Rework of HashMap initialisations

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

@@ -24,6 +24,7 @@
 import de.unijena.cheminf.mortar.gui.views.SettingsView;
 import de.unijena.cheminf.mortar.message.Message;
 import de.unijena.cheminf.mortar.model.fragmentation.algorithm.IMoleculeFragmenter;
+import de.unijena.cheminf.mortar.model.util.CollectionUtil;
 import javafx.beans.property.Property;
 import javafx.scene.Scene;
 import javafx.scene.control.Tab;
@@ -85,7 +86,7 @@ public class FragmentationSettingsViewController {
      */
     public FragmentationSettingsViewController(Stage aStage, IMoleculeFragmenter[] anArrayOfFragmenters, String aSelectedFragmenterAlgorithmName){
         this.mainStage = aStage;
-        this.recentProperties = new HashMap<>(anArrayOfFragmenters.length);
+        this.recentProperties = new HashMap<>(CollectionUtil.calculateInitialHashCollectionCapacity(anArrayOfFragmenters.length));
         this.fragmenters = anArrayOfFragmenters;
         this.selectedFragmenterName = aSelectedFragmenterAlgorithmName;
         this.openFragmentationSettingsView();
@@ -111,7 +112,7 @@ private void openFragmentationSettingsView(){
         //
         this.addListener();
         for (IMoleculeFragmenter tmpFragmenter : this.fragmenters) {
-            HashMap<String, Object> tmpRecentProperties = new HashMap<>(tmpFragmenter.settingsProperties().size());
+            HashMap<String, Object> tmpRecentProperties = new HashMap<>(CollectionUtil.calculateInitialHashCollectionCapacity(tmpFragmenter.settingsProperties().size()));
             this.recentProperties.put(tmpFragmenter.getFragmentationAlgorithmName(), tmpRecentProperties);
             Tab tmpTab = this.settingsView.addTab(this.fragmentationSettingsViewStage,
                     tmpFragmenter.getFragmentationAlgorithmName(), tmpFragmenter.settingsProperties(),

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

@@ -27,7 +27,7 @@
 import de.unijena.cheminf.mortar.model.data.FragmentDataModel;
 import de.unijena.cheminf.mortar.model.data.MoleculeDataModel;
 import de.unijena.cheminf.mortar.model.depict.DepictionUtil;
-import de.unijena.cheminf.mortar.model.util.ListUtil;
+import de.unijena.cheminf.mortar.model.util.CollectionUtil;
 
 import javafx.beans.binding.Bindings;
 import javafx.beans.value.ObservableValue;
@@ -269,7 +269,7 @@ private BarChart createHistogram(int aFragmentNumber, HistogramView aHistogramVi
         ArrayList<String> tmpFullSmilesLength = new ArrayList<>();
         String tmpSelectedData = (String) aHistogramView.getChooseDataComoBox().getValue();
         if (tmpSelectedData.equals(Message.get("HistogramView.chooseDataComboBoxFragmentFrequency.text"))) {
-            ListUtil.sortGivenFragmentListByPropertyAndSortType(this.copyList, "absoluteFrequency", "ASCENDING");
+            CollectionUtil.sortGivenFragmentListByPropertyAndSortType(this.copyList, "absoluteFrequency", "ASCENDING");
             for (MoleculeDataModel tmpMoleculeData : this.copyList) {
                 tmpFragmentData = (FragmentDataModel) tmpMoleculeData;
                 if (tmpFragmentData.getUniqueSmiles().length() > aSmilesLength) {
@@ -284,7 +284,7 @@ private BarChart createHistogram(int aFragmentNumber, HistogramView aHistogramVi
                 tmpFrequencyList.add(tmpFragmentData.getAbsoluteFrequency());
             }
         } else {
-            ListUtil.sortGivenFragmentListByPropertyAndSortType(this.copyList, "moleculeFrequency", "ASCENDING");
+            CollectionUtil.sortGivenFragmentListByPropertyAndSortType(this.copyList, "moleculeFrequency", "ASCENDING");
             for (MoleculeDataModel tmpMoleculeData : this.copyList) {
                 tmpFragmentData = (FragmentDataModel) tmpMoleculeData;
                 if (tmpFragmentData.getUniqueSmiles().length() > aSmilesLength) {

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

@@ -40,6 +40,7 @@
 import de.unijena.cheminf.mortar.model.settings.SettingsContainer;
 import de.unijena.cheminf.mortar.model.util.BasicDefinitions;
 import de.unijena.cheminf.mortar.model.util.ChemUtil;
+import de.unijena.cheminf.mortar.model.util.CollectionUtil;
 import de.unijena.cheminf.mortar.model.util.FileUtil;
 import de.unijena.cheminf.mortar.model.util.LogUtil;
 import javafx.application.Platform;
@@ -239,7 +240,7 @@ public MainViewController(Stage aStage, MainView aMainView, String anAppDir) {
         //</editor-fold>
         this.isImportRunningProperty = new SimpleBooleanProperty(false);
         this.isExportRunningProperty = new SimpleBooleanProperty(false);
-        this.mapOfFragmentDataModelLists = new HashMap<>(5);
+        this.mapOfFragmentDataModelLists = new HashMap<>(CollectionUtil.calculateInitialHashCollectionCapacity(5));
         this.threadList = new CopyOnWriteArrayList();
         this.addListener();
         this.addFragmentationAlgorithmCheckMenuItems();

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

@@ -24,6 +24,7 @@
 import de.unijena.cheminf.mortar.gui.views.SettingsView;
 import de.unijena.cheminf.mortar.message.Message;
 import de.unijena.cheminf.mortar.model.settings.SettingsContainer;
+import de.unijena.cheminf.mortar.model.util.CollectionUtil;
 import javafx.application.Platform;
 import javafx.beans.property.Property;
 import javafx.scene.Scene;
@@ -86,7 +87,7 @@ public SettingsViewController(Stage aStage, SettingsContainer aSettingsContainer
         this.mainStage = aStage;
         this.settingsContainer = aSettingsContainer;
         this.recentSettingsContainer = aSettingsContainer;
-        this.recentProperties = new HashMap<>(this.settingsContainer.settingsProperties().size());
+        this.recentProperties = new HashMap<>(CollectionUtil.calculateInitialHashCollectionCapacity(this.settingsContainer.settingsProperties().size()));
         this.showSettingsView();
     }
     //

src/main/java/de/unijena/cheminf/mortar/gui/util/GuiUtil.java

@@ -28,7 +28,7 @@
 import de.unijena.cheminf.mortar.model.data.MoleculeDataModel;
 import de.unijena.cheminf.mortar.model.depict.DepictionUtil;
 import de.unijena.cheminf.mortar.model.settings.SettingsContainer;
-import de.unijena.cheminf.mortar.model.util.ListUtil;
+import de.unijena.cheminf.mortar.model.util.CollectionUtil;
 import javafx.scene.control.Alert;
 import javafx.scene.control.Button;
 import javafx.scene.control.ButtonType;
@@ -212,7 +212,7 @@ public static void sortTableViewGlobally(SortEvent<TableView> anEvent, Paginatio
             return;
         String tmpSortProp = ((PropertyValueFactory)((TableColumn) anEvent.getSource().getSortOrder().get(0)).cellValueFactoryProperty().getValue()).getProperty().toString();
         TableColumn.SortType tmpSortType = ((TableColumn) anEvent.getSource().getSortOrder().get(0)).getSortType();
-        ListUtil.sortGivenFragmentListByPropertyAndSortType(((IDataTableView)anEvent.getSource()).getItemsList(), tmpSortProp, tmpSortType.toString());
+        CollectionUtil.sortGivenFragmentListByPropertyAndSortType(((IDataTableView)anEvent.getSource()).getItemsList(), tmpSortProp, tmpSortType.toString());
         int fromIndex = tmpPagination.getCurrentPageIndex() * tmpRowsPerPage;
         int toIndex = Math.min(fromIndex + tmpRowsPerPage, ((IDataTableView)anEvent.getSource()).getItemsList().size());
         anEvent.getSource().getItems().clear();

src/main/java/de/unijena/cheminf/mortar/model/fragmentation/FragmentationService.java

@@ -31,6 +31,7 @@
 import de.unijena.cheminf.mortar.model.settings.SettingsContainer;
 import de.unijena.cheminf.mortar.model.util.BasicDefinitions;
 import de.unijena.cheminf.mortar.model.util.ChemUtil;
+import de.unijena.cheminf.mortar.model.util.CollectionUtil;
 import de.unijena.cheminf.mortar.model.util.FileUtil;
 import de.unijena.cheminf.mortar.model.util.SimpleEnumConstantNameProperty;
 import de.unijena.cheminf.mortar.preference.BooleanPreference;
@@ -1063,23 +1064,26 @@ private void updatePropertiesFromPreferences(List<Property> aPropertiesList, Pre
      * anything does not meet the requirements.
      */
     private void checkFragmenters() throws Exception {
-        HashSet<String> tmpAlgorithmNames = new HashSet<>(this.fragmenters.length + 6, 1.0f);
+        int tmpAlgorithmNamesSetInitCapacity = CollectionUtil.calculateInitialHashCollectionCapacity(this.fragmenters.length,
+                BasicDefinitions.DEFAULT_HASH_COLLECTION_LOAD_FACTOR);
+        HashSet<String> tmpAlgorithmNamesSet = new HashSet<>(tmpAlgorithmNamesSetInitCapacity, BasicDefinitions.DEFAULT_HASH_COLLECTION_LOAD_FACTOR);
         for (IMoleculeFragmenter tmpFragmenter : this.fragmenters) {
             //algorithm name should be singleton and must be persistable
             String tmpAlgName = tmpFragmenter.getFragmentationAlgorithmName();
             if (!PreferenceUtil.isValidName(tmpAlgName) || !SingleTermPreference.isValidContent(tmpAlgName)) {
                 throw new Exception("Algorithm name " + tmpAlgName + " is invalid.");
             }
-            if (tmpAlgorithmNames.contains(tmpAlgName)) {
+            if (tmpAlgorithmNamesSet.contains(tmpAlgName)) {
                 throw new Exception("Algorithm name " + tmpAlgName + " is used multiple times.");
             } else {
-                tmpAlgorithmNames.add(tmpAlgName);
+                tmpAlgorithmNamesSet.add(tmpAlgName);
             }
             //setting names must be singletons within the respective class
             //setting names and values must adhere to the preference input restrictions
             //setting values are only tested for their current state, not the entire possible input space! It is tested again at persistence
             List<Property> tmpSettingsList = tmpFragmenter.settingsProperties();
-            HashSet<String> tmpSettingNames = new HashSet<>(tmpSettingsList.size() + 6, 1.0f);
+            int tmpSettingNamesSetInitCapacity = CollectionUtil.calculateInitialHashCollectionCapacity(tmpSettingsList.size(), BasicDefinitions.DEFAULT_HASH_COLLECTION_LOAD_FACTOR);
+            HashSet<String> tmpSettingNames = new HashSet<>(tmpSettingNamesSetInitCapacity, BasicDefinitions.DEFAULT_HASH_COLLECTION_LOAD_FACTOR);
             for (Property tmpSetting : tmpSettingsList) {
                 if (!PreferenceUtil.isValidName(tmpSetting.getName())) {
                     throw new Exception("Setting " + tmpSetting.getName() + " has an invalid name.");

src/main/java/de/unijena/cheminf/mortar/model/fragmentation/FragmentationTask.java

@@ -24,6 +24,7 @@
 import de.unijena.cheminf.mortar.model.data.MoleculeDataModel;
 import de.unijena.cheminf.mortar.model.fragmentation.algorithm.IMoleculeFragmenter;
 import de.unijena.cheminf.mortar.model.util.ChemUtil;
+import de.unijena.cheminf.mortar.model.util.CollectionUtil;
 import org.openscience.cdk.exception.CDKException;
 import org.openscience.cdk.interfaces.IAtomContainer;
 
@@ -134,7 +135,7 @@ public Integer call() throws Exception{
                     continue;
                 }
                 List<FragmentDataModel> tmpFragmentsOfMolList = new ArrayList<>(tmpFragmentsList.size());
-                HashMap<String, Integer> tmpFragmentFrequenciesOfMoleculeMap = new HashMap<>(tmpFragmentsList.size());
+                HashMap<String, Integer> tmpFragmentFrequenciesOfMoleculeMap = new HashMap<>(CollectionUtil.calculateInitialHashCollectionCapacity(tmpFragmentsList.size()));
                 for(IAtomContainer tmpFragment : tmpFragmentsList){
                     String tmpSmiles = ChemUtil.createUniqueSmiles(tmpFragment);
                     if (tmpSmiles == null) {

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

@@ -28,7 +28,9 @@
 import de.unijena.cheminf.mortar.gui.util.GuiUtil;
 import de.unijena.cheminf.mortar.message.Message;
 import de.unijena.cheminf.mortar.model.io.Importer;
+import de.unijena.cheminf.mortar.model.util.BasicDefinitions;
 import de.unijena.cheminf.mortar.model.util.ChemUtil;
+import de.unijena.cheminf.mortar.model.util.CollectionUtil;
 import de.unijena.cheminf.mortar.model.util.SimpleEnumConstantNameProperty;
 import javafx.beans.property.Property;
 import javafx.beans.property.SimpleBooleanProperty;
@@ -338,7 +340,8 @@ public static enum CycleFinderOption {
      * Constructor, all settings are initialised with their default values as declared in the respective public constants.
      */
     public ErtlFunctionalGroupsFinderFragmenter() {
-        this.settingNameTooltipTextMap = new HashMap(10, 0.9f);
+        int tmpInitialCapacityForSettingNameTooltipTextMap = CollectionUtil.calculateInitialHashCollectionCapacity(6, 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) {
             @Override
@@ -805,7 +808,8 @@ public List<IAtomContainer> fragmentMolecule(IAtomContainer aMolecule)
             this.logger.log(Level.WARNING, anException.toString(), anException);
             throw new IllegalArgumentException("Unexpected error at aromaticity detection: " + anException.toString());
         }
-        HashMap<Integer, IAtom> tmpIdToAtomMap = new HashMap<>(tmpMoleculeClone.getAtomCount() + 1, 1);
+        int tmpInitialCapacityForIdToAtomMap = CollectionUtil.calculateInitialHashCollectionCapacity(tmpMoleculeClone.getAtomCount(), BasicDefinitions.DEFAULT_HASH_COLLECTION_LOAD_FACTOR);
+        HashMap<Integer, IAtom> tmpIdToAtomMap = new HashMap<>(tmpInitialCapacityForIdToAtomMap, BasicDefinitions.DEFAULT_HASH_COLLECTION_LOAD_FACTOR);
         for (int i = 0; i < tmpMoleculeClone.getAtomCount(); i++) {
             IAtom tmpAtom = tmpMoleculeClone.getAtom(i);
             tmpAtom.setProperty(ErtlFunctionalGroupsFinderFragmenter.INTERNAL_INDEX_PROPERTY_KEY, i);

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

@@ -22,6 +22,8 @@
 
 import de.unijena.cheminf.mortar.gui.util.GuiUtil;
 import de.unijena.cheminf.mortar.message.Message;
+import de.unijena.cheminf.mortar.model.util.BasicDefinitions;
+import de.unijena.cheminf.mortar.model.util.CollectionUtil;
 import de.unijena.cheminf.mortar.model.util.SimpleEnumConstantNameProperty;
 import de.unijena.cheminf.scaffoldGenerator.ScaffoldGenerator;
 import javafx.beans.property.Property;
@@ -340,7 +342,8 @@ public static enum FragmentationTypeOption {
      */
     public ScaffoldGeneratorFragmenter() {
         this.scaffoldGeneratorInstance = new ScaffoldGenerator();
-        this.settingNameTooltipTextMap = new HashMap(16, 0.9f);
+        int tmpInitialCapacityForSettingNameTooltipTextMap = CollectionUtil.calculateInitialHashCollectionCapacity(16, 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) {
             @Override

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

@@ -28,7 +28,9 @@
 import de.unijena.cheminf.deglycosylation.SugarRemovalUtility;
 import de.unijena.cheminf.mortar.gui.util.GuiUtil;
 import de.unijena.cheminf.mortar.message.Message;
+import de.unijena.cheminf.mortar.model.util.BasicDefinitions;
 import de.unijena.cheminf.mortar.model.util.ChemUtil;
+import de.unijena.cheminf.mortar.model.util.CollectionUtil;
 import de.unijena.cheminf.mortar.model.util.SimpleEnumConstantNameProperty;
 import javafx.beans.property.Property;
 import javafx.beans.property.SimpleBooleanProperty;
@@ -235,7 +237,8 @@ public static enum SRUFragmenterReturnedFragmentsOption {
     public SugarRemovalUtilityFragmenter() {
         this.sugarRUInstance = new SugarRemovalUtility(SilentChemObjectBuilder.getInstance());
         this.settings = new ArrayList<>(15);
-        this.settingNameTooltipTextMap = new HashMap<>(20, 0.9f);
+        int tmpInitialCapacityForSettingNameTooltipTextMap = CollectionUtil.calculateInitialHashCollectionCapacity(20, 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) {
             @Override

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

@@ -28,6 +28,7 @@
 import de.unijena.cheminf.mortar.gui.util.GuiUtil;
 import de.unijena.cheminf.mortar.message.Message;
 import de.unijena.cheminf.mortar.model.util.BasicDefinitions;
+import de.unijena.cheminf.mortar.model.util.CollectionUtil;
 import de.unijena.cheminf.mortar.model.util.FileUtil;
 import de.unijena.cheminf.mortar.model.util.SimpleEnumConstantNameProperty;
 import de.unijena.cheminf.mortar.preference.BooleanPreference;
@@ -609,7 +610,8 @@ public void reloadGlobalSettings() {
      * to the list of settings for display to the user.
      */
     private void initialiseSettings() {
-        this.settingNameTooltipTextMap = new HashMap<String, String>(10, 0.9f);
+        int tmpInitialCapacityForSettingNameTooltipTextMap = CollectionUtil.calculateInitialHashCollectionCapacity(10, 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",
                 SettingsContainer.ROWS_PER_PAGE_SETTING_DEFAULT) {
@@ -752,15 +754,16 @@ private void checkSettings() throws Exception {
         //setting names and values must adhere to the preference input restrictions
         //setting values are only tested for their current state, not the entire possible input space! It is tested again at persistence
         List<Property> tmpSettingsList = this.settings;
-        HashSet<String> tmpSettingNames = new HashSet<>(tmpSettingsList.size() + 6, 1.0f);
+        int tmpSettingNamesSetInitCapacity = CollectionUtil.calculateInitialHashCollectionCapacity(tmpSettingsList.size(), BasicDefinitions.DEFAULT_HASH_COLLECTION_LOAD_FACTOR);
+        HashSet<String> tmpSettingNamesSet = new HashSet<>(tmpSettingNamesSetInitCapacity, BasicDefinitions.DEFAULT_HASH_COLLECTION_LOAD_FACTOR);
         for (Property tmpSetting : tmpSettingsList) {
             if (!PreferenceUtil.isValidName(tmpSetting.getName())) {
                 throw new Exception("Setting " + tmpSetting.getName() + " has an invalid name.");
             }
-            if (tmpSettingNames.contains(tmpSetting.getName())) {
+            if (tmpSettingNamesSet.contains(tmpSetting.getName())) {
                 throw new Exception("Setting name " + tmpSetting.getName() + " is used multiple times.");
             } else {
-                tmpSettingNames.add(tmpSetting.getName());
+                tmpSettingNamesSet.add(tmpSetting.getName());
             }
             if (tmpSetting instanceof SimpleBooleanProperty) {
                 //nothing to do here, booleans cannot have invalid values

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

@@ -186,5 +186,9 @@ public final class BasicDefinitions {
      * Default distance between image and text
      */
     public static final int DEFAULT_IMAGE_TEXT_DISTANCE = 15;
+    /**
+     * Default load factor for HashMap and HashSet instances, defined based on default value given in the Java documentation.
+     */
+    public static final float DEFAULT_HASH_COLLECTION_LOAD_FACTOR = 0.75f;
     //</editor-fold>
 }