Configure Gradle build. Implements VerisimilitudeX#117.

Configures a basic Gradle Java app build. To stick to Gradle convention as closely as possible, this commit
- adds several Gradle-specific directories / files to the git ignore
list
- moves the source code from src/ to app/src/main/java/
- adds a (dummy) test class in app/src/test/java

It also updates the README and provides basic information on how to
build + run the DNAnalyzer.

.gitattributes

@@ -0,0 +1,9 @@
+#
+# https://help.github.com/articles/dealing-with-line-endings/
+#
+# Linux start script should use lf
+/gradlew        text eol=lf
+
+# These are Windows script files and should use crlf
+*.bat           text eol=crlf
+

.gitignore

@@ -1,4 +1,43 @@
 .idea/*
 .config/*
 bin/*
-.vs/*
+.vs/*
+
+### Java ###
+*.class
+
+# BlueJ files
+*.ctxt
+
+# Mobile Tools for Java (J2ME)
+.mtj.tmp/
+
+# Package Files #
+*.jar
+*.war
+*.ear
+
+# virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
+hs_err_pid*
+
+
+### Gradle ###
+.gradle
+/build/
+
+# Ignore Gradle GUI config
+gradle-app.setting
+
+# Avoid ignoring Gradle wrapper jar file (.jar files are usually ignored)
+!gradle-wrapper.jar
+
+# Cache of project
+.gradletasknamecache
+
+# # Work around https://youtrack.jetbrains.com/issue/IDEA-116898
+# gradle/wrapper/gradle-wrapper.properties
+
+# End of https://www.gitignore.io/api/java,gradle
+
+# Ignore Gradle build output directory
+build

README.md

@@ -21,6 +21,27 @@
 <p>DNAnalyzer identifies proteins, amino acids, start and stop codons, high coverage regions, regions susceptible to neurodevelopment disorders, transcription factors, and regulatory elements. Researchers are working to extract valuable information from such software to better understand human health and disease. Currently, we are working on developing a Command-Line-Interface (CLI) and Graphical User Interface (GUI) that will enable physicians to quickly and more easily interact with the software, enabling them to identify genetic mutations that may cause disease. 
 </p>
 
+<h2 id="requirements">System Requirements
+</h2>
+To build and run the DNAnalyzer, you need
+* JDK 17 or greater
+* a JAVA\_HOME environment variabl pointing to your JDK 17, or the java executable in your PATH
+
+<h2 id="build_and_run">Build & Run</h2>
+We use [Gradle|https://gradle.org] for the build. The Gradle wrapper takes care of downloading the dependencies etc. - simply run
+```
+gradlew build
+```
+On UNIX-like operating systems, you might have to prefix this with './' to ensure the OS looks in the current directory, so the above becomes
+```
+./gradlew build
+```
+
+Afterwards, you can run the DNAnalyzer with
+```
+java -cp app/build/classes/java/main/ DNAnalyzer.Main
+```
+
 <h2 id="background">Background
 </h2>
 

app/build.gradle.kts

@@ -0,0 +1,35 @@
+/*
+ * This file was generated by the Gradle 'init' task.
+ *
+ * This generated file contains a sample Java application project to get you started.
+ * For more details take a look at the 'Building Java & JVM projects' chapter in the Gradle
+ * User Manual available at https://docs.gradle.org/7.5.1/userguide/building_java_projects.html
+ */
+
+plugins {
+    // Apply the application plugin to add support for building a CLI application in Java.
+    application
+}
+
+repositories {
+    // Use Maven Central for resolving dependencies.
+    mavenCentral()
+}
+
+dependencies {
+    // Use JUnit test framework.
+    testImplementation("junit:junit:4.13.2")
+
+    // This dependency is used by the application.
+    implementation("com.google.guava:guava:31.0.1-jre")
+}
+
+application {
+    // Define the main class for the application.
+    mainClass.set("DNAnalyzer.Main")
+}
+
+tasks.named<JavaExec>("run") {
+    // ensure STDIN works correctly (see https://stackoverflow.com/a/13172566/610979)
+    standardInput = System.`in`
+}

app/src/test/java/DNAnalyzer/MainTest.java

@@ -0,0 +1,14 @@
+/*
+ * This Java source file was generated by the Gradle 'init' task.
+ */
+package DNAnalyzer;
+
+import org.junit.Test;
+import static org.junit.Assert.*;
+
+public class MainTest {
+    @Test public void mainClassshouldExist() {
+        Main classUnderTest = new Main();
+        assertNotNull("main should be not null", classUnderTest);
+    }
+}

gradle/wrapper/gradle-wrapper.properties

@@ -0,0 +1,5 @@
+distributionBase=GRADLE_USER_HOME
+distributionPath=wrapper/dists
+distributionUrl=https\://services.gradle.org/distributions/gradle-7.5.1-bin.zip
+zipStoreBase=GRADLE_USER_HOME
+zipStorePath=wrapper/dists

gradlew

@@ -0,0 +1,240 @@
+#!/bin/sh
+
+#
+# Copyright © 2015-2021 the original authors.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      https://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+##############################################################################
+#
+#   Gradle start up script for POSIX generated by Gradle.
+#
+#   Important for running:
+#
+#   (1) You need a POSIX-compliant shell to run this script. If your /bin/sh is
+#       noncompliant, but you have some other compliant shell such as ksh or
+#       bash, then to run this script, type that shell name before the whole
+#       command line, like:
+#
+#           ksh Gradle
+#
+#       Busybox and similar reduced shells will NOT work, because this script
+#       requires all of these POSIX shell features:
+#         * functions;
+#         * expansions «$var», «${var}», «${var:-default}», «${var+SET}»,
+#           «${var#prefix}», «${var%suffix}», and «$( cmd )»;
+#         * compound commands having a testable exit status, especially «case»;
+#         * various built-in commands including «command», «set», and «ulimit».
+#
+#   Important for patching:
+#
+#   (2) This script targets any POSIX shell, so it avoids extensions provided
+#       by Bash, Ksh, etc; in particular arrays are avoided.
+#
+#       The "traditional" practice of packing multiple parameters into a
+#       space-separated string is a well documented source of bugs and security
+#       problems, so this is (mostly) avoided, by progressively accumulating
+#       options in "$@", and eventually passing that to Java.
+#
+#       Where the inherited environment variables (DEFAULT_JVM_OPTS, JAVA_OPTS,
+#       and GRADLE_OPTS) rely on word-splitting, this is performed explicitly;
+#       see the in-line comments for details.
+#
+#       There are tweaks for specific operating systems such as AIX, CygWin,
+#       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
+#       within the Gradle project.
+#
+#       You can find Gradle at https://github.com/gradle/gradle/.
+#
+##############################################################################
+
+# Attempt to set APP_HOME
+
+# Resolve links: $0 may be a link
+app_path=$0
+
+# Need this for daisy-chained symlinks.
+while
+    APP_HOME=${app_path%"${app_path##*/}"}  # leaves a trailing /; empty if no leading path
+    [ -h "$app_path" ]
+do
+    ls=$( ls -ld "$app_path" )
+    link=${ls#*' -> '}
+    case $link in             #(
+      /*)   app_path=$link ;; #(
+      *)    app_path=$APP_HOME$link ;;
+    esac
+done
+
+APP_HOME=$( cd "${APP_HOME:-./}" && pwd -P ) || exit
+
+APP_NAME="Gradle"
+APP_BASE_NAME=${0##*/}
+
+# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
+
+# Use the maximum available, or set MAX_FD != -1 to use that value.
+MAX_FD=maximum
+
+warn () {
+    echo "$*"
+} >&2
+
+die () {
+    echo
+    echo "$*"
+    echo
+    exit 1
+} >&2
+
+# OS specific support (must be 'true' or 'false').
+cygwin=false
+msys=false
+darwin=false
+nonstop=false
+case "$( uname )" in                #(
+  CYGWIN* )         cygwin=true  ;; #(
+  Darwin* )         darwin=true  ;; #(
+  MSYS* | MINGW* )  msys=true    ;; #(
+  NONSTOP* )        nonstop=true ;;
+esac
+
+CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
+
+
+# Determine the Java command to use to start the JVM.
+if [ -n "$JAVA_HOME" ] ; then
+    if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
+        # IBM's JDK on AIX uses strange locations for the executables
+        JAVACMD=$JAVA_HOME/jre/sh/java
+    else
+        JAVACMD=$JAVA_HOME/bin/java
+    fi
+    if [ ! -x "$JAVACMD" ] ; then
+        die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME
+
+Please set the JAVA_HOME variable in your environment to match the
+location of your Java installation."
+    fi
+else
+    JAVACMD=java
+    which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
+
+Please set the JAVA_HOME variable in your environment to match the
+location of your Java installation."
+fi
+
+# Increase the maximum file descriptors if we can.
+if ! "$cygwin" && ! "$darwin" && ! "$nonstop" ; then
+    case $MAX_FD in #(
+      max*)
+        MAX_FD=$( ulimit -H -n ) ||
+            warn "Could not query maximum file descriptor limit"
+    esac
+    case $MAX_FD in  #(
+      '' | soft) :;; #(
+      *)
+        ulimit -n "$MAX_FD" ||
+            warn "Could not set maximum file descriptor limit to $MAX_FD"
+    esac
+fi
+
+# Collect all arguments for the java command, stacking in reverse order:
+#   * args from the command line
+#   * the main class name
+#   * -classpath
+#   * -D...appname settings
+#   * --module-path (only if needed)
+#   * DEFAULT_JVM_OPTS, JAVA_OPTS, and GRADLE_OPTS environment variables.
+
+# For Cygwin or MSYS, switch paths to Windows format before running java
+if "$cygwin" || "$msys" ; then
+    APP_HOME=$( cygpath --path --mixed "$APP_HOME" )
+    CLASSPATH=$( cygpath --path --mixed "$CLASSPATH" )
+
+    JAVACMD=$( cygpath --unix "$JAVACMD" )
+
+    # Now convert the arguments - kludge to limit ourselves to /bin/sh
+    for arg do
+        if
+            case $arg in                                #(
+              -*)   false ;;                            # don't mess with options #(
+              /?*)  t=${arg#/} t=/${t%%/*}              # looks like a POSIX filepath
+                    [ -e "$t" ] ;;                      #(
+              *)    false ;;
+            esac
+        then
+            arg=$( cygpath --path --ignore --mixed "$arg" )
+        fi
+        # Roll the args list around exactly as many times as the number of
+        # args, so each arg winds up back in the position where it started, but
+        # possibly modified.
+        #
+        # NB: a `for` loop captures its iteration list before it begins, so
+        # changing the positional parameters here affects neither the number of
+        # iterations, nor the values presented in `arg`.
+        shift                   # remove old arg
+        set -- "$@" "$arg"      # push replacement arg
+    done
+fi
+
+# Collect all arguments for the java command;
+#   * $DEFAULT_JVM_OPTS, $JAVA_OPTS, and $GRADLE_OPTS can contain fragments of
+#     shell script including quotes and variable substitutions, so put them in
+#     double quotes to make sure that they get re-expanded; and
+#   * put everything else in single quotes, so that it's not re-expanded.
+
+set -- \
+        "-Dorg.gradle.appname=$APP_BASE_NAME" \
+        -classpath "$CLASSPATH" \
+        org.gradle.wrapper.GradleWrapperMain \
+        "$@"
+
+# Stop when "xargs" is not available.
+if ! command -v xargs >/dev/null 2>&1
+then
+    die "xargs is not available"
+fi
+
+# Use "xargs" to parse quoted args.
+#
+# With -n1 it outputs one arg per line, with the quotes and backslashes removed.
+#
+# In Bash we could simply go:
+#
+#   readarray ARGS < <( xargs -n1 <<<"$var" ) &&
+#   set -- "${ARGS[@]}" "$@"
+#
+# but POSIX shell has neither arrays nor command substitution, so instead we
+# post-process each arg (as a line of input to sed) to backslash-escape any
+# character that might be a shell metacharacter, then use eval to reverse
+# that process (while maintaining the separation between arguments), and wrap
+# the whole thing up as a single "set" statement.
+#
+# This will of course break if any of these variables contains a newline or
+# an unmatched quote.
+#
+
+eval "set -- $(
+        printf '%s\n' "$DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS" |
+        xargs -n1 |
+        sed ' s~[^-[:alnum:]+,./:=@_]~\\&~g; ' |
+        tr '\n' ' '
+    )" '"$@"'
+
+exec "$JAVACMD" "$@"