Merge branch 'main' into tests

VerisimilitudeX · Jan 11, 2023 · a759453 · a759453
2 parents eb8928f + 377bbe5
commit a759453
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Showing 7 changed files with 11 additions and 46 deletions.
diff --git a/.classpath b/.classpath
@@ -1,14 +1,3 @@
-<!--
- * Copyright © 2023 DNAnalyzer. Some rights reserved.
- * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
- *
- * You are entirely responsible for the use of this application, including any and all activities that occur.
- * While DNAnalyzer strives to fix all major bugs that may be either reported by a user or discovered while debugging,
- * they will not be held liable for any loss that the user may incur as a result of using this application, under any circumstances.
- *
- * For further inquiries, please reach out to contact@dnanalyzer.live
- -->
-
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
 	<classpathentry kind="src" output="bin/main" path="src/main/java">
@@ -17,19 +6,19 @@
 			<attribute name="gradle_used_by_scope" value="main,test"/>
 		</attributes>
 	</classpathentry>
+	<classpathentry kind="src" output="bin/main" path="src/main/resources">
+		<attributes>
+			<attribute name="gradle_scope" value="main"/>
+			<attribute name="gradle_used_by_scope" value="main,test"/>
+		</attributes>
+	</classpathentry>
 	<classpathentry kind="src" output="bin/test" path="src/test/java">
 		<attributes>
 			<attribute name="gradle_scope" value="test"/>
 			<attribute name="gradle_used_by_scope" value="test"/>
 			<attribute name="test" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="src" output="bin/main" path="src/main/resources">
-		<attributes>
-			<attribute name="gradle_scope" value="main"/>
-			<attribute name="gradle_used_by_scope" value="main,test"/>
-		</attributes>
-	</classpathentry>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-17/"/>
 	<classpathentry kind="con" path="org.eclipse.buildship.core.gradleclasspathcontainer"/>
 	<classpathentry kind="output" path="bin/default"/>

diff --git a/.vscode/launch.json b/.vscode/launch.json
@@ -6,7 +6,7 @@
       "request": "launch",
       "mainClass": "DNAnalyzer.Main",
       "projectName": "DNAnalyzer",
-      "args": "assets/dna/random/dnalong.fa --amino=ser --min=0 --max=100 -r"
+      "args": "assets/dna/random/dnalong.fa --amino=ser --min=16450 --max=520218 -r"
     }
   ]
 }
diff --git a/README.md b/README.md
@@ -83,7 +83,7 @@ java -jar build/libs/DNAnalyzer.jar
 DNAnalyzer uses CLI arguments instead of `stdin`. For example, you can do:
 
 ```pwsh
-assets/dna/random/dnalong.fa --amino=ser --min=0 --max=100 -r
+assets/dna/random/dnalong.fa --amino=arg --min=16450 --max=520218 -r
 ```
 
 ### Example
@@ -105,7 +105,7 @@ If you prefer, you can also run it directly from Gradle:
 DNAnalyzer also comes with a (very basic) GUI; to start DNAnalyzer with the GUI, run:
 
 ```pwsh
-./gradlew run --args="--gui"
+./gradlew run --args="--gui assets/dna/random/dnalong.fa"
 ```
 
 Then:

diff --git a/src/main/java/DNAnalyzer/Main.java b/src/main/java/DNAnalyzer/Main.java
@@ -16,11 +16,6 @@
 import DNAnalyzer.ui.cli.CmdArgs;
 import picocli.CommandLine;
 
-import io.sentry.Sentry;
-import io.sentry.ITransaction;
-import io.sentry.Sentry;
-import io.sentry.SpanStatus;
-
 /**
  * Main Class for the DNAnalyzer program.
  *
@@ -47,30 +42,13 @@ public static void clearTerminal() throws InterruptedException, IOException {
 		}
 	}
 
-	/**
-	 * Configures sentry.io to handle error monitoring.
-	 */
-	private static void configureSentry() {
-		Sentry.init(options -> {
-			options.setDsn(
-					"https://82c129bee6214ef39638e4d06e16f157@o4504358029099008.ingest.sentry.io/4504358032965633");
-			// Set tracesSampleRate to 1.0 to capture 100% of transactions for performance
-			// monitoring.
-			// We recommend adjusting this value in production.
-			options.setTracesSampleRate(1.0);
-			// When first trying Sentry it's good to see what the SDK is doing:
-			options.setDebug(true);
-		});
-	}
-
 	/**
 	 * Main method for the DNAnalyzer program (run this).
 	 *
 	 * @param args Command line arguments
 	 *             {@code @category} Main
 	 */
 	public static void main(final String[] args) {
-		configureSentry();
 		new CommandLine(new CmdArgs()).execute(args);
 	}
 }
diff --git a/src/main/java/DNAnalyzer/ui/gui/DNAnalyzerGUI.java b/src/main/java/DNAnalyzer/ui/gui/DNAnalyzerGUI.java
@@ -28,7 +28,7 @@ public class DNAnalyzerGUI extends Application {
 	 */
 	public void start(Stage stage) throws Exception {
 		// Parent root = FXMLLoader.load(getClass().getResource("DNAnalyzerGUI.fxml"));
-		Parent root = FXMLLoader.load(getClass().getResource("fxml/DNAnalyzerGUI.fxml"));
+		Parent root = FXMLLoader.load(DNAnalyzerGUI.class.getResource("/DNAnalyzer/gui/fxml/DNAnalyzerGUI.fxml"));
 		Scene scene = new Scene(root);
 		// scene.getStylesheets().add(getClass().getResource("styles.css").toExternalForm());
 

diff --git a/src/main/java/DNAnalyzer/utils/traits/Traits.java b/src/main/java/DNAnalyzer/utils/traits/Traits.java
@@ -11,8 +11,6 @@
 
 package DNAnalyzer.utils.traits;
 
-import java.util.HashMap;
-
 public class Traits {
     /**
      * Check if the DNA sequence has at least three distinct occurrences of the

diff --git a/src/main/resources/DNAnalyzer/gui/fxml/DNAnalyzerGUI.fxml b/src/main/resources/DNAnalyzer/gui/fxml/DNAnalyzerGUI.fxml
@@ -52,7 +52,7 @@
 <?import javafx.scene.text.Font?>
 
 <VBox prefHeight="600.0" prefWidth="900.0" xmlns="http://javafx.com/javafx/19" xmlns:fx="http://javafx.com/fxml/1"
-      fx:controller="DNAnalyzer.gui.DNAnalyzerGUIFXMLController">
+      fx:controller="DNAnalyzer.ui.gui.DNAnalyzerGUIFXMLController">
     <children>
         <MenuBar VBox.vgrow="NEVER">
             <menus>