Merge pull request #99 from FelixBaensch/issue-84-column-swap

Issue 84 column swap

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

@@ -1303,7 +1303,7 @@ private Tab createFragmentsTab(String aFragmentationName){
         int tmpRowsPerPage = this.settingsContainer.getRowsPerPageSetting();
         tmpFragmentsDataTableView.setOnSort((EventHandler<SortEvent<TableView>>) event -> GuiUtil.sortTableViewGlobally(event, tmpPagination, tmpRowsPerPage));
         tmpFragmentsDataTableView.widthProperty().addListener((observable, oldValue, newValue) -> {
-            for(Object tmpObject : tmpFragmentsDataTableView.getItems()) {
+            for (Object tmpObject : tmpFragmentsDataTableView.getItems()) {
                 ((MoleculeDataModel) tmpObject).setStructureImageWidth(tmpFragmentsDataTableView.getStructureColumn().getWidth());
                 ((FragmentDataModel) tmpObject).getFirstParentMolecule().setStructureImageWidth(tmpFragmentsDataTableView.getParentMolColumn().getWidth());
             }
@@ -1365,7 +1365,7 @@ private Tab createItemsTab(String aFragmentationName){
         int tmpRowsPerPage = this.settingsContainer.getRowsPerPageSetting();
         tmpItemizationDataTableView.setOnSort((EventHandler<SortEvent<TableView>>) event -> GuiUtil.sortTableViewGlobally(event, tmpPagination, tmpRowsPerPage));
         tmpItemizationDataTableView.widthProperty().addListener((observable, oldValue, newValue) -> {
-            for(Object tmpObject : tmpItemizationDataTableView.getItems()) {
+            for (Object tmpObject : tmpItemizationDataTableView.getItems()) {
                 ((MoleculeDataModel) tmpObject).setStructureImageWidth(tmpItemizationDataTableView.getMoleculeStructureColumn().getWidth());
             }
         });

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

@@ -536,7 +536,7 @@ public static void setImageStructureHeight(TableView aTableView, double aHeight,
                         / aRowsPerPage;
         if (aTableView.getClass().equals(ItemizationDataTableView.class)) {
             tmpHeight =
-                    (aHeight - 2*GuiDefinitions.GUI_TABLE_VIEW_HEADER_HEIGHT - GuiDefinitions.GUI_PAGINATION_CONTROL_PANEL_HEIGHT)
+                    (aHeight - 2 * GuiDefinitions.GUI_TABLE_VIEW_HEADER_HEIGHT - GuiDefinitions.GUI_PAGINATION_CONTROL_PANEL_HEIGHT)
                             / aRowsPerPage;
         }
         if (tmpHeight < GuiDefinitions.GUI_STRUCTURE_IMAGE_MIN_HEIGHT) {

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

@@ -131,6 +131,28 @@ public FragmentsDataTableView(IConfiguration aConfiguration){
         //activate for future bulk export?
         //this.getSelectionModel().setSelectionMode(SelectionMode.MULTIPLE);
         DecimalFormat tmpPercentageForm = new DecimalFormat("#.##%");
+        //-smilesColumn
+        this.smilesColumn = new TableColumn<>(Message.get("MainTabPane.fragmentsTab.tableView.smilesColumn.header"));
+        this.smilesColumn.setMinWidth(80);
+        this.smilesColumn.prefWidthProperty().bind(
+                this.widthProperty().multiply(0.075) //magic number
+        );
+        this.smilesColumn.setResizable(true);
+        this.smilesColumn.setEditable(false);
+        this.smilesColumn.setSortable(true);
+        this.smilesColumn.setCellValueFactory(new PropertyValueFactory(DataModelPropertiesForTableView.UNIQUE_SMILES.getText()));
+        this.smilesColumn.setCellFactory(tableColumn ->{
+            TableCell<FragmentDataModel, String> tmpCell = new TableCell<>();
+            Text tmpText = new Text();
+            tmpText.setTextAlignment(TextAlignment.CENTER);
+            tmpCell.setGraphic(tmpText);
+            tmpCell.setPrefHeight(Region.USE_COMPUTED_SIZE);
+            tmpText.wrappingWidthProperty().bind(this.smilesColumn.widthProperty());
+            tmpText.textProperty().bind(tmpCell.itemProperty());
+            return tmpCell;
+        });
+        this.smilesColumn.setStyle("-fx-alignment: CENTER");
+        this.getColumns().add(this.smilesColumn);
         //-structureColumn
         this.structureColumn = new TableColumn<>(Message.get("MainTabPane.fragmentsTab.tableView.structureColumn.header"));
         this.structureColumn.setMinWidth(150); //magic number
@@ -143,28 +165,31 @@ public FragmentsDataTableView(IConfiguration aConfiguration){
         this.structureColumn.setCellValueFactory(new PropertyValueFactory(DataModelPropertiesForTableView.STRUCTURE.getText()));
         this.structureColumn.setStyle("-fx-alignment: CENTER");
         this.getColumns().add(this.structureColumn);
-        //-smilesColumn
-        this.smilesColumn = new TableColumn<>(Message.get("MainTabPane.fragmentsTab.tableView.smilesColumn.header"));
-        this.smilesColumn.setMinWidth(50);
-        this.smilesColumn.prefWidthProperty().bind(
+        //-parentMolNameColumn
+        this.parentMolNameColumn = new TableColumn<>();
+        Label tmpParentNameLabel = new Label(Message.get("MainTabPane.fragmentsTab.tableView.parentMolNameColumn.header"));
+        tmpParentNameLabel.setTooltip(GuiUtil.createTooltip(Message.get("MainTabPane.fragmentsTab.tableView.parentMolNameColumn.tooltip")));
+        this.parentMolNameColumn.setGraphic(tmpParentNameLabel);
+        this.parentMolNameColumn.setMinWidth(80);
+        this.parentMolNameColumn.prefWidthProperty().bind(
                 this.widthProperty().multiply(0.075) //magic number
         );
-        this.smilesColumn.setResizable(true);
-        this.smilesColumn.setEditable(false);
-        this.smilesColumn.setSortable(true);
-        this.smilesColumn.setCellValueFactory(new PropertyValueFactory(DataModelPropertiesForTableView.UNIQUE_SMILES.getText()));
-        this.smilesColumn.setCellFactory(tableColumn ->{
+        this.parentMolNameColumn.setResizable(true);
+        this.parentMolNameColumn.setEditable(false);
+        this.parentMolNameColumn.setSortable(true);
+        this.parentMolNameColumn.setCellValueFactory(new PropertyValueFactory(DataModelPropertiesForTableView.PARENT_MOLECULE_NAME.getText()));
+        this.parentMolNameColumn.setCellFactory(tableColumn ->{
             TableCell<FragmentDataModel, String> tmpCell = new TableCell<>();
             Text tmpText = new Text();
             tmpText.setTextAlignment(TextAlignment.CENTER);
             tmpCell.setGraphic(tmpText);
             tmpCell.setPrefHeight(Region.USE_COMPUTED_SIZE);
-            tmpText.wrappingWidthProperty().bind(this.smilesColumn.widthProperty());
+            tmpText.wrappingWidthProperty().bind(this.parentMolNameColumn.widthProperty());
             tmpText.textProperty().bind(tmpCell.itemProperty());
             return tmpCell;
         });
-        this.smilesColumn.setStyle("-fx-alignment: CENTER");
-        this.getColumns().add(this.smilesColumn);
+        this.parentMolNameColumn.setStyle("-fx-alignment: CENTER");
+        this.getColumns().add(this.parentMolNameColumn);
         //-parentMolColumn
         this.parentMolColumn = new TableColumn<>();
         Label tmpParentMolLabel = new Label(Message.get("MainTabPane.fragmentsTab.tableView.parentMolColumn.header"));
@@ -180,25 +205,11 @@ public FragmentsDataTableView(IConfiguration aConfiguration){
         this.parentMolColumn.setCellValueFactory(new PropertyValueFactory(DataModelPropertiesForTableView.PARENT_MOLECULE_STRUCTURE.getText()));
         this.parentMolColumn.setStyle("-fx-alignment: CENTER");
         this.getColumns().add(this.parentMolColumn);
-        //-parentMolNameColumn
-        this.parentMolNameColumn = new TableColumn<>();
-        Label tmpParentNameLabel = new Label(Message.get("MainTabPane.fragmentsTab.tableView.parentMolNameColumn.header"));
-        tmpParentNameLabel.setTooltip(GuiUtil.createTooltip(Message.get("MainTabPane.fragmentsTab.tableView.parentMolNameColumn.tooltip")));
-        this.parentMolNameColumn.setGraphic(tmpParentNameLabel);
-        this.parentMolNameColumn.prefWidthProperty().bind(
-                this.widthProperty().multiply(0.075) //magic number
-        );
-        this.parentMolNameColumn.setResizable(true);
-        this.parentMolNameColumn.setEditable(false);
-        this.parentMolNameColumn.setSortable(true);
-        this.parentMolNameColumn.setCellValueFactory(new PropertyValueFactory(DataModelPropertiesForTableView.PARENT_MOLECULE_NAME.getText()));
-        this.parentMolNameColumn.setStyle("-fx-alignment: CENTER");
-        this.getColumns().add(this.parentMolNameColumn);
         //-frequencyColumn
         this.frequencyColumn = new TableColumn<>(Message.get("MainTabPane.fragmentsTab.tableView.frequencyColumn.header"));
         this.frequencyColumn.setMinWidth(50); //magic number
         this.frequencyColumn.prefWidthProperty().bind(
-                this.widthProperty().multiply(0.1) //magic number
+                this.widthProperty().multiply(0.098) //magic number
         );
         this.frequencyColumn.setResizable(true);
         this.frequencyColumn.setEditable(false);
@@ -208,9 +219,9 @@ public FragmentsDataTableView(IConfiguration aConfiguration){
         this.getColumns().add(this.frequencyColumn);
         //-percentageColumn
         this.percentageColumn = new TableColumn<>(Message.get("MainTabPane.fragmentsTab.tableView.percentageColumn.header"));
-        this.percentageColumn.setMinWidth(20); //magic number
+        this.percentageColumn.setMinWidth(50); //magic number
         this.percentageColumn.prefWidthProperty().bind(
-                this.widthProperty().multiply(0.1) //magic number
+                this.widthProperty().multiply(0.098) //magic number
         );
         this.percentageColumn.setResizable(true);
         this.percentageColumn.setEditable(false);
@@ -229,23 +240,29 @@ protected void updateItem(Double value, boolean empty){
         });
         this.percentageColumn.setStyle("-fx-alignment: CENTER-RIGHT");
         this.getColumns().add(this.percentageColumn);
-        //-frequencyColumn
-        this.moleculeFrequencyColumn = new TableColumn<>(Message.get("MainTabPane.fragmentsTab.tableView.moleculeFrequencyColumn.header"));
+        //-moleculeFrequencyColumn
+        this.moleculeFrequencyColumn = new TableColumn<>();
+        Label tmpMolFrequencyLabel = new Label(Message.get("MainTabPane.fragmentsTab.tableView.moleculeFrequencyColumn.header"));
+        tmpMolFrequencyLabel.setTooltip(GuiUtil.createTooltip(Message.get("MainTabPane.fragmentsTab.tableView.moleculeFrequencyColumn.tooltip")));
+        this.moleculeFrequencyColumn.setGraphic(tmpMolFrequencyLabel);
         this.moleculeFrequencyColumn.setMinWidth(50); //magic number
         this.moleculeFrequencyColumn.prefWidthProperty().bind(
-                this.widthProperty().multiply(0.1) //magic number
+                this.widthProperty().multiply(0.098) //magic number
         );
         this.moleculeFrequencyColumn.setResizable(true);
         this.moleculeFrequencyColumn.setEditable(false);
         this.moleculeFrequencyColumn.setSortable(true);
         this.moleculeFrequencyColumn.setCellValueFactory(new PropertyValueFactory(DataModelPropertiesForTableView.MOLECULE_FREQUENCY.getText()));
         this.moleculeFrequencyColumn.setStyle("-fx-alignment: CENTER-RIGHT");
         this.getColumns().add(this.moleculeFrequencyColumn);
-        //-percentageColumn
-        this.moleculePercentageColumn = new TableColumn<>(Message.get("MainTabPane.fragmentsTab.tableView.moleculePercentageColumn.header"));
-        this.moleculePercentageColumn.setMinWidth(20); //magic number
+        //-moleculePercentageColumn
+        this.moleculePercentageColumn = new TableColumn<>();
+        Label tmpMolPercentageLabel = new Label(Message.get("MainTabPane.fragmentsTab.tableView.moleculePercentageColumn.header"));
+        tmpMolPercentageLabel.setTooltip(GuiUtil.createTooltip(Message.get("MainTabPane.fragmentsTab.tableView.moleculePercentageColumn.tooltip")));
+        this.moleculePercentageColumn.setGraphic(tmpMolPercentageLabel);
+        this.moleculePercentageColumn.setMinWidth(50); //magic number
         this.moleculePercentageColumn.prefWidthProperty().bind(
-                this.widthProperty().multiply(0.0975) //magic number
+                this.widthProperty().multiply(0.098) //magic number
         );
         this.moleculePercentageColumn.setResizable(true);
         this.moleculePercentageColumn.setEditable(false);

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

@@ -139,7 +139,7 @@ public MoleculesDataTableView(IConfiguration aConfiguration) {
         this.structureColumn = new TableColumn<>(Message.get("MainTabPane.moleculesTab.tableView.structureColumn.header"));
         this.structureColumn.setMinWidth(150); //magic number
         this.structureColumn.prefWidthProperty().bind(
-                this.widthProperty().multiply(0.7975) //magic number
+                this.widthProperty().multiply(0.796) //magic number
         );
         this.structureColumn.setResizable(true);
         this.structureColumn.setEditable(false);
@@ -184,7 +184,7 @@ public Node createMoleculeTableViewPage(int aPageIndex, SettingsContainer aSetti
             }
             this.selectionAllCheckBoxAction = false;
         });
-        this.itemsObservableList.addListener((ListChangeListener) change -> {
+        this.itemsObservableList.addListener((ListChangeListener<? super MoleculeDataModel>) change -> {
             if (this.selectionAllCheckBoxAction) {
                 // No further action needed with column checkbox data when the select all checkbox is operated on
                 return;

src/main/java/de/unijena/cheminf/mortar/model/io/Exporter.java

@@ -611,8 +611,8 @@ private List<String> createFragmentsTabPdfFile(File aPdfFile,
             Chunk tmpHeader = new Chunk(Message.get("Exporter.fragmentationTab.pdfCellHeader.header"),
                     FontFactory.getFont(FontFactory.TIMES_ROMAN, 18, Font.UNDERLINE));
             Paragraph tmpSpace = new Paragraph(" ");
-            tmpFragmentationTable.addCell(tmpFragmentCell);
             tmpFragmentationTable.addCell(tmpSmilesStringCell);
+            tmpFragmentationTable.addCell(tmpFragmentCell);
             tmpFragmentationTable.addCell(tmpFrequencyCell);
             tmpFragmentationTable.addCell(tmpPercentageCell);
             tmpFragmentationTable.addCell(tmpMolFrequencyCell);
@@ -656,8 +656,8 @@ private List<String> createFragmentsTabPdfFile(File aPdfFile,
                 PdfPCell tmpCellOfMolPercentage = new PdfPCell(new Paragraph(tmpStringMoleculePercentage));
                 tmpCellOfMolPercentage.setHorizontalAlignment(Element.ALIGN_RIGHT);
                 tmpImageFragmentCell.addElement(tmpImageFragment);
-                tmpFragmentationTable.addCell(tmpImageFragmentCell);
                 tmpFragmentationTable.addCell(tmpFragmentDataModel.getUniqueSmiles());
+                tmpFragmentationTable.addCell(tmpImageFragmentCell);
                 tmpFragmentationTable.addCell(tmpCellOfFrequency);
                 tmpFragmentationTable.addCell(tmpCellOfPercentage);
                 tmpFragmentationTable.addCell(tmpCellOfMolFrequency);

src/main/resources/de/unijena/cheminf/mortar/message/Message_en_GB.properties

@@ -96,12 +96,14 @@ MainTabPane.fragmentsTab.tableView.structureColumn.header = Structure
 MainTabPane.fragmentsTab.tableView.smilesColumn.header = SMILES
 MainTabPane.fragmentsTab.tableView.frequencyColumn.header = Frequency
 MainTabPane.fragmentsTab.tableView.percentageColumn.header = Percentage
-MainTabPane.fragmentsTab.tableView.moleculeFrequencyColumn.header = Molecule Frequency
-MainTabPane.fragmentsTab.tableView.moleculePercentageColumn.header = Molecule Percentage
-MainTabPane.fragmentsTab.tableView.parentMolColumn.header = Sample Parent
-MainTabPane.fragmentsTab.tableView.parentMolColumn.tooltip = First occurred molecule which contains fragment
-MainTabPane.fragmentsTab.tableView.parentMolNameColumn.header = Sample Parent
-MainTabPane.fragmentsTab.tableView.parentMolNameColumn.tooltip = First occurred molecule which contains fragment
+MainTabPane.fragmentsTab.tableView.moleculeFrequencyColumn.header = Mol. Frequency
+MainTabPane.fragmentsTab.tableView.moleculeFrequencyColumn.tooltip = Molecule Frequency
+MainTabPane.fragmentsTab.tableView.moleculePercentageColumn.header = Mol. Percentage
+MainTabPane.fragmentsTab.tableView.moleculePercentageColumn.tooltip = Molecule Percentage
+MainTabPane.fragmentsTab.tableView.parentMolColumn.header = Parent Structure
+MainTabPane.fragmentsTab.tableView.parentMolColumn.tooltip = Sample Parent Structure: first fragmented molecule which contained the fragment
+MainTabPane.fragmentsTab.tableView.parentMolNameColumn.header = Parent Name
+MainTabPane.fragmentsTab.tableView.parentMolNameColumn.tooltip = Sample Parent Name: name of first fragmented molecule which contained the fragment
 #ItemizationTab#
 MainTabPane.itemizationTab.title = Items
 MainTabPane.itemizationTab.csvButton.txt = CSV
@@ -147,9 +149,9 @@ Exporter.fragmentationTab.pdfCellHeader.header = MORTAR Fragmentation Tab Export
 Exporter.fragmentationTab.pdfCellHeader.smiles = SMILES
 Exporter.fragmentationTab.pdfCellHeader.frequency = Frequency
 Exporter.fragmentationTab.pdfCellHeader.percentage = Percentage
-Exporter.fragmentationTab.pdfCellHeader.moleculeFrequency = Molecule Frequency
-Exporter.fragmentationTab.pdfCellHeader.moleculePercentage = Molecule Percentage
-Exporter.fragmentationTab.pdfCellHeader.fragment = Fragment
+Exporter.fragmentationTab.pdfCellHeader.moleculeFrequency = Mol. Frequency
+Exporter.fragmentationTab.pdfCellHeader.moleculePercentage = Mol. Percentage
+Exporter.fragmentationTab.pdfCellHeader.fragment = Structure
 Exporter.itemsTab.pdfCellHeader.header = MORTAR Itemization Tab Export
 Exporter.itemsTab.pdfCellHeader.name = Name
 Exporter.itemsTab.pdfCellHeader.structure = Structure