Add instructions on how to run the program

Miscellaneous changes

See merge request oysteikt/h20-tdt4100-project!7

.gitignore

@@ -10,4 +10,6 @@ target/
 .idea/
 
 #VSCode
-.vscode/
+.vscode/
+
+dependency-reduced-pom.xml

.gitlab-ci.yml

@@ -3,15 +3,33 @@
 # and
 # https://gitlab.stud.idi.ntnu.no/tdt4140-staff/examples/-/blob/master/.gitlab-ci.yml
 
-image: maven:3.6.3-openjdk-15
+image: maven:3-openjdk-15-slim
 
 variables:
+
   # This will suppress any download for dependencies and plugins or upload messages which would clutter the console log.
   # `showDateTime` will show the passed time in milliseconds. You need to specify `--batch-mode` to make this work.
-  MAVEN_OPTS: "-Dhttps.protocols=TLSv1.2 -Dmaven.repo.local=$CI_PROJECT_DIR/.m2/repository -Dorg.slf4j.simpleLogger.log.org.apache.maven.cli.transfer.Slf4jMavenTransferListener=WARN -Dorg.slf4j.simpleLogger.showDateTime=true -Djava.awt.headless=true"
+  MAVEN_OPTS: " \
+    -Dhttps.protocols=TLSv1.2 \
+    -Dmaven.repo.local=$CI_PROJECT_DIR/.m2/repository \
+    -Dorg.slf4j.simpleLogger.log.org.apache.maven.cli.transfer.Slf4jMavenTransferListener=WARN \
+    -Dorg.slf4j.simpleLogger.showDateTime=true \
+    -Djava.awt.headless=true"
+
   # As of Maven 3.3.0 instead of this you may define these options in `.mvn/maven.config` so the same config is used
   # when running from the command line.
-  MAVEN_CLI_OPTS: "--batch-mode --errors --fail-at-end --show-version"
+  MAVEN_CLI_OPTS: " \
+  --batch-mode \
+  --errors \
+  --fail-at-end \
+  --show-version \
+  -Dprism.verbose=true \
+  -Dtestfx.robot=glass \
+  -Dtestfx.headless=true \
+  -Dglass.platform=Monocle \
+  -Dprism.order=sw \
+  -Dprism.text=t2k \
+  -Dtestfx.setup.timeout=60000"
 
 # Cache downloaded dependencies and plugins between builds.
 # To keep cache across branches add 'key: "$CI_JOB_NAME"'
@@ -38,6 +56,8 @@ unittest:
   stage: test
   needs: [build]
   script:
+    - "apt update"
+    - "apt install -y openjfx"
     - "mvn package $MAVEN_CLI_OPTS"
   artifacts:
     paths:
@@ -46,12 +66,13 @@ unittest:
     reports:
       junit:
         - target/surefire-reports/TEST-*.xml
-        - target/failsafe-reports/TEST-*.xml
 
 generate-coverage:
   stage: docs
   script:
-    - 'mvn clean jacoco:prepare-agent test jacoco:report'
+    - "apt update"
+    - "apt install -y openjfx"
+    - 'mvn clean jacoco:prepare-agent test $MAVEN_CLI_OPTS jacoco:report'
     - 'cat target/site/jacoco/index.html'
   coverage: '/Total.*?([0-9]{1,3})%/'
   artifacts:

README.md

@@ -4,37 +4,64 @@
 
 <img src="src/main/resources/graphics/logo.svg"  width="160" height="130">
 
-
 Probably tastes better than any Apple editor and NetBeans combined.
 
+--> [See project requirement details here][requirements.md] <--
+
+
+In order to run the program, use run.bat if using Windows or run.sh if using UNIX based OS
+
+<img src=".gitlab/graphics/main-screenshot.png">
+
 </div>
 
 ---
 
-## TODO:
-- [X] ~~Tabs~~
-- [X] Modeline w/ linenumbers
-- [X] Syntax highlighting
-- [ ] Filetree
-- [X] Line numbers
-- [X] Shortcuts
-- [X] Change languages
-- [X] Toggle line comment
-- [X] Soft wrap
-- [X] Darkmode/Lightmode or color themes
-- [ ] Add icons for files/folders in filetree
-- [X] Add [code coverage check](https://docs.gitlab.com/ee/user/project/merge_requests/test_coverage_visualization.html) to verify quality of unit tests
+[![Pipeline Status](https://gitlab.stud.idi.ntnu.no/oysteikt/h20-tdt4100-project/badges/master/pipeline.svg)](https://gitlab.stud.idi.ntnu.no/oysteikt/h20-tdt4100-project/commits/master/)
+[![Coverage](https://gitlab.stud.idi.ntnu.no/oysteikt/h20-tdt4100-project/badges/master/coverage.svg?)](http://oysteikt.pages.stud.idi.ntnu.no/h20-tdt4100-project/)
+[![Documentation](https://img.shields.io/badge/Documentation-pages-blue)](http://oysteikt.pages.stud.idi.ntnu.no/h20-tdt4100-project/apidocs)
+[![License](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 
-## Maybe TODO?
-- [ ] List Chooser
-- [ ] Search
-- [ ] And replace
+## TODO:
+
+- [x] ~~Tabs~~
+- [x] Modeline w/ linenumbers
+- [x] Syntax highlighting
+- [x] Filetree
+- [x] Line numbers
+- [x] Shortcuts
+- [x] Change languages
+- [x] Toggle line comment
+- [x] Soft wrap
+- [x] Darkmode/Lightmode or color themes
+- [x] Add icons for files/folders in filetree
+- [x] Add [code coverage check](https://docs.gitlab.com/ee/user/project/merge_requests/test_coverage_visualization.html) to verify quality of unit tests
+- [ ] ~~Search~~
+- [ ] ~~And replace~~
 
 ## Credits/Sources
+
 - [james-d/SimpleMVP](https://github.com/james-d/SimpleMVP/tree/master/src/examples/mvp) -> Demonstration of JavaFX Model/View/Controller application
 - [FXMisc/RichTextFX](https://github.com/FXMisc/RichTextFX) -> Library for handling rich text and line numbers
 - [richtextfx-demos](https://github.com/FXMisc/RichTextFX/blob/master/richtextfx-demos/README.md) -> Examples and demos of how to use RichTextFX, including [Java Keywords Demo](https://github.com/FXMisc/RichTextFX/blob/master/richtextfx-demos/src/main/java/org/fxmisc/richtext/demo/JavaKeywordsAsyncDemo.java)
 - [Pixabay/311788](https://pixabay.com/vectors/bananas-fruits-pair-yellow-bananas-311788/) -> Banana logo
 - [Guava Event Bus](https://github.com/google/guava/wiki/EventBusExplained) -> Library for handling communication between controllers
 - [JFX Moderna](https://github.com/openjdk/jfx/blob/master/modules/javafx.controls/src/main/resources/com/sun/javafx/scene/control/skin/modena/modena.css) -> CSS reference
-- [devicons/devicon](https://github.com/devicons/devicon) -> icons for files and languages
+<!---
+- [devicons/devicon](https://github.com/devicons/devicon) -> Icon languages
+  -->
+- [Papirus](https://github.com/PapirusDevelopmentTeam/papirus-icon-theme) -> Icons for filetree
+- [StackOverflow/38278601](https://stackoverflow.com/questions/38278601/javafx-treeview-directory-listing) ->
+  Example of how to generate and show a filetree recursively.
+- [Youtube/ProgrammingKnowledge](https://www.youtube.com/watch?v=RY_Rb2UVQKQ) -> Introduction to the fundamentals
+  to create a filetree.
+- [GenuineCoder](https://www.genuinecoder.com/save-files-javafx-filechooser/) -> Examples of how to use FileChooser
+  and setting extensionfilters. Also included a nice method to save files.
+- [Tutorialspoint](https://www.tutorialspoint.com/how-to-save-files-using-a-file-chooser-in-javafx) -> Example
+  of how to use the openSaveDialog with FileChooser.
+- [mkyoung](https://mkyong.com/java/how-to-create-directory-in-java/) -> Example of how to create a directory/folder.
+- [Youtube/Cool IT Help](https://www.youtube.com/watch?v=gnXRI3pHxrU&t=727s) -> Showing how to cast (Stage). Example of how FXML, listener/event and DirectyChooser nicely can cooperate.
+- [Code Makery](https://code.makery.ch/blog/javafx-dialogs-official/) -> Examples of many different javafx dialogs.
+- [Oracle](https://docs.oracle.com/javase/tutorial/uiswing/components/dialog.html#button) -> How to use JOption.
+
+[requirements.md]: https://gitlab.stud.idi.ntnu.no/oysteikt/h20-tdt4100-project/-/blob/master/REQUIREMENTS.md

REQUIREMENTS.md

@@ -0,0 +1,204 @@
+
+# Krav til applikasjonen
+
+## Delbeskrivelser
+
+
+### Del 1 - Grunnklasser og brukergrensesnitt
+
+```
+I denne delen skal dere lage de grunnleggende klassene i appen deres. Klassene skal realisere
+hovedfunksjonaliteten i appen, men dere trenger ikke å implementere feilhåndtering og lagring i
+denne delen (det kommer senere). Tilstanden til objektene i appen deres skal være innkapslet,
+og et objekt skal administrere sin egen tilstand.
+I tillegg til grunnklassene skal dere lage et brukergrensesnitt i FXML. Vi anbefaler at dere
+tenker litt over dette grensesnittet, gjerne skissér det på forhånd for å se at det virker greit å
+bruke. Om dere har tatt eller tar TDT4180 - Menneske-maskin-interaksjon kan det være lærerikt
+å bruke noen av konseptene dere har lært der (men merk at dere ikke vurderes ut i fra det i dette
+faget).
+
+Dere skal også lage Controller- og App-klasser som starter appen og kobler sammen brukergrensesnitt 
+og underliggende klasser. Merk at appen deres skal bygges etter Model-ViewController-prinsippet. 
+Det betyr at det skal være et klart skille mellom modell (model), grensesnitt (view), og 
+kontroller (controller) i appen. Her er grensesnittet definert av FXML-filene deres,
+og modellene er de underliggende klassene. Kontrollerens jobb er å binde sammen grensesnitt og
+modeller, altså å holde verdiene i grensesnittet oppdatert i forhold til modellene, og å reagere på
+brukerinput i grensesnittet og kalle passende metoder i modellene.
+```
+
+
+### Del 2 - Filbehandling
+
+```
+Her skal dere utvide appen til å kunne lese fra og skrive til filer. Dere må selv bestemme hva som
+skal lagres, og formatet det skal lagres på. Altså må dere finne en måte å strukturere tilstanden
+i objektene deres som en tekstfil.
+
+For å gjøre det enklere å bytte filformat på et senere tidspunkt, eller å gjøre det mulig å lagre
+i forskjellige formater, skal dere lage et grensesnitt (interface) med metoder for lesing fra og
+skriving til fil. Deretter må dere lage minimum en ny klasse (altså ikke en av klassene dere har
+lagd tidligere i prosjektet) som implementerer grensesnittet og realiserer funksjonaliteten.
+```
+
+
+
+### Del 3 - Feilhåndtering
+
+```
+I de aller fleste programmer vil det være mulighet for at feil skjer under kjøring, uavhengig av
+om koden er skrevet riktig. Det kan f.eks. være ved ugyldig input fra brukere, filer som ikke
+eksisterer, manglende internett, eller lignende. Om denne type feil ikke håndteres, vil det enten
+føre til at appen oppfører seg feil, eller at den krasjer.
+
+I denne delen av prosjektet skal dere utvide appen deres til å håndtere feil på passende måter.
+For å gjøre dette må dere finne ut:
+
+• Hvor i appen deres det kan oppstå feil.
+• Hvordan appen bør respondere på slik feil.
+
+Deretter må dere implementere feilhånderingen dere har funnet ut at er hensiktsmessig.
+```
+
+### Del 4 - Testing
+
+```
+Siste del av prosjektet handler om å skrive enhetstester til appen deres. Dere bør teste alle
+metoder med funksjonalitet utover helt enkle get- og set-metoder. Dere trenger heller ikke å
+teste Controller- og App-klassene deres, da det ikke skal være logikk i disse. Har dere logikk
+liggende i Controller-klassen bør dere flytte dette til en passende underliggende klasse før dere
+begynner på denne delen.
+
+Når dere skriver testene bør dere først tenke over hvilke deler av koden det er viktig å sjekke
+at fungerer som den skal. Deretter bør dere prøve å komme på (kombinasjoner av) input-verdier
+og tilstander som kan føre til uventet oppførsel i disse delene. Slike edge-cases bør det skrives
+tester for, i tillegg til å teste for at funksjonaliteten fungerer med ”snillere” verdier. Til slutt er
+det viktig at testene skal sjekke at koden fungerer, ikke motsatt. Om dere er sikre på at en testen
+er riktig, men den feiler, så må dere sannsynligvis endre koden i klassen som testes – ikke testen
+deres.
+```
+
+## Detaljerte krav
+
+### Del 1 - Grunnklasser og brukergrensesnitt
+
+1. **Appen skal bestå av minimum to interagerende klasser, i tillegg til Controller- og Appklassene, og brukergrensesnittet laget i FXML.**
+
+Andre klasser:
+  - [service/][service-folder]
+  - [model/][model-folder]
+
+App-klasse:
+  - [Main.java][Main-file]
+
+Controller klasser:
+  - [MainController.java][MainController-file]
+  - [controllers/][controllers-folder]
+
+Brukergrensesnitt:
+  [resources/fxml/][fxml-folder]
+
+I denne delen har vi laget én Application-klasse som laster én hoved-FXML-fil + kontroller, som internt linker til flere andre fxml filer med hver sine kontrollere. Kontrollerne binder sammen sine relevante grensesnittsparametere med en global [`Model`][Model-file]-klasse og setter opp event-lyttere på de relevante FXML-elementene, i tillegg til å sette opp en eventbus mellom seg og de andre kontrollerne for kommunikasjon dem imellom. Eventbus bruker dataklasser arvet fra [`Event`][Event-file]-klassen, som beskrivelse på hvilken type melding som blir sendt. Basert på typen av meldingen skiller eventbusen hvilke funksjoner som skal fyres av. Dette er en variant av observatør-observert metoden.
+
+Her er et diagram over koblingene i programmet:
+
+<div align="center">
+<img src=".gitlab/graphics/FXML-diagram.png">
+</div>
+
+
+2. **Minimum en av klassene må ha noe funksjonalitet utover ren datalagring, en form for kalkulasjoner (i en utvidet betydning av begrepet).**
+
+Klassene som blir brukt for kalkulasjon har vi lagt i [app/service][service-folder]
+
+3. **Det skal implementeres korrekt innkapsling og validering for tilstandene til objektene i appen.**
+
+Ettersom vi bruker en eventbus, så ligger innkapslingen og valideringen for tilstandene i events og i funksjonene som tar input fra brukergrensesnittet. 
+Eksempler på dette kan dere se her: 
+
+- [events/LanguageChangedEvent.java][LanguageChangedEvent-file]
+- [events/EditorChangedEvent.java][EditorChangedEvent-file]
+- [events/ThemeChangedEvent.java][ThemeChangedEvent-file]
+
+4. **Appen skal organiseres etter Model-View-Controller prinsippet, som beskrevet ovenfor.**
+
+Hovedbitene med state som skal være global for hele applikasjonen ligger i en klasse som heter [Model][Model-file]. All annen tilstand er lokal til FXML-elementene hvor den hører hjemme, og ved enhver oppdatering av den tilstanden vil det bli sent ut relevante events til alle andre kontrollere for at de skal oppdatere sine FXML-elementer sin indre tilstand. Dermed er Model, View, og Controllers separert.
+
+### Del 2 - Filbehandling
+
+1. **Et grensesnitt som minimum har en metode for lesing fra og en for skriving til fil.**
+
+Dette finner dere i [settings/SettingsProviderI.java][interface-file]
+Her er metodene for lesing fra og skriving til fil som innebærer programtilstandene.  
+
+2. **Minimum en ny klasse (altså ikke en av klassene dere har lagd tidligere i prosjketet) som implementerer grensesnittet. Klassen skal altså lagre (deler av) tilstanden til appen deres til et valgfritt format og lese inn det samme formatet til appen.**
+
+Dette finner dere i [settings/SettingsProvider.java][settings-file]
+SettingsProvider-filen implementerer grensesnittet og realiserer funksjonaliteten. Her blir tilstandene til innstillings-objektene strukturert over til et tekstformat. 
+
+
+3. **Brukergrensesnittet i appen må utvides med mulighet for å skrive tilstanden til og lese fra fil.**
+
+Dette finner dere i [MenubarController.java][MenubarController-file]
+
+### Del 3 - Feilhåndtering
+
+1. **Det skal være implementert hensiktsmessig feilhåndtering i alle utsatte deler av appen deres.**
+
+På lik måte som det er lagt inn innkapsling der hvor programmet får input ifra brukeren, er det er det meste av feilhåndteringen blir gjort. Et eksempel på dette finner dere i [service/FileTreeOperations.java][FileTreeOperations-file]
+
+I FileOperations er det lagt inn omfattende feilhåndtering for filer.
+Dette finner dere i [service/FileOperations.java][FileOperations-file]
+
+
+### Del 4 - Testing
+
+[![Coverage](https://gitlab.stud.idi.ntnu.no/oysteikt/h20-tdt4100-project/badges/master/coverage.svg?)](https://oysteikt.pages.stud.idi.ntnu.no/h20-tdt4100-project/)
+
+1. **Alle relevante deler av koden deres skal enhetstestes.**
+
+Dere finner testene i [src/test/java/app][tests-folder]
+
+**OBS: se nederst angående `FileOperations` og `DialogBoxes`**
+
+2. **Enhetstestene skal skrives i JUnit 5.**
+
+Alle testene er skrevet i JUnit 5, med hjelp fra et par andre biblioteker og plugins som bygger på toppen av JUnit.
+
+Disse inluderer:
+
+  - [TestFX](http://testfx.github.io/TestFX/)
+  - [Hamcrest](http://hamcrest.org/JavaHamcrest/)
+  - [Mockito](https://site.mockito.org/)
+  - [Monocle](https://wiki.openjdk.java.net/display/OpenJFX/Monocle)
+  - [Jacoco](https://www.eclemma.org/jacoco/)
+
+På grunn av hvordan noen av klassene er skrevet statisk, så mangler vi to tester for [`FileOperations`][FileOperations-file] og [`DialogBoxes`][DialogBoxes-file]
+
+Grunnen til at vi ikke fikk testet disse er fordi at Mockito selv ikke kan teste kode som inneholder `static`/`final` properties, eller inline bruk av konstruktør. For disse brukstilfellene har det vært vanlig å bruke [Powermock][powermock], men dette støttet ikke JUnit5 enda. I [`FileOperationsTest.java`][FileOperationsTest-file] finner dere kommentert ut kode som ville vært hvordan vi hadde skrevet koden om powermock var tilgjengelig for JUnit5
+
+Se [aggarwal-rohan17.medium.com](https://aggarwal-rohan17.medium.com/simplifying-junit-mockito-and-powermock-d1392059ce87#48d4) for detaljer
+
+
+[Model-file]: https://gitlab.stud.idi.ntnu.no/oysteikt/h20-tdt4100-project/-/blob/master/src/main/java/app/model/Model.java
+[Event-file]: https://gitlab.stud.idi.ntnu.no/oysteikt/h20-tdt4100-project/-/blob/master/src/main/java/app/events/Event.java
+[model-folder]: https://gitlab.stud.idi.ntnu.no/oysteikt/h20-tdt4100-project/-/tree/master/src/main/java/app/model
+[service-folder]: https://gitlab.stud.idi.ntnu.no/oysteikt/h20-tdt4100-project/-/tree/master/src/main/java/app/service
+[Main-file]: https://gitlab.stud.idi.ntnu.no/oysteikt/h20-tdt4100-project/-/tree/master/src/main/java/app/Main.java
+[MainController-file]: https://gitlab.stud.idi.ntnu.no/oysteikt/h20-tdt4100-project/-/tree/master/src/main/java/app/MainController.java
+[controllers-folder]: https://gitlab.stud.idi.ntnu.no/oysteikt/h20-tdt4100-project/-/tree/master/src/main/java/app/controllers
+[fxml-folder]: https://gitlab.stud.idi.ntnu.no/oysteikt/h20-tdt4100-project/-/tree/master/src/main/resources/fxml/
+[tests-folder]: https://gitlab.stud.idi.ntnu.no/oysteikt/h20-tdt4100-project/-/tree/master/src/test/java/app
+[interface-file]: https://gitlab.stud.idi.ntnu.no/oysteikt/h20-tdt4100-project/-/blob/master/src/main/java/app/settings/SettingsProviderI.java
+[settings-file]: https://gitlab.stud.idi.ntnu.no/oysteikt/h20-tdt4100-project/-/blob/master/src/main/java/app/settings/SettingsProvider.java
+[MenubarController-file]: https://gitlab.stud.idi.ntnu.no/oysteikt/h20-tdt4100-project/-/blob/master/src/main/java/app/controllers/MenubarController.java
+[LanguageChangedEvent-file]: https://gitlab.stud.idi.ntnu.no/oysteikt/h20-tdt4100-project/-/blob/master/src/main/java/app/events/LanguageChangedEvent.java
+[EditorChangedEvent-file]: https://gitlab.stud.idi.ntnu.no/oysteikt/h20-tdt4100-project/-/blob/master/src/main/java/app/events/EditorChangedEvent.java
+[ThemeChangedEvent-file]: https://gitlab.stud.idi.ntnu.no/oysteikt/h20-tdt4100-project/-/blob/master/src/main/java/app/events/ThemeChangedEvent.java
+[FileOperations-file]: https://gitlab.stud.idi.ntnu.no/oysteikt/h20-tdt4100-project/-/blob/master/src/main/java/app/service/FileOperations.java
+[FileTreeOperations-file]: https://gitlab.stud.idi.ntnu.no/oysteikt/h20-tdt4100-project/-/blob/master/src/main/java/app/service/FiletreeOperations.java
+[DialogBoxes-file]: https://gitlab.stud.idi.ntnu.no/oysteikt/h20-tdt4100-project/-/blob/master/src/main/java/app/service/DialogBoxes.java
+[powermock]: https://github.com/powermock/powermock
+[FileOperationsTest-file]: https://gitlab.stud.idi.ntnu.no/oysteikt/h20-tdt4100-project/-/blob/master/src/test/java/app/service/FileOperationsTest.java
+
+
+

pom.xml

@@ -1,5 +1,4 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-  xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
 
   <!-- Please read https://maven.apache.org/guides/introduction/introduction-to-the-pom.html -->
 
@@ -30,9 +29,9 @@
 
     <!-- RichTextFX -->
     <dependency>
-        <groupId>org.fxmisc.richtext</groupId>
-        <artifactId>richtextfx</artifactId>
-        <version>0.10.5</version>
+      <groupId>org.fxmisc.richtext</groupId>
+      <artifactId>richtextfx</artifactId>
+      <version>0.10.5</version>
     </dependency>
 
     <!-- Guava Eventbus -->
@@ -42,13 +41,12 @@
       <version>3.2.0-01</version>
     </dependency>
 
-
     <!-- JUnit 5 -->
     <dependency>
-        <groupId>org.junit.jupiter</groupId>
-        <artifactId>junit-jupiter</artifactId>
-        <version>5.8.0-M1</version>
-        <scope>test</scope>
+      <groupId>org.junit.jupiter</groupId>
+      <artifactId>junit-jupiter</artifactId>
+      <version>5.8.0-M1</version>
+      <scope>test</scope>
     </dependency>
 
     <!-- TestFX -->
@@ -65,6 +63,36 @@
       <scope>test</scope>
     </dependency>
 
+    <!-- Hamcrest - Matchers to help testing the JavaFX UI -->
+    <dependency>
+      <groupId>org.hamcrest</groupId>
+      <artifactId>hamcrest</artifactId>
+      <version>2.1</version>
+      <scope>test</scope>
+    </dependency>
+
+    <!-- Monocle - Headless UI testing in CI -->
+    <dependency>
+      <groupId>org.testfx</groupId>
+      <artifactId>openjfx-monocle</artifactId>
+      <version>jdk-12.0.1+2</version>
+      <scope>test</scope>
+    </dependency>
+
+    <!-- Mockito - Mocking Library for performing isolated unit tests -->
+    <dependency>
+      <groupId>org.mockito</groupId>
+      <artifactId>mockito-inline</artifactId>
+      <version>3.8.0</version>
+      <scope>test</scope>
+    </dependency>
+    <dependency>
+      <groupId>org.mockito</groupId>
+      <artifactId>mockito-junit-jupiter</artifactId>
+      <version>2.23.0</version>
+      <scope>test</scope>
+    </dependency>
+
     <!-- JavaDoc -->
     <dependency>
       <groupId>org.apache.maven.plugins</groupId>
@@ -73,6 +101,26 @@
       <type>maven-plugin</type>
     </dependency>
 
+    <!-- JavaFX Graphics - For completeness when packaging uber-jar -->
+    <dependency>
+      <groupId>org.openjfx</groupId>
+      <artifactId>javafx-graphics</artifactId>
+      <version>17-ea+7</version>
+      <classifier>win</classifier>
+    </dependency>
+    <dependency>
+      <groupId>org.openjfx</groupId>
+      <artifactId>javafx-graphics</artifactId>
+      <version>17-ea+7</version>
+      <classifier>linux</classifier>
+    </dependency>
+    <dependency>
+      <groupId>org.openjfx</groupId>
+      <artifactId>javafx-graphics</artifactId>
+      <version>17-ea+7</version>
+      <classifier>mac</classifier>
+    </dependency>
+
   </dependencies>
   <build>
     <plugins>
@@ -90,7 +138,7 @@
           </compilerArgs>
         </configuration>
       </plugin>
-      
+
       <!-- Plugin to test all junit tests with 'surefire:test' -->
       <plugin>
         <artifactId>maven-surefire-plugin</artifactId>
@@ -112,6 +160,7 @@
         </configuration>
       </plugin>
 
+      <!-- Plugin to generate code coverage reports -->
       <plugin>
         <groupId>org.jacoco</groupId>
         <artifactId>jacoco-maven-plugin</artifactId>
@@ -133,6 +182,27 @@
         </executions>
       </plugin>
 
+      <!-- Plugin to bundle dependencies to generate a jar file -->
+      <plugin>
+        <groupId>org.apache.maven.plugins</groupId>
+        <artifactId>maven-shade-plugin</artifactId>
+        <version>3.0.0</version>
+        <executions>
+          <execution>
+            <phase>package</phase>
+            <goals>
+              <goal>shade</goal>
+            </goals>
+            <configuration>
+              <transformers>
+                <transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
+                  <mainClass>app.MainLauncher</mainClass>
+                </transformer>
+              </transformers>
+            </configuration>
+          </execution>
+        </executions>
+      </plugin>
 
     </plugins>
   </build>

run.bat

@@ -0,0 +1,7 @@
+@ECHO OFF
+
+call mvn clean package -Dmaven.test.skip=true  
+
+java -jar --enable-preview target/banana-editor-1.0.0.jar
+
+pause

run.sh

@@ -0,0 +1,5 @@
+#!/bin/sh
+
+mvn clean package -Dmaven.test.skip=true
+
+java -jar --enable-preview target/banana-editor-1.0.0.jar

src/main/java/app/Main.java

@@ -1,6 +1,7 @@
 package app;
 
 import java.io.IOException;
+import java.util.Optional;
 
 import javafx.application.Application;
 import javafx.fxml.FXMLLoader;
@@ -9,9 +10,9 @@ import javafx.scene.Scene;
 import javafx.scene.image.Image;
 import javafx.stage.Stage;
 import app.events.FileSaveStateChangedEvent;
-import app.events.LanguageChangedEvent;
-import app.events.ThemeChangedEvent;
 import app.model.Model;
+import app.service.DialogBoxes;
+import app.settings.SettingsProvider;
 
 public class Main extends Application {
 
@@ -24,6 +25,8 @@ public class Main extends Application {
 
   /**
    * Boilerplate function to launch the application.
+   * 
+   * @param args Additional arguments from commandline
    */
   public static void main(String[] args) {
     launch(args);
@@ -34,17 +37,25 @@ public class Main extends Application {
    */
   private void setupWindow(Stage window) {
     window.setTitle(TITLE);
-    window.getIcons().add(new Image(getClass().getResourceAsStream(ICON_PATH)));
+    if (window.getIcons().isEmpty())
+      window.getIcons().add(new Image(getClass().getResourceAsStream(ICON_PATH)));
   }
 
   /**
-   * Loads all FXML documents of the main UI and initializes all correlated subcontrollers
+   * Loads all FXML documents of the main UI and initializes all correlated
+   * subcontrollers
+   * 
    * @throws IOException
    */
-  private void loadFXML() throws IOException {
-    // TODO: Error handle this function.
-    this.fxmlLoader = new FXMLLoader(getClass().getResource("/fxml/Main.fxml"));
-    this.fxmlRoot = fxmlLoader.load();
+  private void loadFXML() {
+    try {
+      this.fxmlLoader = new FXMLLoader(getClass().getResource("/fxml/Main.fxml"));
+      this.fxmlRoot = fxmlLoader.load();
+    } catch (Exception e) {
+      DialogBoxes.showErrorMessage("There is an error within the program. Please try to reinstall.");
+      System.exit(1);
+    }
+
   }
 
   /**
@@ -52,6 +63,7 @@ public class Main extends Application {
    */
   private void createScene() {
     this.scene = new Scene(fxmlRoot);
+    this.scene.setUserData(this.fxmlLoader);
     Model.setScene(scene);
   }
 
@@ -62,14 +74,17 @@ public class Main extends Application {
     scene.getStylesheets().setAll("", "");
 
     MainController mainController = fxmlLoader.getController();
-    mainController.getEventBus().post(new LanguageChangedEvent("Java"));
-    mainController.getEventBus().post(new ThemeChangedEvent("Monokai"));
+    SettingsProvider SP = new SettingsProvider(mainController.getEventBus());
+    SP.loadSettings();
+    Model.setActiveFilePath(Optional.empty());
+    Model.setProjectPath(Optional.empty());
     mainController.getEventBus().post(new FileSaveStateChangedEvent(true));
     mainController.setHostServices(getHostServices());
   }
 
   /**
    * The entrypoint of the application.
+   * 
    * @param window The primary window of the application
    */
   @Override

src/main/java/app/MainController.java

@@ -4,6 +4,8 @@ import java.net.URL;
 import java.util.List;
 import java.util.ResourceBundle;
 
+import javax.swing.JOptionPane;
+
 import com.google.common.eventbus.EventBus;
 import com.google.common.eventbus.Subscribe;
 
@@ -18,6 +20,9 @@ import javafx.application.Platform;
 import javafx.fxml.FXML;
 import javafx.fxml.Initializable;
 
+/**
+ * An FXML controller that controls the application and all subcontrollers
+ */
 public class MainController implements Initializable {
 
   @FXML
@@ -64,8 +69,16 @@ public class MainController implements Initializable {
     return hostServices;
   }
 
+  /**
+   * @return All subcontrollers of this controller
+   */
+  public List<Controller> getInnerControllers() {
+    return List.of(editorController, filetreeController, modelineController, menubarController);
+  }
+
   /**
    * Set a reference to the global Host Services API
+   * 
    * @param hostServices The JavaFX HostServices object
    * @see #getHostServices()
    */
@@ -75,52 +88,69 @@ public class MainController implements Initializable {
 
   /**
    * Replace a CSS file in a specific location in the application CSS array
+   * 
    * @param position The position of the CSS file to replace
-   * @param cssPath The path in resources to the new CSS file
+   * @param cssPath  The path in resources to the new CSS file
    */
   private void setCSSAt(int position, String cssPath) {
-    //TODO: Error check that position in range 0 to 1
+    if ((position != 0) && (position != 1)) {
+      throw new IllegalArgumentException("Range of position must be either 0 or 1");
+    } 
     String nextStyleSheet = getClass().getResource(cssPath).toExternalForm();
 
     Model.getScene().getStylesheets().set(position, nextStyleSheet);
   }
 
+  /* ------------------------------------------------------------------------ */
+  /*                            EVENT BUS LISTENERS                           */
+  /* ------------------------------------------------------------------------ */
+
   /**
    * Change the CSS according to which language is being used
+   * 
    * @param event
    */
   @Subscribe
-  private void handle(LanguageChangedEvent event) {
+  public void handle(LanguageChangedEvent event) {
     this.setCSSAt(1, "/styling/languages/" + event.getLanguage().toLowerCase() + ".css");
   }
 
   /**
    * Change the CSS according to which theme the user chooses
+   * 
    * @param event
    */
   @Subscribe
-  private void handle(ThemeChangedEvent event) {
+  public void handle(ThemeChangedEvent event) {
     this.setCSSAt(0, "/styling/themes/" + event.getTheme().toLowerCase().replace(" ", "-") + ".css");
   }
 
   /**
    * Open a link in the browser.
+   * 
    * @param event
    */
   @Subscribe
-  private void handle(OpenLinkInBrowserEvent event) {
+  public void handle(OpenLinkInBrowserEvent event) {
     this.getHostServices().showDocument(event.getLink());
   }
 
   /**
-   * Handle an exit request for the whole program
+   * Handle an exit request for the whole program. Checking if all is saved before
+   * closing the app. The user can either choose to exit or go back to the
+   * application and save.
+   * 
    * @param event
    */
   @Subscribe
-  private void handle(ExitApplicationEvent event) {
-    // TODO: send save file event, exit application safely.
+  public void handle(ExitApplicationEvent event) {
+    if (!Model.getFileIsSaved()) {
+      int g = JOptionPane.showConfirmDialog(null, "Your files are not saved.\nSave before exit?", "Exit",
+          JOptionPane.YES_NO_OPTION);
 
+      if (g == JOptionPane.YES_OPTION)
+        this.editorController.saveCodeArea(Model.getActiveFilePath().isEmpty());
+    }
     Platform.exit();
   }
-
-}
+}

src/main/java/app/MainLauncher.java

@@ -0,0 +1,15 @@
+package app;
+
+/**
+ * A launcher class to point towards as the start point for a packaged JAR
+ */
+public class MainLauncher {
+  /**
+   * The root function of the call stack
+   * 
+   * @param args Commandline arguments
+   */
+    public static void main(String[] args) {
+        Main.main(args);
+    }
+}

src/main/java/app/controllers/Controller.java

@@ -3,12 +3,12 @@ package app.controllers;
 import com.google.common.eventbus.EventBus;
 
 /**
- * Interface to make a controller that contains an EventBus
+ * Interface describing a JavaFX controller that contains an EventBus
  */
 public interface Controller {  
   /**
    * Registers the main EventBus into the controller.
-   * @param eventBus the main EventBus
+   * @param eventBus
    */
   public void setEventBus(EventBus eventBus);
 }

src/main/java/app/controllers/EditorController.java

@@ -1,11 +1,8 @@
 package app.controllers;
 
-import java.io.File;
-import java.io.FileNotFoundException;
 import java.net.URL;
 import java.util.Collection;
 import java.util.ResourceBundle;
-import java.util.Scanner;
 
 import com.google.common.eventbus.EventBus;
 import com.google.common.eventbus.Subscribe;
@@ -19,19 +16,26 @@ import org.fxmisc.richtext.model.TwoDimensional.Position;
 import app.events.CopyEvent;
 import app.events.CutEvent;
 import app.events.EditorChangedEvent;
+
 import app.events.LanguageChangedEvent;
+import app.events.OpenFileEvent;
 import app.events.PasteEvent;
 import app.events.RedoEvent;
+import app.events.SaveFileEvent;
 import app.events.ToggleCommentEvent;
 import app.events.ToggleWrapTextEvent;
 import app.events.UndoEvent;
 import app.events.FileSaveStateChangedEvent;
-import app.events.FileSelectedEvent;
 import app.model.Model;
+import app.service.FileOperations;
 import app.service.LanguageOperations;
 import javafx.fxml.FXML;
 import javafx.fxml.Initializable;
+import javafx.stage.Stage;
 
+/**
+ * An FXML controller that controls the CodeArea
+ */
 public class EditorController implements Initializable, Controller {
 
   @FXML
@@ -59,7 +63,7 @@ public class EditorController implements Initializable, Controller {
   /**
    * Applies highlighting to the editor.
    * 
-   * @param highlighting highlighting data
+   * @param highlighting Syntax highlighting data
    */
   private void setHighlighting(StyleSpans<Collection<String>> highlighting) {
     this.editor.setStyleSpans(0, highlighting);
@@ -73,8 +77,12 @@ public class EditorController implements Initializable, Controller {
   }
 
   /**
-   * Uses Model.language to determine whether the current line/selection is
-   * commented or not, and toggles the comment.
+   * Uses the {@link app.model.ProgrammingLanguage ProgrammingLanguage} in
+   * {@link app.model.Model Model} to determine whether the current line/selection
+   * is commented or not, and toggles the comment.
+   * 
+   * @see app.model.ProgrammingLanguage#commentLine(String)
+   *      ProgrammingLanguage.commentLine(line)
    */
   private void toggleComment() {
     if (editor.getSelectedText().equals("")) {
@@ -101,6 +109,11 @@ public class EditorController implements Initializable, Controller {
     }
   }
 
+  /**
+   * Updates the wraptext setting of the code area
+   * 
+   * @param isWrapText The updated setting value
+   */
   private void setWrapText(boolean isWrapText) {
     this.editor.setWrapText(isWrapText);
   }
@@ -120,70 +133,143 @@ public class EditorController implements Initializable, Controller {
   }
 
   /**
-   * Refreshes the editor whenever the language is changed.
+   * Updates the content of the editor. 
+   * 
+   * @param newContent The String to be inserted into the editor
+   */
+  private void setEditorContent(String newContent) {
+      editor.clear();
+      editor.appendText(newContent);
+  }
+
+  /**
+   * Saving/Writing to the file based on the active filepath in {@link app.model.Model Model}
+   * if it is a new File. Otherwise it will open a dialog to ask the user where to save the file.
+   * 
+   * @param isNewFile Whether or not the file already has a path
+   */
+  public void saveCodeArea(boolean isNewFile) {
+    Stage stage = (Stage) editor.getScene().getWindow();
+
+    if (isNewFile && FileOperations.saveFileWithDialog(stage, editor.getText())) {
+      this.eventBus.post(new OpenFileEvent(Model.getActiveFilePath()));
+      this.eventBus.post(new FileSaveStateChangedEvent(true));
+    }
+    else if (FileOperations.saveFile(Model.getActiveFilePath().orElseThrow(), editor.getText())) {
+      this.eventBus.post(new FileSaveStateChangedEvent(true));
+    }    
+  }
+
+  /* ------------------------------------------------------------------------ */
+  /*                            EVENT BUS LISTENERS                           */
+  /* ------------------------------------------------------------------------ */
+
+  /**
+   * Updates the CodeArea whenever a new file is opened.
    * 
    * @param event
    */
-
   @Subscribe
-  private void handle(FileSelectedEvent event) {
-    try (Scanner sc = new Scanner(new File(event.getPath()))) {
-      editor.clear();
-      while (sc.hasNextLine()) {
-        editor.appendText(sc.nextLine());
-        editor.appendText("\n");
-      }
-    } catch (FileNotFoundException ex) {
-      System.out.println(event.getPath());
-    }
+  public void handle(OpenFileEvent event) {
+    String newContent =
+      event
+        .getPath()
+        .map(path -> FileOperations.readFile(path))
+        .orElse("");
+    this.setEditorContent(newContent);
   }
 
+  /**
+   * Saves the editor content to a file
+   * 
+   * @param event
+   */
   @Subscribe
-  private void handle(LanguageChangedEvent event) {
+  public void handle(SaveFileEvent event) {
+    this.saveCodeArea(event.getIsNewFile());
+  }
+
+  /**
+   * Refreshes the syntax highlighting when the Programming language is changed
+   * 
+   * @param event
+   */
+  @Subscribe
+  public void handle(LanguageChangedEvent event) {
     this.refreshHighlighting();
   }
 
   /**
-   * Toggles a language specific comment of the line/selection
+   * Toggles a comment based on the editor state
    * 
    * @param event
    */
   @Subscribe
-  private void handle(ToggleCommentEvent event) {
+  public void handle(ToggleCommentEvent event) {
     this.toggleComment();
   }
 
+  /**
+   * Toggles the WrapText setting
+   * 
+   * @param event
+   */
   @Subscribe
-  private void handle(ToggleWrapTextEvent event) {
+  public void handle(ToggleWrapTextEvent event) {
     this.setWrapText(event.getIsWrapped());
   }
 
+  /**
+   * Undo if focused
+   * 
+   * @param event
+   */
   @Subscribe
-  private void handle(UndoEvent event) {
+  public void handle(UndoEvent event) {
     if (this.editor.isFocused())
       this.editor.undo();
   }
 
+  /**
+   * Redo if focused
+   * 
+   * @param event
+   */
   @Subscribe
-  private void handle(RedoEvent event) {
+  public void handle(RedoEvent event) {
     if (this.editor.isFocused())
       this.editor.redo();
   }
 
+  /**
+   * Copy selected content if focused
+   * 
+   * @param event
+   */
   @Subscribe
-  private void handle(CopyEvent event) {
+  public void handle(CopyEvent event) {
     if (this.editor.isFocused())
       this.editor.copy();
   }
 
+  /**
+   * Cut selected content if focused
+   * 
+   * @param event
+   */
   @Subscribe
-  private void handle(CutEvent event) {
+  public void handle(CutEvent event) {
     if (this.editor.isFocused())
       this.editor.cut();
   }
 
+  /**
+   * Paste from clipboard if focused
+   * 
+   * @param event
+   */
   @Subscribe
-  private void handle(PasteEvent event) {
+  public void handle(PasteEvent event) {
     if (this.editor.isFocused())
       this.editor.paste();
   }

src/main/java/app/controllers/FiletreeController.java

@@ -4,42 +4,39 @@ import javafx.fxml.FXML;
 import javafx.scene.control.CheckBoxTreeItem;
 import javafx.scene.control.TreeItem;
 import javafx.scene.control.TreeView;
-import javafx.scene.image.Image;
-import javafx.scene.image.ImageView;
 import javafx.scene.input.MouseEvent;
 
 import java.io.File;
+import java.io.FileNotFoundException;
 import java.net.URL;
-import java.util.ArrayList;
-import java.util.List;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.Optional;
 import java.util.ResourceBundle;
 
 import com.google.common.eventbus.EventBus;
 import com.google.common.eventbus.Subscribe;
 
-import app.events.FileSelectedEvent;
+import app.events.OpenFileEvent;
 import app.events.OpenProjectEvent;
+import app.events.SaveFileEvent;
 import app.model.Model;
+import app.service.DialogBoxes;
+import app.service.FiletreeOperations;
 import javafx.fxml.Initializable;
 
+/**
+ * An FXML controller that controls the Filetree
+ */
 public class FiletreeController implements Initializable, Controller {
 
   private EventBus eventBus;
 
-  // Creating the images for the icons.
-  Image folder = new Image(getClass().getResourceAsStream("/graphics/folder.png"));
-  Image md = new Image(getClass().getResourceAsStream("/graphics/md.png"));
-  Image java = new Image(getClass().getResourceAsStream("/graphics/java.png"));
-  Image placeholder = new Image(getClass().getResourceAsStream("/graphics/placeholder.png"));
-
-  // Creating the variable.
   @FXML
   private TreeView<String> filetree;
 
   @Override
-  public void initialize(URL url, ResourceBundle resourceBundle) {
-    //
-  }
+  public void initialize(URL url, ResourceBundle resourceBundle) {}
 
   @Override
   public void setEventBus(EventBus eventBus) {
@@ -48,106 +45,78 @@ public class FiletreeController implements Initializable, Controller {
   }
 
   /**
-   * The displaying of the fileTree. The inputChosen(the path) is aquired from the
-   * eventBus (OpeFileProjectEvent). The root is created as a CheckBoxItems and
-   * sends it to generateTree, and after that setting it to the root.
+   * Generate a tree structure of a directory, and set the filetree to
+   * show the new tree
+   * 
+   * @param rootDir Path to the directory to be the root of the tree
    */
-  private void showTree(String inputChosen) {
-    CheckBoxTreeItem<String> root = new CheckBoxTreeItem<>(inputChosen);
+  private void showTree(Path rootDir) {
+    CheckBoxTreeItem<String> root = new CheckBoxTreeItem<>(rootDir.getFileName().toString());
     filetree.setShowRoot(false);
-    File fileInputChosen = new File(inputChosen);
+    File fileInputChosen = rootDir.toFile();
 
-    generateTree(fileInputChosen, root);
+    try {
+      FiletreeOperations.generateTree(fileInputChosen, root);
 
-    filetree.setRoot(root);
-  }
-
-  /**
-   * The method to generate the fileTree recursively. If it is a directory a
-   * CheckBoxStringItem is created and the method is called again. It goes through
-   * all until every directory or file inside the orginal CheckBoxItem is made. If
-   * the item is a file it sends it to the help function checkExtension which is
-   * described below.
-   */
-  private void generateTree(File file, CheckBoxTreeItem<String> parent) {
-
-    if (file.isDirectory()) {
-      CheckBoxTreeItem<String> element = new CheckBoxTreeItem<>(file.getName(), new ImageView(folder));
-      parent.getChildren().add(element);
-
-      List<File> dirList = new ArrayList<>();
-      List<File> fileList = new ArrayList<>();
-
-      sortFiles(dirList, fileList, file);
-
-      for (File f : dirList) {
-        generateTree(f, element);
-      }
-
-    } else {
-      checkExtensions(file, parent);
+      filetree.setRoot(root);
+    } catch (Exception e) {
+      Model.setProjectPath(Optional.empty());
+      DialogBoxes.showErrorMessage(
+        "Could not open directory.\n\n"
+        + "Do you have the right permissions for this directory?\n"
+        + "Or does the directory contain any shortcut to somewhere within itself?"
+      );
     }
   }
 
   /**
-   * A helping function to sort the files/folders in the fileTree so that it shows
-   * in the correct order.
-   */
-  private void sortFiles(List<File> dirList, List<File> fileList, File file) {
-    for (File f : file.listFiles()) {
-      if (f.isDirectory())
-        dirList.add(f);
-      else {
-        fileList.add(f);
-      }
-
-    }
-    dirList.addAll(fileList);
-
-  }
-
-  /**
-   * A help function to check if the extensions match .java or.md to insert the
-   * spesific icons and sending it to another help funtion createExtension to
-   * create the new CheckboxTreeItem<String> that will add to the parent.
-   */
-  private void checkExtensions(File file, CheckBoxTreeItem<String> parent) {
-    String name = file.getName();
-    String ext = (name.substring(file.getName().lastIndexOf(".") + 1, file.getName().length()));
-
-    if ("java".equals(ext))
-      createExtension(name, java, parent);
-    else if ("md".equals(ext))
-      createExtension(name, md, parent);
-    else
-      createExtension(name, placeholder, parent);
-  }
-
-  private void createExtension(String name, Image image, CheckBoxTreeItem<String> parent) {
-    CheckBoxTreeItem<String> element = new CheckBoxTreeItem<>(name, new ImageView(image));
-    parent.getChildren().add(element);
-  }
-
+   * Handles opening a file whenever a filetree item is clicked twice. */
   @FXML
   private void handleMouseClick(MouseEvent event) {
     if (event.getClickCount() == 2) {
       TreeItem<String> item = filetree.getSelectionModel().getSelectedItem();
 
-      String root = Model.getProjectPath().getFileName().toString();
-      String path = "";
-      while (!root.equals(item.getValue())) {
-        path = File.separator + item.getValue() + path;
-        item = item.getParent();
-      }
+      try {
+        Path path = FiletreeOperations.getPathOfTreeItem(item);
 
-      path = Model.getProjectPath() + path;
-      this.eventBus.post(new FileSelectedEvent(path));
+        if (!Files.isDirectory(path)) {
+          this.eventBus.post(new OpenFileEvent(Optional.ofNullable(path)));
+        }
+      } catch (FileNotFoundException e) {
+        System.err.println("[ERROR] Could not find filepath from filetree");
+        System.err.print(e);
+      }
     }
   }
 
+  /* ------------------------------------------------------------------------ */
+  /*                            EVENT BUS LISTENERS                           */
+  /* ------------------------------------------------------------------------ */
+
+  /**
+   * Updates the filetree whenever a new project is opened
+   * 
+   * @param event
+   */
   @Subscribe
   private void handle(OpenProjectEvent event) {
-    this.showTree(event.getPath());
+    event.getPath().ifPresentOrElse(
+      path -> this.showTree(path),
+      () -> System.err.println("[ERROR] OpenProjectEvent was empty")
+    );
+  }
+
+  /**
+   * Updates the filetree whenever a new file gets saved
+   * 
+   * @param event
+   */
+  @Subscribe
+  private void handle(SaveFileEvent event) {
+    if (event.getIsNewFile())
+      Model
+        .getProjectPath()
+        .ifPresent(path -> this.showTree(path));
   }
 
 }

src/main/java/app/controllers/MenubarController.java

@@ -1,7 +1,9 @@
 package app.controllers;
 
 import java.io.File;
+import java.io.FileNotFoundException;
 import java.net.URL;
+import java.util.Optional;
 import java.util.ResourceBundle;
 
 import com.google.common.eventbus.EventBus;
@@ -10,17 +12,19 @@ import com.google.common.eventbus.Subscribe;
 import app.events.CopyEvent;
 import app.events.CutEvent;
 import app.events.ExitApplicationEvent;
-import app.events.FileSelectedEvent;
 import app.events.LanguageChangedEvent;
+import app.events.OpenFileEvent;
 import app.events.OpenLinkInBrowserEvent;
 import app.events.OpenProjectEvent;
 import app.events.PasteEvent;
 import app.events.RedoEvent;
+import app.events.SaveFileEvent;
 import app.events.ThemeChangedEvent;
 import app.events.ToggleCommentEvent;
 import app.events.ToggleWrapTextEvent;
 import app.events.UndoEvent;
-import app.model.Model;
+import app.service.DialogBoxes;
+import app.service.FileOperations;
 import javafx.event.ActionEvent;
 import javafx.fxml.FXML;
 import javafx.fxml.Initializable;
@@ -28,10 +32,11 @@ import javafx.scene.control.CheckMenuItem;
 import javafx.scene.control.MenuBar;
 import javafx.scene.control.RadioMenuItem;
 import javafx.scene.control.ToggleGroup;
-import javafx.stage.DirectoryChooser;
-import javafx.stage.FileChooser;
 import javafx.stage.Stage;
 
+/**
+ * A FXML controller that controls the MenuBar
+ */
 public class MenubarController implements Initializable, Controller {
 
   private EventBus eventBus;
@@ -42,9 +47,11 @@ public class MenubarController implements Initializable, Controller {
   @FXML
   private ToggleGroup languageToggleGroup;
 
+  @FXML
+  private ToggleGroup themeToggleGroup;
+
   @Override
   public void initialize(URL url, ResourceBundle resourceBundle) {
-    // TODO: implement
   }
 
   @Override
@@ -53,53 +60,75 @@ public class MenubarController implements Initializable, Controller {
     this.eventBus.register(this);
   }
 
-  /* ------------------------------------------------------------------------ */
-  /* FILE */
-  /* ------------------------------------------------------------------------ */
-
-  @FXML
-  public void handleOpenFile() {
-    FileChooser fc = new FileChooser();
-    fc.setTitle("Open File");
-    Stage stage = (Stage) menubar.getScene().getWindow();
-
-    File chosenFile = fc.showOpenDialog(stage);
-    String correctFormat = chosenFile.getAbsolutePath().replace("\\", "\\\\");
-
-    Model.setActiveFilePath(chosenFile.toPath());
-    this.eventBus.post(new FileSelectedEvent(correctFormat));
-  }
-
-  @FXML
-  private void handleOpenProject() {
-    DirectoryChooser dc = new DirectoryChooser();
-    dc.setTitle("Open Project");
-    Stage stage = (Stage) menubar.getScene().getWindow();
-
-    File chosenDir = dc.showDialog(stage);
-    String correctFormat = chosenDir.getAbsolutePath().replace("\\", "\\\\");
-
-    Model.setProjectPath(chosenDir.toPath());
-    this.eventBus.post(new OpenProjectEvent(correctFormat));
-
-  }
-
-  // @FXML
-  // public void handleSaveFile() {
-  // FileChooser fc = new FileChooser();
-  // fc.setTitle("Save File");
-  // Stage stage = (Stage) menubar.getScene().getWindow();
-
-  // FileChooser.ExtensionFilter extentionjava = new
-  // FileChooser.ExtensionFilter(".java");
-  // FileChooser.ExtensionFilter extentionmd = new
-  // FileChooser.ExtensionFilter(".md");
-  // fc.getExtensionFilters().addAll(extentionjava, extentionmd);
-  // fc.showOpenDialog(stage);
-  // }
+  /* ---------------------------------- File ---------------------------------- */
 
   /**
-   * Handles the event where the language was change from the menu.
+   * Handles whenever the New File button is pressed in the menubar
+   * 
+   * @param event
+   */
+  @FXML
+  private void handleNewFile() {
+    this.eventBus.post(new OpenFileEvent(Optional.empty()));
+  }
+
+  /**
+   * Handles whenever the Open File button is pressed in the menubar
+   * 
+   * @param event
+   */
+  @FXML
+  private void handleOpenFile() {
+    Stage stage = (Stage) menubar.getScene().getWindow();
+
+    try {
+      File file = FileOperations.openFileWithDialog(stage);
+
+      this.eventBus.post(new OpenFileEvent(Optional.ofNullable(file.toPath())));
+    } catch (FileNotFoundException e) {
+      DialogBoxes.showErrorMessage("File not found!");
+    }
+  }
+
+  /**
+   * Handles whenever the Open Project button is pressed in the menubar
+   * 
+   * @param event
+   */
+  @FXML
+  private void handleOpenProject() {
+    Stage stage = (Stage) menubar.getScene().getWindow();
+
+    try {
+      File dir = FileOperations.openDirectoryWithDialog(stage);
+
+      this.eventBus.post(new OpenProjectEvent(Optional.of(dir.toPath())));
+    } catch (FileNotFoundException e) {}
+  }
+
+
+  /**
+   * Handles whenever the Save button is pressed in the menubar
+   * 
+   * @param event
+   */
+  @FXML
+  private void handleSaveFile() {
+    this.eventBus.post(new SaveFileEvent());
+  }
+
+  /**
+   * Handles whenever the Save as button is pressed in the menubar
+   * 
+   * @param event
+   */
+  @FXML
+  private void handleSaveAsFile() {
+    this.eventBus.post(new SaveFileEvent(true));
+  }
+
+  /**
+   * Handles whenever the programming language is changed from the menubar.
    * 
    * @param event
    */
@@ -108,19 +137,29 @@ public class MenubarController implements Initializable, Controller {
     this.eventBus.post(new LanguageChangedEvent(((RadioMenuItem) event.getSource()).getText()));
   }
 
+  /**
+   * Handles whenever the wraptext togglebutton is pressed in the menubar
+   * 
+   * @param event
+   */
   @FXML
   private void handleToggleWraptext(ActionEvent event) {
     var isSelected = ((CheckMenuItem) event.getSource()).selectedProperty().get();
     this.eventBus.post(new ToggleWrapTextEvent(isSelected));
   }
 
+  /**
+   * Handles whenever the theme is changed from the menubar
+   * 
+   * @param event
+   */
   @FXML
   private void handleThemeChange(ActionEvent event) {
     this.eventBus.post(new ThemeChangedEvent(((RadioMenuItem) event.getSource()).getText()));
   }
 
   /**
-   * Handles the event where there was an exit request from the menu.
+   * Handles whenever the exit button is pressed in the menubar
    * 
    * @param event
    */
@@ -129,44 +168,75 @@ public class MenubarController implements Initializable, Controller {
     this.eventBus.post(new ExitApplicationEvent());
   }
 
-  /* ------------------------------------------------------------------------ */
-  /* EDIT */
-  /* ------------------------------------------------------------------------ */
+  /* ---------------------------------- Edit ---------------------------------- */
 
+  /**
+   * Handles whenever the undo button is pressed in the menubar
+   * 
+   * @param event
+   */
   @FXML
   private void handleUndo(ActionEvent event) {
     this.eventBus.post(new UndoEvent());
   }
 
+  /**
+   * Handles whenever the redo button is pressed in the menubar
+   * 
+   * @param event
+   */
   @FXML
   private void handleRedo(ActionEvent event) {
     this.eventBus.post(new RedoEvent());
   }
 
+  /**
+   * Handles whenever the copy button is pressed in the menubar
+   * 
+   * @param event
+   */
   @FXML
   private void handleCopy(ActionEvent event) {
     this.eventBus.post(new CopyEvent());
   }
 
+  /**
+   * Handles whenever the cut button is pressed in the menubar
+   * 
+   * @param event
+   */
   @FXML
   private void handleCut(ActionEvent event) {
     this.eventBus.post(new CutEvent());
   }
 
+  /**
+   * Handles whenever the paste button is pressed in the menubar
+   * 
+   * @param event
+   */
   @FXML
   private void handlePaste(ActionEvent event) {
     this.eventBus.post(new PasteEvent());
   }
 
+  /**
+   * Handles whenever the Toggle Comment button is pressed in the menubar
+   * 
+   * @param event
+   */
   @FXML
   private void handleToggleComment(ActionEvent event) {
     this.eventBus.post(new ToggleCommentEvent());
   }
 
-  /* ------------------------------------------------------------------------ */
-  /* ABOUT */
-  /* ------------------------------------------------------------------------ */
+  /* ---------------------------------- About --------------------------------- */
 
+  /**
+   * Handles whenever the About button is pressed in the menubar
+   * 
+   * @param event
+   */
   @FXML
   private void handleAbout(ActionEvent event) {
     String aboutLink = "https://gitlab.stud.idi.ntnu.no/oysteikt/tdt4100-project-2021v/-/blob/master/README.md";
@@ -183,9 +253,33 @@ public class MenubarController implements Initializable, Controller {
    * @param event
    */
   @Subscribe
-  private void handle(LanguageChangedEvent event) {
-    this.languageToggleGroup.getToggles().stream().map(RadioMenuItem.class::cast)
-        .filter(t -> t.getId().equals("toggle" + event.getLanguage())).findFirst().orElseThrow().setSelected(true);
+  public void handle(LanguageChangedEvent event) {
+    this.languageToggleGroup
+      .getToggles()
+      .stream()
+      .map(RadioMenuItem.class::cast)
+      .filter(t -> t.getId().equals("toggle" + event.getLanguage()))
+      .findFirst()
+      // This should never happen!
+      .orElseThrow(() -> new IllegalStateException("Language button missing: " + event.getLanguage()))
+      .setSelected(true);
   }
 
+  /**
+   * Updates menubuttons whenever the theme is changed
+   * 
+   * @param event
+   */
+  @Subscribe
+  public void handle(ThemeChangedEvent event) {
+    this.themeToggleGroup
+      .getToggles()
+      .stream()
+      .map(RadioMenuItem.class::cast)
+      .filter(t -> t.getId().equals("toggle" + event.getTheme().replace(" ", "_")))
+      .findFirst()
+      // This should never happen!
+      .orElseThrow(() -> new IllegalStateException("Theme button missing: " + event.getTheme()))
+      .setSelected(true);
+  }
 }

src/main/java/app/controllers/ModelineController.java

@@ -8,12 +8,19 @@ import com.google.common.eventbus.Subscribe;
 
 import app.events.EditorChangedEvent;
 import app.events.LanguageChangedEvent;
+import app.events.OpenFileEvent;
 import app.events.FileSaveStateChangedEvent;
 import javafx.fxml.FXML;
 import javafx.fxml.Initializable;
 import javafx.scene.control.Label;
 
+/**
+ * A FXML controller that controls the Modeline
+ */
 public class ModelineController implements Initializable, Controller {
+
+  @FXML
+  private Label filename; 
   
   @FXML
   private Label saveState;
@@ -46,34 +53,50 @@ public class ModelineController implements Initializable, Controller {
     this.columnrow.setText(String.format("[%d:%d]", row, column));
   }
 
+  /* ------------------------------------------------------------------------ */
+  /* SUBSCRIPTIONS */
+  /* ------------------------------------------------------------------------ */
+
   /**
    * Updates the column-row number display whenever the editor cursor
    * changes position.
+   * 
    * @param event
    */
   @Subscribe
-  private void handle(EditorChangedEvent event) {
+  public void handle(EditorChangedEvent event) {
     this.setColumnRow(event.getColumn(), event.getLine());
   }
 
   /**
    * Updates the saveState label whenever the file either is saved or modified
+   * 
    * @param event
    */
   @Subscribe
-  private void handle(FileSaveStateChangedEvent event) {
-    // TODO: Add CSS styleclass for coloring the saveState label
-    //       whenever it changes
+  public void handle(FileSaveStateChangedEvent event) {
     this.saveState.setText(event.getIsSaved() ? "Saved!" : "Modified");
   }
 
   /**
-   * Updates the modeline to display a new language
-   * whenever it is changed.
+   * Updates the modeline to display a new language when changed.
+   * 
    * @param event
    */
   @Subscribe
   private void handle(LanguageChangedEvent event) {
     this.language.setText(event.getLanguage());
   }
+
+  /**
+   * Updates the modeline to display the name of the current file when changed
+   * 
+   * @param event
+   */
+  @Subscribe
+  private void handle(OpenFileEvent event) {
+    this.filename.setText(
+      event.getPath().map(path -> path.getFileName().toString()).orElse("New file")
+    );
+  }
 }

src/main/java/app/events/Event.java

@@ -3,4 +3,4 @@ package app.events;
 /**
  * Base class for any type of event of the eventbus
  */
-abstract class Event {}
+public abstract class Event {}

src/main/java/app/events/ExitApplicationEvent.java

@@ -4,5 +4,5 @@ package app.events;
  * Event signalizing a shutdown request for the whole applicaton
  */
 public class ExitApplicationEvent extends Event {
-  
+
 }

src/main/java/app/events/FileSelectedEvent.java

@@ -1,29 +0,0 @@
-package app.events;
-
-/**
- * Event signalizing that a file was selected in the filetree.
- * 
- * Not to be confused with {@link OpenFileEvent}
- */
-public class FileSelectedEvent extends Event {
-
-  private String path;
-
-  /**
-   * Event signalizing that a file was selected in the filetree.
-   * 
-   * Not to be confused with {@link OpenFileEvent}
-   * @param path The path of the selected file
-   */
-  public FileSelectedEvent(String path) {
-    this.path = path;
-  }
-
-  /**
-   * @return The path of the selected file
-   */
-  public String getPath() {
-    return this.path;
-  }
-
-}

src/main/java/app/events/LanguageChangedEvent.java

@@ -17,18 +17,22 @@ public class LanguageChangedEvent extends Event {
   public LanguageChangedEvent(String language) {
     this.language = language;
 
-    switch (language) {
+    switch (language.toLowerCase()) {
 
-      case "Java":
+      case "java":
         Model.setLanguage(new Java());
         break;
 
-      case "Markdown":
+      case "markdown":
         Model.setLanguage(new Markdown());
         break;
 
-      default:
+      case "empty":
+        Model.setLanguage(new Empty());
         break;
+
+      default:
+        throw new IllegalArgumentException("Could not recognize language: " + language);
     }
   }
 

src/main/java/app/events/OpenFileEvent.java

@@ -1,27 +1,31 @@
 package app.events;
 
+import java.nio.file.Path;
+import java.util.Optional;
+
+import app.model.Model;
+
 /**
  * Event signalizing that a file outside the current project is supposed to be opened in the editor.
- * 
- * Not to be confused with {@link FileSelectedEvent}
  */
 public class OpenFileEvent extends Event {
 
-    private String path;
+  private Optional<Path> path;
 
-    /**
-     * Event signalizing that a file outside the current project is supposed to be opened in the editor.
-     * @param path The path of the file to be opened
-     */
-    public OpenFileEvent(String path) {
-        this.path = path;
-    }
+  /**
+   * Event signalizing that a file outside the current project is supposed to be opened in the editor.
+   * @param path The path of the file to be opened
+   */
+  public OpenFileEvent(Optional<Path> path) {
+    this.path = path;
+    Model.setActiveFilePath(path);
+  }
 
-    /**
-     * @return The path of the file to be opened
-     */
-    public String getPath() {
-        return this.path;
-    }
+  /**
+   * @return The path of the file to be opened
+   */
+  public Optional<Path> getPath() {
+    return this.path;
+  }
 
 }

src/main/java/app/events/OpenProjectEvent.java

@@ -1,24 +1,30 @@
 package app.events;
 
+import java.nio.file.Path;
+import java.util.Optional;
+
+import app.model.Model;
+
 /**
- * Event signalizing that a folder is supposed to be opened in the filetree.
+ * Event signalizing that a directory is supposed to be opened in the filetree.
  */
 public class OpenProjectEvent extends Event {
 
-    private String path;
+    private Optional<Path> path;
 
     /**
-     * Event signalizing that a folder is supposed to be opened in the filetree.
-     * @param path The path of the folder to be opened
+     * Event signalizing that a directory is supposed to be opened in the filetree.
+     * @param path The path of the directory to be opened
      */
-    public OpenProjectEvent(String path) {
+    public OpenProjectEvent(Optional<Path> path) {
         this.path = path;
+        Model.setProjectPath(path);
     }
 
     /**
-     * @return The path of the folder to be opened
+     * @return The path of the directory to be opened
      */
-    public String getPath() {
+    public Optional<Path> getPath() {
         return this.path;
     }
 }

src/main/java/app/events/SaveFileEvent.java

@@ -0,0 +1,35 @@
+package app.events;
+
+import app.model.Model;
+
+/**
+ * Event signalizing that the current file should be saved to disk
+ */
+public class SaveFileEvent extends Event {
+
+    private boolean isNewFile;
+
+    /**
+     * Event signalizing that a file is to be saved.
+     */
+    public SaveFileEvent() {
+        this.isNewFile = Model.getActiveFilePath().isEmpty();
+    }
+
+    /**
+     * Event signalizing that a file is to be saved.
+     * 
+     * @param isNewFile The path of the selected file
+     */
+    public SaveFileEvent(boolean isNewFile) {
+        this.isNewFile = isNewFile;
+    }
+
+    /**
+     * @return Whether or not 
+     */
+    public boolean getIsNewFile() {
+        return this.isNewFile;
+    }
+
+}

src/main/java/app/events/ThemeChangedEvent.java

@@ -1,5 +1,7 @@
 package app.events;
 
+import app.model.Model;
+
 /**
  * Event signalizing that the theme of the applicaton has been changed
  */
@@ -9,12 +11,14 @@ public class ThemeChangedEvent extends Event {
 
   /**
    * Event signalizing that the theme of the applicaton has been changed
+   * 
    * @param theme The name of the theme
    */
   public ThemeChangedEvent(String theme) {
+    Model.setTheme(theme);
     this.theme = theme;
   }
-  
+
   /**
    * @return The name of the theme
    */

src/main/java/app/model/Model.java

@@ -1,7 +1,9 @@
 package app.model;
 
 import java.nio.file.Path;
+import java.util.Optional;
 
+import app.settings.SettingsProvider;
 import javafx.scene.Scene;
 
 /**
@@ -12,44 +14,68 @@ import javafx.scene.Scene;
  */
 public class Model {
   private static boolean fileIsSaved;
-  private static Path activeFilePath;
-  private static Path currentProjectPath;
-  private static ProgrammingLanguage currentProgrammingLanguage;
+  private static Optional<Path> activeFilePath;
+  private static Optional<Path> activeProjectPath;
+  private static ProgrammingLanguage activeProgrammingLanguage;
+  private static String theme;
   private static Scene scene;
+  private static SettingsProvider settings;
 
-  public static Path getActiveFilePath() {
+  public static Optional<Path> getActiveFilePath() {
     return activeFilePath;
   }
 
-  public static void setActiveFilePath(Path path) {
+  public static void setActiveFilePath(Optional<Path> path) {
+    if (path == null)
+      throw new IllegalArgumentException("path can not be null");
     Model.activeFilePath = path;
   }
 
-  public static Path getProjectPath() {
-    return currentProjectPath;
+  public static Optional<Path> getProjectPath() {
+    return activeProjectPath;
   }
 
-  public static void setProjectPath(Path path) {
-    Model.currentProjectPath = path;
+  public static void setProjectPath(Optional<Path> path) {
+    if (path == null)
+      throw new IllegalArgumentException("path can not be null");
+    Model.activeProjectPath = path;
   }
 
   public static ProgrammingLanguage getLanguage() {
-    return currentProgrammingLanguage;
+    return activeProgrammingLanguage;
   }
 
   public static Scene getScene() {
     return scene;
   }
 
+  public static String getTheme() {
+    return theme;
+  }
+
   public static boolean getFileIsSaved() {
     return fileIsSaved;
   }
 
+  public static SettingsProvider getSettingsProvider() {
+    return settings;
+  }
+
+  public static void setTheme(String theme) {
+    if (theme == null)
+      throw new IllegalArgumentException("theme can not be null");
+    Model.theme = theme;
+  }
+
   public static void setLanguage(ProgrammingLanguage language) {
-    Model.currentProgrammingLanguage = language;
+    if (language == null)
+      throw new IllegalArgumentException("language can not be null");
+    Model.activeProgrammingLanguage = language;
   }
 
   public static void setScene(Scene scene) {
+    if (scene == null)
+      throw new IllegalArgumentException("scene can not be null");
     Model.scene = scene;
   }
 
@@ -57,4 +83,10 @@ public class Model {
     Model.fileIsSaved = fileIsSaved;
   }
 
+  public static void setSettingsProvider(SettingsProvider settings) {
+    if (settings == null)
+      throw new IllegalArgumentException("settings can not be null");
+    Model.settings = settings;
+  }
+
 }

src/main/java/app/model/ProgrammingLanguage.java

@@ -1,37 +1,66 @@
 package app.model;
 
-import java.net.URL;
 import java.util.Map;
 import java.util.regex.Pattern;
 
+/**
+ * An interface describing functions required for a class to
+ * provide language specific details and functionality.
+ */
 public interface ProgrammingLanguage {
   /**
-   * The name of the programming language
+   * @return The name of the programming language
    */
   public String getName();
   
   /**
-   * The icon of the programming language
-   * @return The path of the icon
-   */
-  public URL getIcon();
-
-  /**
-   * The map containing the regex and corresponding style-classes to be used for syntax highlighting
+   * @return The map containing the regexes and corresponding style-classes to be used for syntax highlighting
    */
   public Map<Pattern,String> getPatternMap();
 
   /**
-   * The pattern containing all regexes for syntax highlighting
+   * @return A combined regex for syntax highlighting
    */
   public Pattern getPattern();
 
+  /**
+   * Comment out a line
+   * @param line The text of the line to comment out
+   * @return The commented line
+   */
   public String commentLine(String line);
+
+  /**
+   * Uncomment a line
+   * @param line The text of the line to uncomment
+   * @return The uncommented line
+   */
   public String unCommentLine(String line);
+
+  /**
+   * @param line The text of the line
+   * @return Whether or not a line is commented
+   */
   public boolean isCommentedLine(String line);
 
+  /**
+   * Comment out an area of text
+   * @param selection The text of the area to comment out
+   * @return The commented area
+   */
   public String commentSelection(String selection);
+
+  /**
+   * Uncomment an area of text
+   * @param selection The text of the area to uncomment
+   * @return The uncommented area
+   */
   public String unCommentSelection(String selection);
+
+  /**
+   * @param selection The content of the area
+   * @return Whether or not an area of text is commented
+   */
   public boolean isCommentedSelection(String selection);
 
 }

src/main/java/app/model/languages/Empty.java

@@ -1,6 +1,5 @@
 package app.model.languages;
 
-import java.net.URL;
 import java.util.regex.Pattern;
 import java.util.Map;
 
@@ -9,15 +8,11 @@ import app.model.ProgrammingLanguage;
 public class Empty implements ProgrammingLanguage {
   
   private String name = "?";
-  private URL iconPath = this.getClass().getResource("");
 
   public String getName() {
     return this.name;
   }
 
-  public URL getIcon() {
-    return this.iconPath;
-  }
 
   public Map<Pattern, String> getPatternMap() {
     return Map.of();

src/main/java/app/model/languages/Java.java

@@ -1,9 +1,10 @@
 package app.model.languages;
 
-import java.net.URL;
-import java.util.AbstractMap;
 import java.util.Arrays;
+import java.util.LinkedHashMap;
+import java.util.List;
 import java.util.Map;
+import java.util.AbstractMap.SimpleEntry;
 import java.util.Map.Entry;
 import java.util.regex.Pattern;
 import java.util.stream.Collectors;
@@ -14,7 +15,7 @@ import app.model.ProgrammingLanguage;
 public class Java implements ProgrammingLanguage {
 
   private String name = "Java";
-  private URL iconPath = this.getClass().getResource("");
+  private static Map<Pattern, String> pattern;
 
   private static final String[] keywords = new String[] {
     "abstract", "assert", "boolean", "break", "byte",
@@ -30,11 +31,12 @@ public class Java implements ProgrammingLanguage {
   };
 
   private static Entry<Pattern, String> e(String k, String v) {
-    return new AbstractMap.SimpleEntry<>(Pattern.compile(k), v);
+    return new SimpleEntry<>(Pattern.compile(k), v);
   }
 
-  private static final Map<Pattern, String> pattern = 
-    Map.ofEntries(
+
+  private static final List<Entry<Pattern, String>> patternList =
+    List.of(
       e("\"([^\"\\\\]|\\\\.)*\"",       "string"),
       e("\\bthis\\b",                   "this"),
       e("\\btrue\\b",                   "true"),
@@ -50,16 +52,23 @@ public class Java implements ProgrammingLanguage {
                                         "keyword"),
       e("(?://.*)|/\\*(?:\\n|.)*?\\*/", "comment")
     );
+  
+  public Java() {
+    this.initializePatternMap();
+  }
+
+  private void initializePatternMap() {
+    pattern = new LinkedHashMap<>();
+    patternList
+      .forEach(e -> pattern.put(e.getKey(), e.getValue()));
+  }
 
   public String getName() {
     return this.name;
   }
 
-  public URL getIcon() {
-    return this.iconPath;
-  }
-
   public Map<Pattern, String> getPatternMap() {
+
     return Java.pattern;
   }
 

src/main/java/app/model/languages/Markdown.java

@@ -1,8 +1,9 @@
 package app.model.languages;
 
-import java.net.URL;
 import java.util.AbstractMap;
 import java.util.Arrays;
+import java.util.LinkedHashMap;
+import java.util.List;
 import java.util.Map;
 import java.util.Map.Entry;
 import java.util.regex.Pattern;
@@ -13,14 +14,14 @@ import app.model.ProgrammingLanguage;
 public class Markdown implements ProgrammingLanguage {
 
   private String name = "Markdown";
-  private URL iconPath = this.getClass().getResource("");
+  private static Map<Pattern, String> pattern;
 
   private static Entry<Pattern, String> e(String k, String v) {
     return new AbstractMap.SimpleEntry<>(Pattern.compile(k), v);
   }
 
-  private static final Map<Pattern, String> pattern = 
-    Map.ofEntries(
+  private static final List<Entry<Pattern, String>> patternList = 
+    List.of(
       e("<!--(?:.|\n)*-->", "comment"),
       e("##### .*", "ssssheader"),
       e("#### .*", "sssheader"),
@@ -38,12 +39,19 @@ public class Markdown implements ProgrammingLanguage {
       e("\\[\\d+\\]: .*", "source")
     );
 
-  public String getName() {
-    return this.name;
+
+  public Markdown() {
+    this.initializePatternMap();
   }
 
-  public URL getIcon() {
-    return this.iconPath;
+  private void initializePatternMap() {
+    pattern = new LinkedHashMap<>();
+    patternList
+      .forEach(e -> pattern.put(e.getKey(), e.getValue()));
+  }
+
+  public String getName() {
+    return this.name;
   }
 
   public Map<Pattern, String> getPatternMap() {
@@ -64,7 +72,7 @@ public class Markdown implements ProgrammingLanguage {
   String cStart     = "<!-- ";
   String cEnd       = " -->";
   String cStartRegex = "<!-- ?";
-  String cEndRegex   = " ?-->\\s{0,}";
+  String cEndRegex   = " ?-->\\s{0,}$";
 
   public String commentLine(String line) {
     return  cStart + line + cEnd;

src/main/java/app/service/DialogBoxes.java

@@ -0,0 +1,84 @@
+package app.service;
+
+import java.io.File;
+
+import app.model.Model;
+import javafx.scene.control.Alert;
+import javafx.scene.control.Alert.AlertType;
+import javafx.stage.DirectoryChooser;
+import javafx.stage.FileChooser;
+import javafx.stage.Stage;
+
+/**
+ * Class containing static methods for different kinds of popup window interactions
+ * with the user.
+ */
+public class DialogBoxes {
+
+  private DialogBoxes() {}
+  private static FileChooser fc = new FileChooser();
+  private static DirectoryChooser dc = new DirectoryChooser();
+  private static Alert error = new Alert(AlertType.ERROR);
+
+  /**
+   * Shows a specified message to the user with an error icon.
+   * 
+   * @param errorMessage The message to show the user
+   */
+  public static void showErrorMessage(String errorMessage) {
+      error.setContentText(errorMessage);
+      error.showAndWait();
+  }
+
+  /**
+   * Shows an OS specific file chooser to choose a file on the disk
+   * 
+   * @param stage The JavaFX stage to connect to the dialog box. This is needed
+   *              for the window to be able to run on the JavaFX thread.
+   * 
+   * @return The file chosen through the dialog window
+   */
+  public static File showopenFileWithDialog(Stage stage) {
+    fc.setTitle("Open File");
+    File chosenFile = fc.showOpenDialog(stage);
+
+    return chosenFile; 
+  }
+
+  /**
+   * Shows an OS specific directory chooser to choose a directory on the disk
+   * 
+   * @param stage The JavaFX stage to connect to the dialog box. This is needed
+   *              for the window to be able to run on the JavaFX thread.
+   * 
+   * @return The file chosen through the dialog window
+   */
+  public static File showOpenDirectoryWithDialog(Stage stage) {
+    dc.setTitle("Open Project");
+    File dir = dc.showDialog(stage);
+
+    return dir;
+  }
+
+  /**
+   * Shows an OS specific file chooser to specifyy a new path on the disk
+   * 
+   * @param stage The JavaFX stage to connect to the dialog box. This is needed
+   *              for the window to be able to run on the JavaFX thread.
+   * 
+   * @return The filepath chosen through the dialog window
+   */
+  public static File showSaveFileWithDialog(Stage stage) {
+    FileChooser fc = new FileChooser();
+    fc.setTitle("Save as");
+
+    Model
+      .getProjectPath()
+      .ifPresent(path -> fc.setInitialDirectory(path.toFile()));
+
+    File chosenLocation = fc.showSaveDialog(stage);
+
+    return chosenLocation;
+  }
+  
+}

src/main/java/app/service/FileOperations.java

@@ -0,0 +1,128 @@
+package app.service;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.PrintWriter;
+import java.nio.file.Path;
+import java.util.NoSuchElementException;
+import java.util.Optional;
+import java.util.Scanner;
+
+import app.model.Model;
+import javafx.stage.Stage;
+
+/**
+ * A class containing operations and logic for choosing, reading and writing to files.
+ */
+public class FileOperations {
+
+  private FileOperations() {}
+
+  /**
+   * A function to get a file through a dialog
+   * 
+   * @param stage A JavaFX stage is required to show the dialog
+   * @return The chosen file
+   * @throws FileNotFoundException if the dialog was canceled
+   */
+  public static File openFileWithDialog(Stage stage) throws FileNotFoundException {
+    File chosenFile = DialogBoxes.showopenFileWithDialog(stage);
+
+    if (chosenFile == null)
+      throw new FileNotFoundException();
+
+    return chosenFile;
+
+  }
+
+  /**
+   * A function to get directory through a dialog
+   * 
+   * @param stage A JavaFX stage is required to show the dialog
+   * @return The chosen directory
+   * @throws FileNotFoundException if the dialog was canceled
+   */
+  public static File openDirectoryWithDialog(Stage stage) throws FileNotFoundException {
+    File dir = DialogBoxes.showOpenDirectoryWithDialog(stage);
+
+    if (dir == null)
+      throw new FileNotFoundException();
+
+    return dir;
+  }
+
+  /**
+   * Saves a file a the specified filepath with the specified content.
+   * Shows an error message to the user if the file was not found at the specified location.
+   * 
+   * @param filepath The path of the file to save the content into
+   * @param content The text content to be saved
+   * @return Whether the file was sucessfully saved
+   */
+  public static boolean saveFile(Path filepath, String content) {
+    try (PrintWriter writer = new PrintWriter(filepath.toFile())) {
+      writer.println(content);
+      return true;
+
+    } catch (FileNotFoundException ex) {
+      DialogBoxes.showErrorMessage("Could not save file at \n" + filepath.toString());
+      return false;
+    }
+  }
+
+  /**
+   * Lets the user choose a file to save the specified content into
+   * 
+   * @param stage A JavaFX stage is needed in order to show the file chooser
+   * @param content The content to be saved
+   * 
+   * @return Whether the file was sucessfully saved
+   */
+  public static boolean saveFileWithDialog(Stage stage, String content) {
+    File chosenLocation;
+
+    try {
+      chosenLocation = DialogBoxes.showSaveFileWithDialog(stage);
+    } catch (NoSuchElementException e) {
+      return false;
+    }
+
+    if (chosenLocation == null) return false;
+
+    if (saveFile(chosenLocation.toPath(), content)) {
+      Model.setActiveFilePath(Optional.of(chosenLocation.toPath()));
+      return true;
+    }
+
+    return false;
+  }
+
+  /**
+   * Tries to read the contents of a file in the specified filepath.
+   * If it fails, it shows the user a corresponding error message.
+   * 
+   * @param filePath The path of the file to be read
+   * 
+   * @return The text content of the file
+   */
+  public static String readFile(Path filePath) {
+
+    if (filePath == null)
+      return "";
+
+    String result = "";
+
+    try (Scanner sc = new Scanner(filePath.toFile())) {
+      while (sc.hasNextLine()) {
+        result += (sc.nextLine() + "\n");
+      }
+
+    } catch (FileNotFoundException e) {
+      DialogBoxes.showErrorMessage("This file could not be opened!");
+      System.err.println("[ERROR] File could not be opened: " + filePath.toString());
+      System.err.print(e);
+    }
+
+    return result;
+  }
+}

src/main/java/app/service/FiletreeOperations.java

@@ -0,0 +1,160 @@
+package app.service;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.io.InputStream;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.ArrayList;
+import java.util.List;
+
+import app.model.Model;
+import javafx.scene.control.CheckBoxTreeItem;
+import javafx.scene.control.TreeItem;
+import javafx.scene.image.Image;
+import javafx.scene.image.ImageView;
+
+/**
+ * A class containing operations for handling files withing a GUI filetree
+ */
+public class FiletreeOperations {
+
+  private static int iconSize = 20;
+
+  private FiletreeOperations() {}
+
+  /**
+   * Generate a filetree recursively, find icons for every file and append them to
+   * the root tree node.
+   * 
+   * @param file The root directory to be at the top of the tree
+   * @param parent The root tree item to append children to
+   */
+  public static void generateTree(File file, CheckBoxTreeItem<String> parent) {
+
+    Image folder = new Image(FiletreeOperations.class.getResourceAsStream("/graphics/folder.png"));
+
+    if (file.isDirectory()) {
+      ImageView icon = new ImageView(folder);
+      icon.setFitHeight(iconSize);
+      icon.setFitWidth(iconSize);
+
+      CheckBoxTreeItem<String> element = new CheckBoxTreeItem<>(file.getName(), icon);
+      parent.getChildren().add(element);
+
+      List<File> dirList = new ArrayList<>();
+      List<File> fileList = new ArrayList<>();
+
+      sortFiles(dirList, fileList, file);
+
+      for (File f : dirList) {
+        generateTree(f, element);
+      }
+
+    } else {
+
+      try {
+        ImageView icon = new ImageView(getIconForFile(file));
+        icon.setFitHeight(iconSize);
+        icon.setFitWidth(iconSize);
+
+        CheckBoxTreeItem<String> element = new CheckBoxTreeItem<>(file.getName(), icon);
+        parent.getChildren().add(element);
+
+      } catch (Exception e) {
+        System.err.println("[ERROR] Default file icon not found");
+        System.err.println(e);
+      }
+    }
+  }
+
+  /**
+   * A helping function to sort the files/directories in the fileTree so that it shows
+   * in the correct order.
+   * 
+   * @param dirList The list of directories to append all directories to
+   * @param fileList The list of files to append all the files to
+   * @param file The directory of which children to sort
+   */
+  private static void sortFiles(List<File> dirList, List<File> fileList, File file) {
+    for (File f : file.listFiles()) {
+      if (f.isDirectory())
+        dirList.add(f);
+      else
+        fileList.add(f);
+    }
+    dirList.addAll(fileList);
+
+  }
+
+  /**
+   * A function to get an icon for a file based on its mimetype.
+   * If no such icon is found, the function will return a default icon
+   * 
+   * @param file The file to probe for a mimetype
+   * @return An image containing the icon
+   * @throws IOException if the default icon was not found. This should not happen
+   */
+  private static Image getIconForFile(File file) throws IOException {
+    Image icon;
+
+    try {
+      String mimeType = Files.probeContentType(file.toPath());
+      if (mimeType == null) throw new IOException();
+
+      String iconPath = "/graphics/filetreeicons/" + mimeType.replace('/', '-') + ".png";
+      InputStream imageData = FiletreeOperations.class.getResourceAsStream(iconPath);
+      if (imageData == null) throw new IOException();
+
+      icon = new Image(imageData);
+
+    } catch (IOException e) {
+      System.err.println("[WARNING] Icon not found: " + file.getPath());
+
+      // String iconPath = "/graphics/filetreeicons/file.png";
+      String iconPath = "/graphics/filetreeicons/unknown.png";
+
+      InputStream imageData = FileOperations.class.getResourceAsStream(iconPath);
+      if (imageData == null) throw new IOException();
+
+      icon = new Image(imageData);
+    }
+      
+    return icon;
+  }
+
+  /**
+   * Determine the absolute path of a file within the filetree.
+   * @param item The treeitem that represents the file of which path is needed
+   * @return The absolute path of the file that the treeitem represents
+   * @throws FileNotFoundException if no path was found within the filetree such that the
+   *         item could be connected with the root tree item. This should not happen
+   */
+  public static Path getPathOfTreeItem(TreeItem<String> item) throws FileNotFoundException {
+    Path projectPath = 
+      Model
+        .getProjectPath()
+        .orElseThrow(() -> new IllegalStateException());
+
+    final String rootDirName =
+      projectPath
+        .getFileName()
+        .toString();
+
+    String path = "";
+    while (!rootDirName.equals(item.getValue())) {
+      path = File.separator + item.getValue() + path;
+      item = item.getParent();
+      if (item == null)
+        throw new FileNotFoundException();
+    }
+
+    path = projectPath.toString() + path;
+
+    Path pathToString = Paths.get(path);
+
+    return pathToString;
+  }  
+}

src/main/java/app/service/LanguageOperations.java

@@ -9,7 +9,13 @@ import org.fxmisc.richtext.model.StyleSpansBuilder;
 
 import app.model.ProgrammingLanguage;
 
-public class LanguageOperations {
+/**
+ * Common static operations that can be executed on any class
+ * that implements {@link app.model.ProgrammingLanguage ProgrammingLanguage}
+ */
+public final class LanguageOperations {
+
+  private LanguageOperations() {}
   
   /**
    * Use a matcher to find the styleclass of the next match

src/main/java/app/settings/SettingsProvider.java

@@ -0,0 +1,112 @@
+package app.settings;
+
+import java.io.File;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.Scanner;
+
+import com.google.common.eventbus.EventBus;
+import com.google.common.eventbus.Subscribe;
+
+import app.events.LanguageChangedEvent;
+import app.events.ThemeChangedEvent;
+import app.model.Model;
+
+/**
+ * A provider for permanent storage of the settings of the application.
+ */
+public class SettingsProvider implements SettingsProviderI {
+
+    private EventBus eventBus;
+
+    private String settingsPath =
+      (System.getProperty("os.name").startsWith("Windows"))
+      ? System.getProperty("user.home") + "\\AppData\\Roaming\\/BNNsettings.dat"
+      : System.getProperty("user.home") + System.getProperty("file.separator") + ".BNNsettings.dat";
+
+    private List<String> legalSettings = 
+       Arrays.asList("Java", "Markdown", "Monokai", "Solarized Light");
+    
+
+    /** Only for testing purposes */
+    protected void setSettingsPath(String settingsPath) {
+      this.settingsPath = settingsPath;
+    }
+
+
+    public SettingsProvider(EventBus eB) {
+        setEventBus(eB);
+        Model.setSettingsProvider(this);
+    }
+
+    public void setEventBus(EventBus eB) {
+        eventBus = eB;
+        eventBus.register(this);
+    }
+
+    @Override
+    public void loadSettings() {
+        List<String> settings = new ArrayList<>();
+        try (Scanner sc = new Scanner(new File(settingsPath))) {
+
+            while (sc.hasNextLine()) {
+                var nextLine = sc.nextLine().trim();
+                if (nextLine.isEmpty() || nextLine.startsWith("-")) {
+                    continue;
+                } else {
+                    settings.add(nextLine.substring(nextLine.indexOf("=") + 2));
+                }
+            }
+
+            if (legalSettings.containsAll(settings)) {
+                eventBus.post(new LanguageChangedEvent(settings.get(0)));
+                eventBus.post(new ThemeChangedEvent(settings.get(1)));
+            } else {
+                throw new IOException();
+            }
+
+        } catch (IOException e) {
+            System.err.println("[WARNING] Couldn't find settings file. Using defaults");
+            eventBus.post(new LanguageChangedEvent("Java"));
+            eventBus.post(new ThemeChangedEvent("Monokai"));
+        }
+
+    }
+
+    @Override
+    public void saveSettings() {
+        try (PrintWriter writer = new PrintWriter(new File(settingsPath))) {
+            writer.println("- Settings:");
+            writer.println("Programming Language = " + Model.getLanguage().getName());
+            writer.println("Theme = " + Model.getTheme());
+        } catch (IOException e) {
+            System.err.println("[ERROR] Couldn't write to settings file.");
+            System.err.println(e);
+        }
+
+    }
+
+    /**
+     * Update the settings whenever the theme gets changed
+     * 
+     * @param event
+     */
+    @Subscribe
+    private void handle(ThemeChangedEvent event) {
+        saveSettings();
+    }
+
+    /**
+     * Update the settings whenever the language gets changed
+     * 
+     * @param event
+     */
+    @Subscribe
+    private void handle(LanguageChangedEvent event) {
+        saveSettings();
+    }
+
+}

src/main/java/app/settings/SettingsProviderI.java

@@ -0,0 +1,15 @@
+package app.settings;
+
+public interface SettingsProviderI {
+
+  /**
+   * Load settings from disk, and fire events to update the program state
+   */
+  void loadSettings();
+
+  /**
+   * Save the state from {@link app.model.Model Model} to disk.
+   */
+  void saveSettings();
+
+}

src/main/resources/BNNsettings/settings.dat

@@ -0,0 +1,3 @@
+- Settings:
+ProgrammingLanguage = Java
+Theme = Solarized Light

src/main/resources/fxml/Main.fxml

@@ -10,7 +10,8 @@
   prefHeight="400"
   xmlns="http://javafx.com/javafx/8.0.65"
   xmlns:fx="http://javafx.com/fxml/1"
-  fx:controller="app.MainController">
+  fx:controller="app.MainController"
+  fx:id="root">
 
   <top>
     <!-- Menubar -->

src/main/resources/fxml/components/Menubar.fxml

@@ -18,14 +18,13 @@
   <menus>
     <Menu mnemonicParsing="false" text="File">
       <items>
-        <MenuItem mnemonicParsing="false" text="New File" accelerator="Shortcut+n"/>
-        <MenuItem mnemonicParsing="false" text="New Folder" accelerator="Shortcut+Shift+N"/>
+        <MenuItem mnemonicParsing="false" text="New File" accelerator="Shortcut+n" onAction="#handleNewFile"/>
         <SeparatorMenuItem/>
         <MenuItem mnemonicParsing="false" text="Open File" accelerator="Shortcut+o" onAction="#handleOpenFile"/>
         <MenuItem mnemonicParsing="false" text="Open Project" accelerator="Shortcut+Shift+O" onAction="#handleOpenProject"/>
         <SeparatorMenuItem/>
-        <MenuItem mnemonicParsing="false" text="Save" accelerator="Shortcut+s"/>
-        <MenuItem mnemonicParsing="false" text="Save as" accelerator="Shortcut+Shift+S"/>
+        <MenuItem mnemonicParsing="false" text="Save" accelerator="Shortcut+s" onAction="#handleSaveFile"/>
+        <MenuItem mnemonicParsing="false" text="Save as" accelerator="Shortcut+Shift+S" onAction="#handleSaveAsFile"/>
         <SeparatorMenuItem/>
 
         <fx:define>
@@ -34,7 +33,6 @@
 
         <Menu mnemonicParsing="false" text="Change programming language">
           <items>
-            <!-- TODO: Generate buttons based on classes -->
             <RadioMenuItem text="Java"
                            fx:id="toggleJava"
                            onAction="#handleLanguageChange"
@@ -56,12 +54,12 @@
 
         <Menu mnemonicParsing="false" text="Change color theme">
           <items>
-            <!-- TODO: Generate buttons based on classes -->
             <RadioMenuItem text="Monokai"
-                           selected="true"
+                           fx:id="toggleMonokai"
                            onAction="#handleThemeChange"
                            toggleGroup="$themeToggleGroup"/>
             <RadioMenuItem text="Solarized Light"
+                           fx:id="toggleSolarized_Light"
                            onAction="#handleThemeChange"
                            toggleGroup="$themeToggleGroup"/>
           </items>

src/main/resources/fxml/components/Modeline.fxml

@@ -11,6 +11,7 @@
   fx:controller="app.controllers.ModelineController"
   alignment="CENTER_LEFT">
   <Label text="Modeline :)"/>
+  <Label fx:id="filename" text="New file"/>
   <Region HBox.hgrow="ALWAYS"/>
   <Label fx:id="saveState" text="Saved!"/>
   <Label fx:id="columnrow" text="[y:x]"/>