Adjustments according to comments, shortened doc on convenience metho…

…d, declared magic numbers in local variables;

src/main/java/de/unijena/cheminf/mortar/model/fragmentation/algorithm/ErtlFunctionalGroupsFinderFragmenter.java

@@ -340,7 +340,10 @@ public static enum CycleFinderOption {
      * Constructor, all settings are initialised with their default values as declared in the respective public constants.
      */
     public ErtlFunctionalGroupsFinderFragmenter() {
-        int tmpInitialCapacityForSettingNameTooltipTextMap = CollectionUtil.calculateInitialHashCollectionCapacity(6, BasicDefinitions.DEFAULT_HASH_COLLECTION_LOAD_FACTOR);
+        int tmpNumberOfSettingsForTooltipMapSize= 6;
+        int tmpInitialCapacityForSettingNameTooltipTextMap = CollectionUtil.calculateInitialHashCollectionCapacity(
+                tmpNumberOfSettingsForTooltipMapSize,
+                BasicDefinitions.DEFAULT_HASH_COLLECTION_LOAD_FACTOR);
         this.settingNameTooltipTextMap = new HashMap(tmpInitialCapacityForSettingNameTooltipTextMap, BasicDefinitions.DEFAULT_HASH_COLLECTION_LOAD_FACTOR);
         this.fragmentSaturationSetting = new SimpleEnumConstantNameProperty(this, "Fragment saturation setting",
                 IMoleculeFragmenter.FRAGMENT_SATURATION_OPTION_DEFAULT.name(), IMoleculeFragmenter.FragmentSaturationOption.class) {

src/main/java/de/unijena/cheminf/mortar/model/fragmentation/algorithm/ScaffoldGeneratorFragmenter.java

@@ -342,7 +342,10 @@ public static enum FragmentationTypeOption {
      */
     public ScaffoldGeneratorFragmenter() {
         this.scaffoldGeneratorInstance = new ScaffoldGenerator();
-        int tmpInitialCapacityForSettingNameTooltipTextMap = CollectionUtil.calculateInitialHashCollectionCapacity(16, BasicDefinitions.DEFAULT_HASH_COLLECTION_LOAD_FACTOR);
+        int tmpNumberOfSettingsForTooltipMapSize= 10;
+        int tmpInitialCapacityForSettingNameTooltipTextMap = CollectionUtil.calculateInitialHashCollectionCapacity(
+                tmpNumberOfSettingsForTooltipMapSize,
+                BasicDefinitions.DEFAULT_HASH_COLLECTION_LOAD_FACTOR);
         this.settingNameTooltipTextMap = new HashMap(tmpInitialCapacityForSettingNameTooltipTextMap, BasicDefinitions.DEFAULT_HASH_COLLECTION_LOAD_FACTOR);
         this.fragmentSaturationSetting = new SimpleEnumConstantNameProperty(this, "Fragment saturation setting",
                 IMoleculeFragmenter.FRAGMENT_SATURATION_OPTION_DEFAULT.name(), IMoleculeFragmenter.FragmentSaturationOption.class) {

src/main/java/de/unijena/cheminf/mortar/model/fragmentation/algorithm/SugarRemovalUtilityFragmenter.java

@@ -236,8 +236,11 @@ public static enum SRUFragmenterReturnedFragmentsOption {
      */
     public SugarRemovalUtilityFragmenter() {
         this.sugarRUInstance = new SugarRemovalUtility(SilentChemObjectBuilder.getInstance());
-        this.settings = new ArrayList<>(15);
-        int tmpInitialCapacityForSettingNameTooltipTextMap = CollectionUtil.calculateInitialHashCollectionCapacity(20, BasicDefinitions.DEFAULT_HASH_COLLECTION_LOAD_FACTOR);
+        int tmpNumberOfSettings = 15;
+        this.settings = new ArrayList<>(tmpNumberOfSettings);
+        int tmpInitialCapacityForSettingNameTooltipTextMap = CollectionUtil.calculateInitialHashCollectionCapacity(
+                tmpNumberOfSettings,
+                BasicDefinitions.DEFAULT_HASH_COLLECTION_LOAD_FACTOR);
         this.settingNameTooltipTextMap = new HashMap<>(tmpInitialCapacityForSettingNameTooltipTextMap, BasicDefinitions.DEFAULT_HASH_COLLECTION_LOAD_FACTOR);
         this.returnedFragmentsSetting = new SimpleEnumConstantNameProperty(this, "Returned fragments setting",
                 SugarRemovalUtilityFragmenter.RETURNED_FRAGMENTS_OPTION_DEFAULT.name(), SugarRemovalUtilityFragmenter.SRUFragmenterReturnedFragmentsOption.class) {

src/main/java/de/unijena/cheminf/mortar/model/settings/SettingsContainer.java

@@ -610,7 +610,10 @@ public void reloadGlobalSettings() {
      * to the list of settings for display to the user.
      */
     private void initialiseSettings() {
-        int tmpInitialCapacityForSettingNameTooltipTextMap = CollectionUtil.calculateInitialHashCollectionCapacity(10, BasicDefinitions.DEFAULT_HASH_COLLECTION_LOAD_FACTOR);
+        int tmpNumberOfSettings = 8;
+        int tmpInitialCapacityForSettingNameTooltipTextMap = CollectionUtil.calculateInitialHashCollectionCapacity(
+                tmpNumberOfSettings,
+                BasicDefinitions.DEFAULT_HASH_COLLECTION_LOAD_FACTOR);
         this.settingNameTooltipTextMap = new HashMap<String, String>(tmpInitialCapacityForSettingNameTooltipTextMap, BasicDefinitions.DEFAULT_HASH_COLLECTION_LOAD_FACTOR);
         this.rowsPerPageSetting = new SimpleIntegerProperty(this,
                 "Rows per page setting",

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

@@ -112,14 +112,14 @@ public static void sortGivenFragmentListByPropertyAndSortType(List<MoleculeDataM
     //
     /**
      * Calculates a suitable initial size for instantiating a new HashMap or HashSet instance based on the number of elements
-     * supposed to be stored in it and the load factor that determines the rehash threshold.
+     * supposed to be stored in it and the load factor that determines the resize threshold.
      * Calculation: initCap = (int) aNumberOfElement * (1/aLoadFactor) + 2
-     * <br>The initial capacity multiplied with the load factor (= rehash threshold) must be higher than the number of
+     * <br>The initial capacity multiplied with the load factor (= resize threshold) must be higher than the number of
      * elements.
      *
      * @param aNumberOfElements number of elements supposed to be stored in the new HashMap or HashSet instance
      * @param aLoadFactor load factor that is specified for the new HashMap or HashSet instance
-     * @return a suitable initial size for the new HashMap or HashSet instance that leads to a rehash threshold that is slightly
+     * @return a suitable initial size for the new HashMap or HashSet instance that leads to a resize threshold that is slightly
      * higher than the number of elements
      * @throws IllegalArgumentException if the number of elements or the load factor is negative or equal to zero
      * or if the load factor is greater than 1.0
@@ -137,14 +137,12 @@ public static int calculateInitialHashCollectionCapacity(int aNumberOfElements,
     }
     //
     /**
-     * Calculates a suitable initial size for instantiating a new HashMap or HashSet instance based on the number of elements
-     * supposed to be stored in it and the default load factor (0.75) that determines the rehash threshold.
-     * Calculation: initCap = (int) aNumberOfElement * (1/0.75) + 2
-     * <br>The initial capacity multiplied with the load factor (= rehash threshold) must be higher than the number of
-     * elements.
+     * Calculates a suitable initial size for instantiating a new HashMap or HashSet instance with the default load factor.
+     * <br>For more details, see {@link #calculateInitialHashCollectionCapacity(int, float) calculateInitialHashCollectionCapacity(int, float)}.
+     *
      *
      * @param aNumberOfElements number of elements supposed to be stored in the new HashMap or HashSet instance
-     * @return a suitable initial size for the new HashMap or HashSet instance that leads to a rehash threshold that is slightly
+     * @return a suitable initial size for the new HashMap or HashSet instance that leads to a resize threshold that is slightly
      * higher than the number of elements
      * @throws IllegalArgumentException if the number of elements is negative or equal to zero
      */