

@@ -0,0 +1,2 @@
+rootProject.name = "GSG"
+

src/main/java/org/b12x/gfe/utilities/preference/ClearPrefs.java

@@ -0,0 +1,19 @@
+package org.b12x.gfe.utilities.preference;
+
+import java.util.prefs.BackingStoreException;
+import java.util.prefs.Preferences;
+
+public class ClearPrefs {
+
+    private static final Preferences preferences = Preferences.userNodeForPackage(PrefsManager.class);
+
+    public ClearPrefs() { }
+
+    /**
+     * Clears all program preferences.
+     *
+     */
+    public static void clearAllPrefs() throws BackingStoreException {
+        preferences.clear();
+    }
+}

src/main/java/org/b12x/gfe/utilities/preference/PrefsManager.java

@@ -0,0 +1,85 @@
+package org.b12x.gfe.utilities.preference;
+
+import java.util.prefs.BackingStoreException;
+import java.util.prefs.Preferences;
+
+public class PrefsManager {
+
+    private static final Preferences preferences = Preferences.userNodeForPackage(PrefsManager.class);
+
+    private PrefsManager() {
+    }
+
+    /**
+     * Sets the integer value of the named preference.
+     *
+     * @param name   the preference to be set
+     * @param newInt the value to be set
+     */
+    public static void setPrefInt(String name, int newInt) {
+        preferences.putInt(name, newInt);
+    }
+
+    /**
+     * Gets the integer value of the named preference.
+     * Returns zero by default.
+     *
+     * @param name the preference to be retrieved
+     * @return the stored integer
+     */
+    public static int getPrefInt(String name) {
+        return preferences.getInt(name, 1);
+    }
+
+    /**
+     * Sets the string value of the named preference.
+     *
+     * @param name      the preference to be set
+     * @param newString the value to be set
+     */
+    public static void setPrefString(String name, String newString) {
+        preferences.put(name, newString);
+    }
+
+    /**
+     * Gets the string value of the named preference.
+     * Returns the string "HLA-A" by default.
+     *
+     * @param name the preference to be retrieved
+     * @return the stored string
+     */
+    public static String getPrefString(String name) {
+        return preferences.get(name, "HLA-A");
+    }
+
+    /**
+     * Sets the boolean value of the named preference.
+     *
+     * @param name       the preference to be set
+     * @param newBoolean the value to be set
+     */
+    public static void setPrefBoolean(String name, Boolean newBoolean) {
+        preferences.putBoolean(name, newBoolean);
+    }
+
+    /**
+     * Gets the boolean value of the named preference.
+     * Returns false by default.
+     *
+     * @param name the preference to be retrieved
+     * @return the stored boolean
+     */
+    public static Boolean getPrefBoolean(String name) {
+        return preferences.getBoolean(name, false);
+    }
+
+    /**
+     * Removes the named preference.
+     *
+     * @param name preference to be removed
+     */
+    public static void wipePref(String name) throws BackingStoreException {
+        preferences.remove(name);
+        preferences.flush();
+    }
+}

src/main/kotlin/org/b12x/gfe/GSG.kt

@@ -0,0 +1,17 @@
+package org.b12x.gfe
+
+import javafx.stage.Stage
+import org.b12x.gfe.core.view.MainView
+import org.b12x.gfe.plugins.gfesearch.view.GfeSearchLayoutData
+import tornadofx.App
+import tornadofx.Stylesheet.Companion.label
+
+class GSG: App(MainView::class, Styles::class) {
+    override fun start(stage: Stage) {
+        super.start(stage)
+        stage.width = 1150.0
+        stage.height = 800.0
+
+    }
+
+}

src/main/kotlin/org/b12x/gfe/Styles.kt

@@ -0,0 +1,40 @@
+package org.b12x.gfe
+
+import javafx.scene.text.Font
+import javafx.scene.text.Font.font
+import javafx.scene.text.FontWeight
+import javafx.scene.text.TextAlignment
+import tornadofx.*
+
+class Styles : Stylesheet() {
+    companion object {
+        val heading by cssclass()
+        val textAreas by cssclass()
+    }
+
+    init {
+
+        root {
+            prefHeight = 600.px
+            prefWidth = 1000.px
+            fontFamily = "sansserif"
+        }
+
+        textAreas {
+            padding = box(20.px)
+            prefWidth = 760.px
+            prefHeight = 300.px
+        }
+
+        textField {
+            prefWidth = 25.px
+//            borderWidth += box(30.px, 30.px, 30.px, 30.px)
+        }
+
+        label and heading {
+//            padding = box(100.px)
+            fontSize = 20.px
+            fontWeight = FontWeight.BOLD
+        }
+    }
+}

src/main/kotlin/org/b12x/gfe/core/controller/PrefsCore.kt

@@ -0,0 +1,15 @@
+package org.b12x.gfe.core.controller
+
+import org.b12x.gfe.GSG
+import org.b12x.gfe.plugins.gfesearch.controller.locistategfesearch.PrefsGfeSearch
+import java.util.prefs.Preferences
+
+object PrefsCore {
+    var prefs: Preferences = Preferences.userNodeForPackage(GSG::class.java)
+
+    fun nuclearOption() {
+        prefs.removeNode()
+        prefs = Preferences.userNodeForPackage(GSG::class.java)
+        PrefsGfeSearch.prefs = prefs
+    }
+}

src/main/kotlin/org/b12x/gfe/core/controller/loci/HlaLoci.kt

@@ -0,0 +1,19 @@
+package org.b12x.gfe.core.controller.loci
+
+enum class HlaLoci(override val fullName: String, override val exons: Int) : LociEnum {
+    A("HLA-A", 8),
+    B("HLA-B", 7),
+    C("HLA-C", 8),
+    DPA1("HLA-DPA1", 4),
+    DPB1("HLA-DPB1", 5),
+    DQA1("HLA-DQA1", 4),
+    DQB1("HLA-DQB1", 6),
+    DRB1("HLA-DRB1", 6),
+    DRB3("HLA-DRB3", 6),
+    DRB4("HLA-DRB4", 6),
+    DRB5("HLA-DRB5", 6);
+
+    override fun toString(): String {
+        return fullName
+    }
+}