Preparations for v1.1.1.0 release and corrected some JavaDoc warnings;

CITATION.cff

@@ -1,6 +1,6 @@
 cff-version: 1.2.0
 title: MORTAR
-version: 1.1.0.0
+version: 1.1.1.0
 message: "If you use this software, please cite it as below."
 type: software
 authors:
@@ -26,7 +26,7 @@ authors:
     given-names: "Achim"    
     orcid: "https://orcid.org/0000-0003-0722-4229"
 doi: "10.5281/zenodo.6984804"
-date-released: 2023-02-21
+date-released: 2023-06-27
 url: "https://github.com/FelixBaensch/MORTAR"
 license: GPL-3.0
 references:

README.md

@@ -50,12 +50,12 @@ Pre-compiled and executable MORTAR distributions can be found attached to the
 
 <p>
 <b>Windows:</b> A convenient Windows OS installer executable for MORTAR is available 
-(click <a href="https://github.com/FelixBaensch/MORTAR/releases/download/v1.1.0.0/MORTAR_v1.1.0.0_WINx64_installer.exe">here</a> to 
+(click <a href="https://github.com/FelixBaensch/MORTAR/releases/download/v1.1.1.0/MORTAR_v1.1.1.0_WINx64_installer.exe">here</a> to 
 automatically download the installer .exe of the latest version). Download the installer 
 executable, start, and follow the instructions to install MORTAR. Note that the installation includes a full 
 Java Runtime Environment (JRE). After installation, create a shortcut to an appropriate MORTAR start batch file on your 
 Windows desktop. E.g. for MORTAR to use up to 4 gigabyte of RAM, copy a shortcut to batch file "MORTAR.bat" which is 
-located in the MORTAR program folder (default "C:\Program Files\MORTAR\MORTARv1.1.0.0\bin" or the path specified at 
+located in the MORTAR program folder (default "C:\Program Files\MORTAR\MORTARv1.1.1.0\bin" or the path specified at 
 installation). To start MORTAR, double click the created shortcut. MORTAR can be uninstalled by the provided 
 Uninstall.exe executable in the MORTAR program folder or standard Windows functions.
 <br>
@@ -72,21 +72,21 @@ with your chosen initially allocated memory (-Xms) and maximum value (-Xmx) acco
 described below. As an alternative way, they should also work on Windows.
 </p>
 
-<p><b>Linux and macOS:</b> Every release has the executable Java ARchive (JAR) "MORTAR-fat-1.1.0.0.jar"
+<p><b>Linux and macOS:</b> Every release has the executable Java ARchive (JAR) "MORTAR-fat-1.1.1.0.jar"
 attached, which contains the packaged MORTAR code together with all dependencies 
-(click <a href="https://github.com/FelixBaensch/MORTAR/releases/download/v1.1.0.0/MORTAR-fat-1.1.0.0.jar">here</a> to 
+(click <a href="https://github.com/FelixBaensch/MORTAR/releases/download/v1.1.1.0/MORTAR-fat-1.1.1.0.jar">here</a> to 
 automatically download the JAR of the latest version). 
 To run MORTAR (with up to 4 GB of RAM available, e.g.), 
 execute the JAR from the command-line using</p>
 
-<p><code>java -jar -Xms512m -Xmx4g [path to]MORTAR-fat-1.1.0.0.jar</code></p>
+<p><code>java -jar -Xms512m -Xmx4g [path to]MORTAR-fat-1.1.1.0.jar</code></p>
 
 A JDK or JRE of version 17.0.4 or higher needs to be installed on your system and linked to the "java" command. 
 Otherwise, replace "java" with the path to the java command of your JDK or JRE.<br>
 
 <p>Please note that MORTAR only supports x64 (on all three platforms) and AArch64 (on macOS and Linux) architectures in general. 
-For the latter, a special "fat JAR" named "MORTAR-fat-aarch64-1.1.0.0.jar" is available from the distributions attached to the releases and must be used 
-(click <a href="https://github.com/FelixBaensch/MORTAR/releases/download/v1.1.0.0/MORTAR-fat-aarch64-1.1.0.0.jar">here</a> to 
+For the latter, a special "fat JAR" named "MORTAR-fat-aarch64-1.1.1.0.jar" is available from the distributions attached to the releases and must be used 
+(click <a href="https://github.com/FelixBaensch/MORTAR/releases/download/v1.1.1.0/MORTAR-fat-aarch64-1.1.1.0.jar">here</a> to 
 automatically download the AArch64 JAR of the latest version).</p>
 Also note that using the Windows Subsystem for Linux (WSL) is not recommended, since a lot of additional configurations 
 have to be made there to run Java GUI applications.
@@ -114,9 +114,9 @@ into it (i.e. sub-folders of "AdoptOpenJDK\jdk-17.0.4_8_jre\" need to be "bin",
 * Chemistry Development Kit (CDK) version 2.8
     * [Chemistry Development Kit on GitHub](https://cdk.github.io/)
     * License: GNU Lesser General Public License 2.1
-* JUnit version 4.13
-    * [JUnit 4](https://junit.org/junit4/)
-    * License: Eclipse Public License 1.0
+* JUnit version 5.9.3
+    * [JUnit 5](https://junit.org/junit5/)
+    * License: Eclipse Public License 2.0
 * LibrePDF OpenPDF version 1.3.26
   * [OpenPDF GitHub repository](https://github.com/LibrePDF/OpenPDF)
   * License: GNU Lesser General Public License 2.1

build.gradle

@@ -6,7 +6,7 @@ plugins {
 }
 
 group 'de.unijena.cheminf'
-version '1.1.0.0'
+version '1.1.1.0'
 
 sourceCompatibility = 1.17
 

src/main/java/de/unijena/cheminf/mortar/controller/IViewToolController.java

@@ -42,6 +42,8 @@ public interface IViewToolController {
     public List<Property> settingsProperties();
     /**
      * Returns a view tool name that can be displayed in the GUI, e.g. in the views menu.
+     *
+     * @return language-specific name for the view tool
      */
     public String getViewToolNameForDisplay();
     /**
@@ -51,6 +53,9 @@ public interface IViewToolController {
     /**
      * Specifies whether the view tool can be used on the given tab type, e.g. the histogram view cannot be used
      * on the molecules tab.
+     *
+     * @param aTabNameEnumConstant enum constant denoting the currently active tab in the GUI
+     * @return true if the view tool can be opened when this specific tab is active
      */
     public boolean canBeUsedOnTab(TabNames aTabNameEnumConstant);
 

src/main/java/de/unijena/cheminf/mortar/controller/OverviewViewController.java

@@ -368,7 +368,7 @@ public boolean canBeUsedOnTab(TabNames aTabNameEnumConstant) {
      * @param aTabName String containing the name of the tab that's content is to be shown in the overview view
      * @param aMoleculeDataModelList List of MoleculeDataModel instances
      * @throws NullPointerException if one of the parameters is null; aTabName is allowed to be null if the value of aDataSource is
-     *      * PARENT_MOLECULES_SAMPLE or ITEM_WITH_FRAGMENTS_SAMPLE
+     *         PARENT_MOLECULES_SAMPLE or ITEM_WITH_FRAGMENTS_SAMPLE
      */
     public void initializeAndShowOverviewView(
             Stage aMainStage,

src/main/java/de/unijena/cheminf/mortar/controller/ViewToolsManager.java

@@ -112,18 +112,31 @@ public ViewToolsManager() {
     //<editor-fold desc="public methods" defaultstate="collapsed">
     /**
      * Returns the array containing the instances of available view tools.
+     *
+     * @return array with one instance per available view tool
      */
     public IViewToolController[] getViewToolControllers() {
         return this.viewToolsArray;
     }
     /**
      * See {@link HistogramViewController#openHistogramView(Stage, List)}.
+     *
+     * @param aMainStage Stage of the MainView
+     * @param aFragmentDataModelList ObservableList that holds FragmentDataModel objects for visualisation in histogram
+     * @throws NullPointerException if any param is null
      */
     public void openHistogramView(Stage aMainStage, List< FragmentDataModel > aFragmentDataModelList) throws NullPointerException {
         this.histogramViewController.openHistogramView(aMainStage, aFragmentDataModelList);
     }
     /**
      * See {@link OverviewViewController#initializeAndShowOverviewView(Stage, OverviewViewController.DataSources, String, List)}.
+     *
+     * @param aMainStage Stage that is to be the owner of the overview view's stage
+     * @param aDataSource Source of the data to be shown in the overview view
+     * @param aTabName String containing the name of the tab that's content is to be shown in the overview view
+     * @param aMoleculeDataModelList List of MoleculeDataModel instances
+     * @throws NullPointerException if one of the parameters is null; aTabName is allowed to be null if the value of aDataSource is
+     *         PARENT_MOLECULES_SAMPLE or ITEM_WITH_FRAGMENTS_SAMPLE
      */
     public void openOverviewView(
             Stage aMainStage,
@@ -135,6 +148,8 @@ public void openOverviewView(
     }
     /**
      * See {@link OverviewViewController#getCachedIndexOfStructureInMoleculeDataModelList()}.
+     *
+     * @return Integer value of the cached index of structure or -1
      */
     public int getCachedIndexOfStructureInMoleculeDataModelList() {
         return this.overviewViewController.getCachedIndexOfStructureInMoleculeDataModelList();

src/main/java/de/unijena/cheminf/mortar/model/util/BasicDefinitions.java

@@ -144,7 +144,7 @@ public final class BasicDefinitions {
     /**
      * Version of application
      */
-    public static final String MORTAR_VERSION = "1.1.0.0";
+    public static final String MORTAR_VERSION = "1.1.1.0";
     //</editor-fold>
     //
     //<editor-fold desc="GitHub repository url">

src/main/java/de/unijena/cheminf/mortar/model/util/ChemUtil.java

@@ -95,11 +95,11 @@ public static String createUniqueSmiles(IAtomContainer anAtomContainer) {
      * atom types are assigned to it (the former through kekulization) if required. Aromaticity flags are set only if
      * there is aromaticity information present in the SMILES code, no aromaticity perception is performed here.
      *
-     * @return IAtomContainer atom container of the molecule
      * @param aSmilesCode SMILES representation
      * @param shouldBeKekulized whether explicit bond orders should be assigned or "aromatic bond" can be used if present;
      *                          does not affect aromaticity flags
      * @param shouldAtomTypesBePerceived whether atom types should be perceived and configured
+     * @return IAtomContainer atom container of the molecule
      * @throws InvalidSmilesException if the given SMILES is invalid
      * @throws CDKException if kekulization or atom type matching fails
      */
@@ -125,6 +125,11 @@ public static IAtomContainer parseSmilesToAtomContainer(String aSmilesCode, bool
     /**
      * Call to {@link #parseSmilesToAtomContainer(String, boolean, boolean)} with kekulization and atom type perception
      * set to true.
+     *
+     * @param aSmilesCode SMILES representation
+     * @return IAtomContainer atom container of the molecule
+     * @throws InvalidSmilesException if the given SMILES is invalid
+     * @throws CDKException if kekulization or atom type matching fails
      */
     public static IAtomContainer parseSmilesToAtomContainer(String aSmilesCode) throws InvalidSmilesException, CDKException {
         return ChemUtil.parseSmilesToAtomContainer(aSmilesCode, true, true);