Fix all bugs!

VerisimilitudeX · Jun 22, 2024 · 553adbc · 553adbc
1 parent 630ed8e
commit 553adbc
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Showing 30 changed files with 80 additions and 57 deletions.
diff --git a/.classpath b/.classpath
@@ -1,9 +1,10 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
-	<classpathentry kind="src" output="bin/main" path="src/main/java">
+	<classpathentry kind="src" output="bin/test" path="src/test/java">
 		<attributes>
-			<attribute name="gradle_scope" value="main"/>
-			<attribute name="gradle_used_by_scope" value="main,test"/>
+			<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">
@@ -12,11 +13,10 @@
 			<attribute name="gradle_used_by_scope" value="main,test"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="src" output="bin/test" path="src/test/java">
+	<classpathentry kind="src" output="bin/main" path="src/main/java">
 		<attributes>
-			<attribute name="gradle_scope" value="test"/>
-			<attribute name="gradle_used_by_scope" value="test"/>
-			<attribute name="test" value="true"/>
+			<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/"/>

diff --git a/.vscode/launch.json b/.vscode/launch.json
@@ -1,5 +1,12 @@
 {
   "configurations": [
+    {
+      "type": "java",
+      "name": "Main",
+      "request": "launch",
+      "mainClass": "DNAnalyzer.Main",
+      "projectName": ""
+    },
     {
       "type": "java",
       "name": "Launch DNAnalyzer",

diff --git a/build.gradle b/build.gradle
@@ -8,6 +8,9 @@ plugins {
     id 'io.spring.dependency-management' version '1.1.3'
 }
 
+sourceCompatibility = '17'
+targetCompatibility = '17'
+
 repositories {
     // Use Maven Central for resolving dependencies.
     mavenCentral()

diff --git a/gradle/wrapper/gradle-wrapper.jar b/gradle/wrapper/gradle-wrapper.jar
diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties
@@ -1,5 +1,7 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-7.5.1-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.6-bin.zip
+networkTimeout=10000
+validateDistributionUrl=true
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
diff --git a/gradlew b/gradlew
@@ -55,7 +55,7 @@
 #       Darwin, MinGW, and NonStop.
 #
 #   (3) This script is generated from the Groovy template
-#       https://github.com/gradle/gradle/blob/master/subprojects/plugins/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt
+#       https://github.com/gradle/gradle/blob/HEAD/subprojects/plugins/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt
 #       within the Gradle project.
 #
 #       You can find Gradle at https://github.com/gradle/gradle/.
@@ -80,13 +80,11 @@ do
     esac
 done
 
-APP_HOME=$( cd "${APP_HOME:-./}" && pwd -P ) || exit
-
-APP_NAME="Gradle"
+# This is normally unused
+# shellcheck disable=SC2034
 APP_BASE_NAME=${0##*/}
-
-# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
-DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
+# Discard cd standard output in case $CDPATH is set (https://github.com/gradle/gradle/issues/25036)
+APP_HOME=$( cd "${APP_HOME:-./}" > /dev/null && pwd -P ) || exit
 
 # Use the maximum available, or set MAX_FD != -1 to use that value.
 MAX_FD=maximum
@@ -133,22 +131,29 @@ location of your Java installation."
     fi
 else
     JAVACMD=java
-    which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
+    if ! command -v java >/dev/null 2>&1
+    then
+        die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
 
 Please set the JAVA_HOME variable in your environment to match the
 location of your Java installation."
+    fi
 fi
 
 # Increase the maximum file descriptors if we can.
 if ! "$cygwin" && ! "$darwin" && ! "$nonstop" ; then
     case $MAX_FD in #(
       max*)
+        # In POSIX sh, ulimit -H is undefined. That's why the result is checked to see if it worked.
+        # shellcheck disable=SC2039,SC3045
         MAX_FD=$( ulimit -H -n ) ||
             warn "Could not query maximum file descriptor limit"
     esac
     case $MAX_FD in  #(
       '' | soft) :;; #(
       *)
+        # In POSIX sh, ulimit -n is undefined. That's why the result is checked to see if it worked.
+        # shellcheck disable=SC2039,SC3045
         ulimit -n "$MAX_FD" ||
             warn "Could not set maximum file descriptor limit to $MAX_FD"
     esac
@@ -193,11 +198,15 @@ if "$cygwin" || "$msys" ; then
     done
 fi
 
-# Collect all arguments for the java command;
-#   * $DEFAULT_JVM_OPTS, $JAVA_OPTS, and $GRADLE_OPTS can contain fragments of
-#     shell script including quotes and variable substitutions, so put them in
-#     double quotes to make sure that they get re-expanded; and
-#   * put everything else in single quotes, so that it's not re-expanded.
+
+# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
+
+# Collect all arguments for the java command:
+#   * DEFAULT_JVM_OPTS, JAVA_OPTS, JAVA_OPTS, and optsEnvironmentVar are not allowed to contain shell fragments,
+#     and any embedded shellness will be escaped.
+#   * For example: A user cannot expect ${Hostname} to be expanded, as it is an environment variable and will be
+#     treated as '${Hostname}' itself on the command line.
 
 set -- \
         "-Dorg.gradle.appname=$APP_BASE_NAME" \

diff --git a/gradlew.bat b/gradlew.bat
@@ -26,6 +26,7 @@ if "%OS%"=="Windows_NT" setlocal
 
 set DIRNAME=%~dp0
 if "%DIRNAME%"=="" set DIRNAME=.
+@rem This is normally unused
 set APP_BASE_NAME=%~n0
 set APP_HOME=%DIRNAME%
 
@@ -42,11 +43,11 @@ set JAVA_EXE=java.exe
 %JAVA_EXE% -version >NUL 2>&1
 if %ERRORLEVEL% equ 0 goto execute
 
-echo.
-echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
-echo.
-echo Please set the JAVA_HOME variable in your environment to match the
-echo location of your Java installation.
+echo. 1>&2
+echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH. 1>&2
+echo. 1>&2
+echo Please set the JAVA_HOME variable in your environment to match the 1>&2
+echo location of your Java installation. 1>&2
 
 goto fail
 
@@ -56,11 +57,11 @@ set JAVA_EXE=%JAVA_HOME%/bin/java.exe
 
 if exist "%JAVA_EXE%" goto execute
 
-echo.
-echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME%
-echo.
-echo Please set the JAVA_HOME variable in your environment to match the
-echo location of your Java installation.
+echo. 1>&2
+echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME% 1>&2
+echo. 1>&2
+echo Please set the JAVA_HOME variable in your environment to match the 1>&2
+echo location of your Java installation. 1>&2
 
 goto fail
 

diff --git a/src/main/java/DNAnalyzer/core/DNAAnalysis.java b/src/main/java/DNAnalyzer/core/DNAAnalysis.java
@@ -1,4 +1,4 @@
-contact@dnanalyzer.org2024/*
+/*
  * Copyright © 2023 DNAnalyzer. Some rights reserved.
  * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
  *

diff --git a/src/main/java/DNAnalyzer/core/Properties.java b/src/main/java/DNAnalyzer/core/Properties.java
@@ -1,4 +1,4 @@
-contact@dnanalyzer.org2024/*
+/*
  * Copyright © 2023 DNAnalyzer. Some rights reserved.
  * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
  *

diff --git a/src/main/java/DNAnalyzer/data/aminoAcid/AminoAcid.java b/src/main/java/DNAnalyzer/data/aminoAcid/AminoAcid.java
@@ -1,4 +1,4 @@
-contact@dnanalyzer.org2024/*
+/*
  * Copyright © 2023 DNAnalyzer. Some rights reserved.
  * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
  *

diff --git a/src/main/java/DNAnalyzer/data/aminoAcid/AminoAcidFactory.java b/src/main/java/DNAnalyzer/data/aminoAcid/AminoAcidFactory.java
@@ -1,4 +1,4 @@
-contact@dnanalyzer.org2024/*
+/*
  * Copyright © 2023 DNAnalyzer. Some rights reserved.
  * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
  *

diff --git a/src/main/java/DNAnalyzer/data/codon/CodonDataConstants.java b/src/main/java/DNAnalyzer/data/codon/CodonDataConstants.java
@@ -1,4 +1,4 @@
-contact@dnanalyzer.org2024/*
+/*
  * Copyright © 2023 DNAnalyzer. Some rights reserved.
  * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
  *

diff --git a/src/main/java/DNAnalyzer/data/codon/CodonDataUtils.java b/src/main/java/DNAnalyzer/data/codon/CodonDataUtils.java
@@ -1,4 +1,4 @@
-contact@dnanalyzer.org2024/*
+/*
  * Copyright © 2023 DNAnalyzer. Some rights reserved.
  * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
  *

diff --git a/src/main/java/DNAnalyzer/data/codon/CodonFrame.java b/src/main/java/DNAnalyzer/data/codon/CodonFrame.java
@@ -1,4 +1,4 @@
-contact@dnanalyzer.org2024/*
+/*
  * Copyright © 2023 DNAnalyzer. Some rights reserved.
  * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
  *

diff --git a/src/main/java/DNAnalyzer/ui/cli/CmdArgs.java b/src/main/java/DNAnalyzer/ui/cli/CmdArgs.java
@@ -1,4 +1,4 @@
-contact@dnanalyzer.org2024/*
+/*
  * Copyright © 2023 DNAnalyzer. Some rights reserved.
  * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
  *

diff --git a/src/main/java/DNAnalyzer/ui/gui/DNAnalyzerGUI.java b/src/main/java/DNAnalyzer/ui/gui/DNAnalyzerGUI.java
@@ -1,4 +1,4 @@
-contact@dnanalyzer.org2024/*
+/*
  * Copyright © 2023 DNAnalyzer. Some rights reserved.
  * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
  *

diff --git a/src/main/java/DNAnalyzer/ui/gui/DNAnalyzerGUIFXMLController.java b/src/main/java/DNAnalyzer/ui/gui/DNAnalyzerGUIFXMLController.java
@@ -1,4 +1,4 @@
-contact@dnanalyzer.org2024/*
+/*
  * Copyright © 2023 DNAnalyzer. Some rights reserved.
  * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
  *

diff --git a/src/main/java/DNAnalyzer/utils/core/BasePairCounter.java b/src/main/java/DNAnalyzer/utils/core/BasePairCounter.java
@@ -1,4 +1,4 @@
-contact@dnanalyzer.org2024/*
+/*
  * Copyright © 2023 DNAnalyzer. Some rights reserved.
  * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
  *

diff --git a/src/main/java/DNAnalyzer/utils/core/DNATools.java b/src/main/java/DNAnalyzer/utils/core/DNATools.java
@@ -1,4 +1,4 @@
-contact@dnanalyzer.org2024/*
+/*
  * Copyright © 2023 DNAnalyzer. Some rights reserved.
  * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
  *

diff --git a/src/main/java/DNAnalyzer/utils/core/ReadingFrames.java b/src/main/java/DNAnalyzer/utils/core/ReadingFrames.java
@@ -1,4 +1,4 @@
-contact@dnanalyzer.org2024/*
+/*
  * Copyright © 2023 DNAnalyzer. Some rights reserved.
  * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
  *

diff --git a/src/main/java/DNAnalyzer/utils/core/Utils.java b/src/main/java/DNAnalyzer/utils/core/Utils.java
@@ -1,4 +1,4 @@
-contact@dnanalyzer.org2024/*
+/*
  * Copyright © 2023 DNAnalyzer. Some rights reserved.
  * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
  *

diff --git a/src/main/java/DNAnalyzer/utils/protein/ProteinAnalysis.java b/src/main/java/DNAnalyzer/utils/protein/ProteinAnalysis.java
@@ -1,4 +1,4 @@
-contact@dnanalyzer.org2024/*
+/*
  * Copyright © 2023 DNAnalyzer. Some rights reserved.
  * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
  *

diff --git a/src/main/java/DNAnalyzer/utils/protein/ProteinFinder.java b/src/main/java/DNAnalyzer/utils/protein/ProteinFinder.java
@@ -1,4 +1,4 @@
-contact@dnanalyzer.org2024/*
+/*
  * Copyright © 2023 DNAnalyzer. Some rights reserved.
  * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
  *

diff --git a/src/test/java/DNAnalyzer/CodonDataUtilsTest.java b/src/test/java/DNAnalyzer/CodonDataUtilsTest.java
@@ -1,4 +1,4 @@
-2024/*
+/*
  * Copyright © 2023 DNAnalyzer. Some rights reserved.
  * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
  *
@@ -11,14 +11,15 @@
 
 package DNAnalyzer;
 
+import java.util.List;
+
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertTrue;
-
-import DNAnalyzer.data.codon.CodonDataUtils;
-import java.util.List;
 import org.junit.jupiter.params.ParameterizedTest;
 import org.junit.jupiter.params.provider.ValueSource;
 
+import DNAnalyzer.data.codon.CodonDataUtils;
+
 /**
  * CodonDataUtilsTest contains 20 unit tests, one for each acid.
  *

diff --git a/src/test/java/DNAnalyzer/MainTest.java b/src/test/java/DNAnalyzer/MainTest.java
@@ -1,4 +1,4 @@
-contact@dnanalyzer.org2024/*
+/*
  * Copyright © 2023 DNAnalyzer. Some rights reserved.
  * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
  *

diff --git a/web/about/about.css b/web/about/about.css
@@ -1,4 +1,4 @@
-contact@dnanalyzer.org2024/*
+/*
  * Copyright © 2023 DNAnalyzer. Some rights reserved.
  * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
  *

diff --git a/web/about/about.html b/web/about/about.html
@@ -1,4 +1,4 @@
-[email protected]<!--
+2024<!--
  * Copyright © 2023 DNAnalyzer. Some rights reserved.
  * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
  *

diff --git a/web/about/about.js b/web/about/about.js
@@ -1,4 +1,4 @@
-contact@dnanalyzer.org2024/*
+/*
  * Copyright © 2023 DNAnalyzer. Some rights reserved.
  * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
  *

diff --git a/web/index.html b/web/index.html
@@ -1,4 +1,4 @@
-[email protected]<!--
+2024<!--
  * Copyright © 2023 DNAnalyzer. Some rights reserved.
  * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
  *

diff --git a/web/style.css b/web/style.css
@@ -1,4 +1,4 @@
-contact@dnanalyzer.org2024/*
+/*
  * Copyright © 2023 DNAnalyzer. Some rights reserved.
  * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
  *