adds fragment frequencies to fragments overview

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

@@ -971,7 +971,7 @@ private StackPane createStackPaneWithContextMenuAndStructureDisplayForBar(ImageV
                     //Note: the used depiction method returns an error image if image creation fails, so nothing else to do here
                 }
             }
-            Image tmpImage = DepictionUtil.depictImageWithZoomAndFillToFitAndWhiteBackground(
+            Image tmpImage = DepictionUtil.depictImage(
                     this.atomContainerForDisplayCache,
                     this.imageZoomFactor,
                     this.imageWidth,
@@ -993,16 +993,17 @@ private StackPane createStackPaneWithContextMenuAndStructureDisplayForBar(ImageV
             Clipboard.getSystemClipboard().setContent(tmpSmilesClipboardContent);
         });
         tmpCopyStructureMenuItem.setOnAction(event -> {
-            ClipboardContent tmpStructureClipboardContent = new ClipboardContent();
-            Image tmpCopyImageOnBar = DepictionUtil.depictImageWithZoomAndFillToFitAndWhiteBackground(
+            //note: making the background transparent leads to problems on Windows, where the background then appears black
+            Image tmpCopyImageOnBar = DepictionUtil.depictImage(
                     this.atomContainerForDisplayCache,
                     12.0,
                     GuiDefinitions.GUI_COPY_IMAGE_IMAGE_WIDTH,
                     GuiDefinitions.GUI_COPY_IMAGE_IMAGE_HEIGHT,
                     true,
                     true);
-            tmpStructureClipboardContent.putImage(tmpCopyImageOnBar);
-            Clipboard.getSystemClipboard().setContent(tmpStructureClipboardContent);
+            ClipboardContent tmpImageClipboardContent = new ClipboardContent();
+            tmpImageClipboardContent.putImage(tmpCopyImageOnBar);
+            Clipboard.getSystemClipboard().setContent(tmpImageClipboardContent);
         });
         tmpNodePane.addEventHandler(MouseEvent.MOUSE_EXITED, event -> {
             tmpNodePane.setStyle("-fx-bar-fill: " + HistogramViewController.HISTOGRAM_BARS_COLOR_HEX_VALUE);

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

@@ -243,7 +243,7 @@ public MainViewController(Stage aStage, MainView aMainView, String anAppDir, ICo
         this.fragmentationService = new FragmentationService();
         this.fragmentationService.reloadFragmenterSettings();
         this.fragmentationService.reloadActiveFragmenterAndPipeline();
-        this.viewToolsManager = new ViewToolsManager(this.configuration);
+        this.viewToolsManager = new ViewToolsManager(this.configuration, this.settingsContainer);
         this.viewToolsManager.reloadViewToolsSettings();
         //<editor-fold desc="show MainView inside primaryStage" defaultstate="collapsed">
         this.mainTabPane = new TabPane();

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

@@ -30,6 +30,7 @@
 import de.unijena.cheminf.mortar.message.Message;
 import de.unijena.cheminf.mortar.model.data.FragmentDataModel;
 import de.unijena.cheminf.mortar.model.data.MoleculeDataModel;
+import de.unijena.cheminf.mortar.model.settings.SettingsContainer;
 import de.unijena.cheminf.mortar.model.util.BasicDefinitions;
 import de.unijena.cheminf.mortar.model.util.FileUtil;
 import de.unijena.cheminf.mortar.preference.PreferenceContainer;
@@ -82,10 +83,6 @@ public class ViewToolsManager {
      * OverviewViewController instance.
      */
     private final OverviewViewController overviewViewController;
-    /**
-     * Configuration class to read resource file paths from.
-     */
-    private final IConfiguration configuration;
     //</editor-fold>
     //
     //<editor-fold desc="constructor" defaultstate="collapsed">
@@ -94,13 +91,13 @@ public class ViewToolsManager {
      * Opens a GUI exception alert if they are not.
      *
      * @param aConfiguration configuration instance to read resource file paths from
+     * @param aSettingsContainer settings container to read settings from
      */
-    public ViewToolsManager(IConfiguration aConfiguration) {
-        this.configuration = aConfiguration;
+    public ViewToolsManager(IConfiguration aConfiguration, SettingsContainer aSettingsContainer) {
         this.viewToolsArray = new IViewToolController[2];
-        this.histogramViewController = new HistogramViewController(this.configuration);
+        this.histogramViewController = new HistogramViewController(aConfiguration);
         this.viewToolsArray[0] = this.histogramViewController;
-        this.overviewViewController = new OverviewViewController(this.configuration);
+        this.overviewViewController = new OverviewViewController(aConfiguration, aSettingsContainer);
         this.viewToolsArray[1] = this.overviewViewController;
         try {
             this.checkViewTools();

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

@@ -485,6 +485,7 @@ public static void copySelectedTableViewCellsToClipboard(TableView<?> aTableView
                 tmpCell = aTableView.getColumns().get(tmpColIndex).getCellData(tmpRowIndex);
             }
             if (tmpCell == null) {
+                GuiUtil.LOGGER.log(Level.WARNING, "Selected cell in table view is empty and could not be copied to clipboard.");
                 return;
             } else {
                 ClipboardContent tmpClipboardContent = new ClipboardContent();
@@ -516,12 +517,21 @@ public static void copySelectedTableViewCellsToClipboard(TableView<?> aTableView
                         } else {
                             tmpAtomContainer = ((MoleculeDataModel) aTableView.getItems().get(tmpRowIndex)).getAtomContainer();
                         }
-                        Image tmpImage = DepictionUtil.depictImageWithZoomAndFillToFitAndWhiteBackground(tmpAtomContainer, 1, GuiDefinitions.GUI_COPY_IMAGE_IMAGE_WIDTH, GuiDefinitions.GUI_COPY_IMAGE_IMAGE_HEIGHT,true, true);
+                        //note: making the background transparent leads to problems on Windows, where the background then appears black
+                        Image tmpImage = DepictionUtil.depictImage(
+                                tmpAtomContainer,
+                                1.0,
+                                GuiDefinitions.GUI_COPY_IMAGE_IMAGE_WIDTH,
+                                GuiDefinitions.GUI_COPY_IMAGE_IMAGE_HEIGHT,
+                                true,
+                                true);
                         tmpClipboardContent.putImage(tmpImage);
                     } catch (CDKException | ClassCastException tmpException) {
+                        //copies the exact image instance already on display in the cell to clipboard, instead of generating a bigger depiction
                         tmpClipboardContent.putImage(((ImageView) tmpCell).getImage());
                     }
                 } else {
+                    GuiUtil.LOGGER.log(Level.WARNING, "Unknown data type in table view cell ({0}) could not be copied to clipboard.", tmpCell.getClass());
                     return;
                 }
                 Clipboard.getSystemClipboard().setContent(tmpClipboardContent);

src/main/java/de/unijena/cheminf/mortar/gui/views/ItemizationDataTableView.java

@@ -31,6 +31,7 @@
 import de.unijena.cheminf.mortar.model.data.DataModelPropertiesForTableView;
 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.settings.SettingsContainer;
 
 import javafx.beans.binding.Bindings;
@@ -47,6 +48,8 @@
 import javafx.scene.image.ImageView;
 import javafx.scene.layout.BorderPane;
 
+import java.awt.FontMetrics;
+import java.awt.Graphics2D;
 import java.util.List;
 
 /**
@@ -95,6 +98,13 @@ public class ItemizationDataTableView extends TableView implements IDataTableVie
      * Configuration class to read resource file paths from.
      */
     private final IConfiguration configuration;
+    /**
+     * Cached {@link FontMetrics} instance (created once in the constructor using
+     * {@link DepictionUtil#getGraphicsInstanceWithStandardFont(int, int)}) that is reused by the
+     * fragment-column cell-value factories to avoid allocating a new {@link java.awt.image.BufferedImage}
+     * and {@link Graphics2D} on every cell render.
+     */
+    private final FontMetrics cachedFontMetrics;
     //</editor-fold>
     //
     /**
@@ -106,6 +116,11 @@ public class ItemizationDataTableView extends TableView implements IDataTableVie
     public ItemizationDataTableView(String aFragmentationName, IConfiguration aConfiguration) {
         super();
         this.configuration = aConfiguration;
+        // Build FontMetrics once; the backing Graphics2D is disposed immediately after extraction.
+        // The FontMetrics object itself is self-contained and can be reused across all cell renders.
+        Graphics2D tmpGraphics2D = DepictionUtil.getGraphicsInstanceWithStandardFont(1, 1);
+        this.cachedFontMetrics = tmpGraphics2D.getFontMetrics();
+        tmpGraphics2D.dispose();
         this.setEditable(false);
         this.fragmentationName = aFragmentationName;
         this.getSelectionModel().setCellSelectionEnabled(true);
@@ -222,11 +237,14 @@ private void resetFragmentStructureColumns(int anItemAmount) {
                     return null;
                 }
                 FragmentDataModel tmpFragment = cellData.getValue().getFragmentsOfSpecificFragmentation(this.fragmentationName).get(tmpIndex);
-                if (!cellData.getValue().hasMoleculeUndergoneSpecificFragmentation(this.fragmentationName)) {
-                    return null;
+                int tmpFrequency = cellData.getValue().getFragmentFrequencyOfSpecificFragmentation(this.fragmentationName).get(tmpFragment.getUniqueSmiles());
+                String tmpFrequencyString = String.valueOf(tmpFrequency);
+                // just a precaution; it is highly unlikely that we get that many fragments of the same type for one(!) molecule
+                // cachedFontMetrics is reused here to avoid allocating a BufferedImage/Graphics2D per cell render
+                if (!DepictionUtil.isTextNarrowerThanImage(tmpFragment.getStructureImageWidth(), tmpFrequencyString, this.cachedFontMetrics)) {
+                    tmpFrequencyString = DepictionUtil.fitIntegerDisplayToImageWidth(tmpFragment.getStructureImageWidth(), tmpFrequency, this.cachedFontMetrics);
                 }
-                String tmpFrequency = cellData.getValue().getFragmentFrequencyOfSpecificFragmentation(this.fragmentationName).get(tmpFragment.getUniqueSmiles()).toString();
-                return tmpFragment.getStructureWithText(tmpFrequency);
+                return tmpFragment.getStructureWithText(tmpFrequencyString);
             }));
             tmpColumn.setMinWidth(300);
             this.fragmentStructureColumn.getColumns().add(tmpColumn);

src/main/java/de/unijena/cheminf/mortar/gui/views/OverviewView.java

@@ -58,7 +58,7 @@
  * @version 1.0.0.0
  */
 public class OverviewView extends AnchorPane {
-    //<editor-fold desc="public static final class constants", defaultstate="collapsed">
+    //<editor-fold desc="public static final class constants" defaultstate="collapsed">
     /**
      * Width of columns and rows per page label of the overview view.
      */
@@ -99,6 +99,10 @@ public class OverviewView extends AnchorPane {
      * Button to apply the default configuration to the structure grid pane.
      */
     private final Button defaultButton;
+    /**
+     * Button to save a screenshot of the structure grid pane.
+     */
+    private final Button screenshotButton;
     /**
      * Button to close the view.
      */
@@ -275,7 +279,10 @@ public OverviewView(int aColumnsPerPage, int aRowsPerPage) throws IllegalArgumen
         this.closeButton = GuiUtil.getButtonOfStandardSize(Message.get("OverviewView.closeButton.text"));
         this.closeButton.setTooltip(GuiUtil.createTooltip(Message.get("OverviewView.closeButton.tooltip")));
         //
-        this.bottomRightHBox.getChildren().add(this.closeButton);
+        this.screenshotButton = GuiUtil.getButtonOfStandardSize(Message.get("OverviewView.screenshotButton.text"));
+        this.screenshotButton.setTooltip(GuiUtil.createTooltip(Message.get("OverviewView.screenshotButton.tooltip")));
+        //
+        this.bottomRightHBox.getChildren().addAll(this.screenshotButton, this.closeButton);
         //
         /*
         initialization of the imageDimensionsBelowLimitVBox that is meant to be shown when the dimensions of the
@@ -413,6 +420,15 @@ public Button getCloseButton() {
         return this.closeButton;
     }
     //
+    /**
+     * Returns the overview view's screenshot button for saving a PNG image of the current structure grid page.
+     *
+     * @return Button
+     */
+    public Button getScreenshotButton() {
+        return this.screenshotButton;
+    }
+    //
     /**
      * Returns the text field for rows per page entry of the user.
      *

src/main/java/de/unijena/cheminf/mortar/model/data/FragmentDataModel.java

@@ -233,21 +233,27 @@ public MoleculeDataModel getFirstParentMolecule() {
      */
     public ImageView getParentMoleculeStructure() throws NullPointerException {
         if (this.parentMolecules.isEmpty()) {
-            return new ImageView(DepictionUtil.depictErrorImage("No parent molecules", 250, 250));
+            return new ImageView(DepictionUtil.depictErrorImage("No parent molecules",
+                    (int) super.getStructureImageWidth(),
+                    (int) super.getStructureImageHeight()));
         }
         if (this.parentMolecule == null) {
             this.parentMolecule = this.parentMolecules.stream().findFirst().orElse(null);
         }
         try {
             // throws NullPointerException if parent molecule is null
             IAtomContainer tmpAtomContainer = this.parentMolecule.getAtomContainer();
-            return new ImageView(DepictionUtil.depictImageWithHeight(tmpAtomContainer, super.getStructureImageHeight()));
+            return new ImageView(
+                    DepictionUtil.depictImageWithDefaultWidthNoZoomNoFillToFitAndTransparentBackground(
+                            tmpAtomContainer, super.getStructureImageHeight()));
         } catch (CDKException | NullPointerException anException) {
             FragmentDataModel.LOGGER.log(
                     Level.SEVERE,
                     String.format("Molecule name: %s; exception: %s", this.parentMolecule.getName(), anException.toString()),
                     anException);
-            return new ImageView(DepictionUtil.depictErrorImage(anException.getMessage(), 250, 250));
+            return new ImageView(DepictionUtil.depictErrorImage(anException.getMessage(),
+                    (int) super.getStructureImageWidth(),
+                    (int) super.getStructureImageHeight()));
         }
     }
     //

src/main/java/de/unijena/cheminf/mortar/model/data/MoleculeDataModel.java

@@ -280,10 +280,10 @@ public boolean hasMoleculeUndergoneSpecificFragmentation(String aKey) {
     public ImageView getStructure() {
         try {
             IAtomContainer tmpAtomContainer = this.getAtomContainer();
-            return new ImageView(DepictionUtil.depictImageWithZoomAndFillToFit(tmpAtomContainer, 1, this.getStructureImageWidth(), this.getStructureImageHeight(), false));
+            return new ImageView(DepictionUtil.depictImageWithTransparentBackground(tmpAtomContainer, 1, this.getStructureImageWidth(), this.getStructureImageHeight(), false));
         } catch (CDKException aCDKException) {
             Logger.getLogger(MoleculeDataModel.class.getName()).log(Level.SEVERE, aCDKException.toString(), aCDKException);
-            return new ImageView(DepictionUtil.depictErrorImage(aCDKException.getMessage(), 250, 250));
+            return new ImageView(DepictionUtil.depictErrorImage(aCDKException.getMessage(), (int) this.getStructureImageWidth(), (int) this.getStructureImageHeight()));
         }
     }
     //
@@ -297,10 +297,10 @@ public ImageView getStructure() {
     public ImageView getStructureWithText(String aText){
         try {
             IAtomContainer tmpAtomContainer = this.getAtomContainer();
-            return new ImageView(DepictionUtil.depictImageWithText(tmpAtomContainer, 1, this.getStructureImageWidth(), this.getStructureImageHeight(), aText));
+            return new ImageView(DepictionUtil.depictImageWithTextNoFillToFitAndTransparentBackground(tmpAtomContainer, 1, this.getStructureImageWidth(), this.getStructureImageHeight(), aText));
         } catch (CDKException aCDKException) {
             Logger.getLogger(MoleculeDataModel.class.getName()).log(Level.SEVERE, aCDKException.toString(), aCDKException);
-            return new ImageView(DepictionUtil.depictErrorImage(aCDKException.getMessage(), 250, 250));
+            return new ImageView(DepictionUtil.depictErrorImage(aCDKException.getMessage(), (int) this.getStructureImageWidth(), (int) this.getStructureImageHeight()));
         }
     }
     //