Examples with FragmentDataModel de.unijena.cheminf.mortar.model.data.FragmentDataModel used on opensource projects

Example 1 with FragmentDataModel

use of de.unijena.cheminf.mortar.model.data.FragmentDataModel in project MORTAR by FelixBaensch.

the class GuiUtil method setImageStructureHeight.

// 
/**
 * Sets the height for structure images to each MoleculeDataModel object of the items list of the tableView.
 * If image height is too small it will be set to GuiDefinitions.GUI_STRUCTURE_IMAGE_MIN_HEIGHT (50.0)
 *
 * @param aTableView TableView
 * @param aHeight double
 * @param aSettingsContainer SettingsContainer
 */
public static void setImageStructureHeight(TableView aTableView, double aHeight, SettingsContainer aSettingsContainer) {
    double tmpHeight = (aHeight - GuiDefinitions.GUI_TABLE_VIEW_HEADER_HEIGHT - GuiDefinitions.GUI_PAGINATION_CONTROL_PANEL_HEIGHT) / aSettingsContainer.getRowsPerPageSetting();
    if (aTableView.getClass().equals(ItemizationDataTableView.class)) {
        tmpHeight = (aHeight - 2 * GuiDefinitions.GUI_TABLE_VIEW_HEADER_HEIGHT - GuiDefinitions.GUI_PAGINATION_CONTROL_PANEL_HEIGHT) / aSettingsContainer.getRowsPerPageSetting();
    }
    if (tmpHeight < GuiDefinitions.GUI_STRUCTURE_IMAGE_MIN_HEIGHT) {
        tmpHeight = GuiDefinitions.GUI_STRUCTURE_IMAGE_MIN_HEIGHT;
    }
    if (aTableView.getClass().equals(ItemizationDataTableView.class)) {
        for (MoleculeDataModel tmpMoleculeDataModel : ((IDataTableView) aTableView).getItemsList()) {
            tmpMoleculeDataModel.setStructureImageHeight(tmpHeight);
            String tmpFragmentationName = ((ItemizationDataTableView) aTableView).getFragmentationName();
            if (!tmpMoleculeDataModel.hasMoleculeUndergoneSpecificFragmentation(tmpFragmentationName)) {
                continue;
            }
            for (FragmentDataModel tmpFragmentDataModel : tmpMoleculeDataModel.getFragmentsOfSpecificAlgorithm(tmpFragmentationName)) {
                tmpFragmentDataModel.setStructureImageHeight(tmpHeight);
            }
        }
    } else {
        for (MoleculeDataModel tmpMoleculeDataModel : ((IDataTableView) aTableView).getItemsList()) {
            tmpMoleculeDataModel.setStructureImageHeight(tmpHeight);
        }
    }
}

Example 2 with FragmentDataModel

use of de.unijena.cheminf.mortar.model.data.FragmentDataModel in project MORTAR by FelixBaensch.

the class Exporter method createFragmentationTabPdfFile.

// 
/**
 * Exports the fragmentation results as they are displayed on the fragments tab as a PDF file. Opens a file chooser
 * dialog for the user to determine a directory and file for the exported data.
 *
 * @param aFragmentDataModelList a list of FragmentDataModel instances to export
 * @param aMoleculeDataModelList a list MoleculeDataModel needed for the fragmentation report at the head of the exported document
 * @param aFragmentationName     fragmentation name to be displayed in the header of the PDF file
 * @return PDF file which contains the results of the fragmentation
 * @throws FileNotFoundException
 * @throws DocumentException
 * @author Betül Sevindik
 */
private List<String> createFragmentationTabPdfFile(File aPdfFile, List<MoleculeDataModel> aFragmentDataModelList, ObservableList<MoleculeDataModel> aMoleculeDataModelList, String aFragmentationName) throws FileNotFoundException, DocumentException {
    if (aPdfFile == null || aFragmentDataModelList == null || aMoleculeDataModelList == null || aFragmentationName == null) {
        return null;
    }
    List<String> tmpFailedExportFragments = new LinkedList<>();
    this.document = new Document(PageSize.A4);
    this.document.setPageSize(this.document.getPageSize().rotate());
    PdfWriter.getInstance(this.document, new FileOutputStream(aPdfFile.getPath()));
    this.document.open();
    // relative sizes
    float[] tmpCellLength = { 70f, 120f, 50f, 50f, 55f, 55f };
    PdfPTable tmpFragmentationTable = new PdfPTable(tmpCellLength);
    PdfPCell tmpSmilesStringCell = new PdfPCell(new Paragraph(Message.get("Exporter.fragmentationTab.pdfCellHeader.smiles"), fontFactory));
    PdfPCell tmpFrequencyCell = new PdfPCell(new Paragraph(Message.get("Exporter.fragmentationTab.pdfCellHeader.frequency"), this.fontFactory));
    PdfPCell tmpPercentageCell = new PdfPCell(new Paragraph(Message.get("Exporter.fragmentationTab.pdfCellHeader.percentage"), this.fontFactory));
    PdfPCell tmpMolFrequencyCell = new PdfPCell(new Paragraph(Message.get("Exporter.fragmentationTab.pdfCellHeader.moleculeFrequency"), this.fontFactory));
    PdfPCell tmpMolPercentageCell = new PdfPCell(new Paragraph(Message.get("Exporter.fragmentationTab.pdfCellHeader.moleculePercentage"), this.fontFactory));
    PdfPCell tmpFragmentCell = new PdfPCell(new Paragraph(Message.get("Exporter.fragmentationTab.pdfCellHeader.fragment"), this.fontFactory));
    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(tmpFrequencyCell);
    tmpFragmentationTable.addCell(tmpPercentageCell);
    tmpFragmentationTable.addCell(tmpMolFrequencyCell);
    tmpFragmentationTable.addCell(tmpMolPercentageCell);
    for (MoleculeDataModel tmpModel : aFragmentDataModelList) {
        if (Thread.currentThread().isInterrupted()) {
            return null;
        }
        FragmentDataModel tmpFragmentDataModel = (FragmentDataModel) tmpModel;
        int tmpAbsoluteFrequency = tmpFragmentDataModel.getAbsoluteFrequency();
        String tmpStringAbsoluteFrequency = String.format("%d", tmpAbsoluteFrequency);
        double tmpAbsolutePercentage = tmpFragmentDataModel.getAbsolutePercentage();
        int tmpMoleculeFrequency = tmpFragmentDataModel.getMoleculeFrequency();
        String tmpStringMoleculeFrequency = String.format("%d", tmpMoleculeFrequency);
        String tmpStringAbsolutePercentage = String.format("%.3f", tmpAbsolutePercentage);
        double tmpMoleculePercentage = tmpFragmentDataModel.getMoleculePercentage();
        String tmpStringMoleculePercentage = String.format("%.2f", tmpMoleculePercentage);
        // creates an image of the fragment
        PdfPCell tmpImageFragmentCell = new PdfPCell();
        tmpImageFragmentCell.setFixedHeight(85f);
        IAtomContainer tmpStructureOfFragment;
        try {
            tmpStructureOfFragment = tmpFragmentDataModel.getAtomContainer();
        } catch (CDKException anException) {
            Exporter.LOGGER.getLogger(MoleculeDataModel.class.getName()).log(Level.SEVERE, anException.toString() + "_" + tmpFragmentDataModel.getName(), anException);
            tmpFailedExportFragments.add(tmpFragmentDataModel.getUniqueSmiles());
            continue;
        }
        javafx.scene.image.Image tmpImageStructureOfFragment = DepictionUtil.depictImageWithZoom(tmpStructureOfFragment, 4.0);
        BufferedImage tmpBufferedImageFragment = SwingFXUtils.fromFXImage(tmpImageStructureOfFragment, null);
        Image tmpImageFragment = this.getITextImage(tmpBufferedImageFragment);
        // inserts the data into the table
        PdfPCell tmpCellOfFrequency = new PdfPCell(new Paragraph(tmpStringAbsoluteFrequency));
        tmpCellOfFrequency.setHorizontalAlignment(Element.ALIGN_RIGHT);
        PdfPCell tmpCellOfPercentage = new PdfPCell(new Paragraph(tmpStringAbsolutePercentage));
        tmpCellOfPercentage.setHorizontalAlignment(Element.ALIGN_RIGHT);
        PdfPCell tmpCellOfMolFrequency = new PdfPCell(new Paragraph(tmpStringMoleculeFrequency));
        tmpCellOfMolFrequency.setHorizontalAlignment(Element.ALIGN_RIGHT);
        PdfPCell tmpCellOfMolPercentage = new PdfPCell(new Paragraph(tmpStringMoleculePercentage));
        tmpCellOfMolPercentage.setHorizontalAlignment(Element.ALIGN_RIGHT);
        tmpImageFragmentCell.addElement(tmpImageFragment);
        tmpFragmentationTable.addCell(tmpImageFragmentCell);
        tmpFragmentationTable.addCell(tmpFragmentDataModel.getUniqueSmiles());
        tmpFragmentationTable.addCell(tmpCellOfFrequency);
        tmpFragmentationTable.addCell(tmpCellOfPercentage);
        tmpFragmentationTable.addCell(tmpCellOfMolFrequency);
        tmpFragmentationTable.addCell(tmpCellOfMolPercentage);
    }
    this.document.add(tmpHeader);
    this.document.add(tmpSpace);
    this.document.add(this.createHeaderTable(aFragmentDataModelList.size(), aMoleculeDataModelList.size(), aFragmentationName));
    this.document.add(tmpSpace);
    this.document.add(tmpFragmentationTable);
    this.document.close();
    return tmpFailedExportFragments;
}

Example 3 with FragmentDataModel

use of de.unijena.cheminf.mortar.model.data.FragmentDataModel in project MORTAR by FelixBaensch.

the class Exporter method createFragmentationTabCsvFile.

// 
/**
 * Exports the fragmentation results as they are displayed on the fragments tab as a CSV file.
 *
 * @param aList      a list of FragmentDataModel instances to export
 * @param aSeparator the separator for the csv file
 * @throws FileNotFoundException
 * @author Betül Sevindik
 */
private void createFragmentationTabCsvFile(File aCsvFile, List<MoleculeDataModel> aList, String aSeparator) throws FileNotFoundException {
    if (aCsvFile == null || aList == null) {
        return;
    }
    PrintWriter tmpWriter = new PrintWriter(aCsvFile.getPath());
    StringBuilder tmpFragmentationCsvHeader = new StringBuilder();
    tmpFragmentationCsvHeader.append(Message.get("Exporter.fragmentationTab.csvHeader.smiles") + aSeparator + Message.get("Exporter.fragmentationTab.csvHeader.frequency") + aSeparator + Message.get("Exporter.fragmentationTab.csvHeader.percentage") + aSeparator + Message.get("Exporter.fragmentationTab.csvHeader.moleculeFrequency") + aSeparator + Message.get("Exporter.fragmentationTab.csvHeader.moleculePercentage") + ("\n"));
    tmpWriter.write(tmpFragmentationCsvHeader.toString());
    for (MoleculeDataModel tmpDataModel : aList) {
        if (Thread.currentThread().isInterrupted()) {
            return;
        }
        FragmentDataModel tmpFragmentDataModel = (FragmentDataModel) tmpDataModel;
        tmpWriter.printf("%s" + aSeparator + "%d" + aSeparator + "%.3f" + aSeparator + "%d" + aSeparator + "%.2f\n", tmpFragmentDataModel.getUniqueSmiles(), tmpFragmentDataModel.getAbsoluteFrequency(), tmpFragmentDataModel.getAbsolutePercentage(), tmpFragmentDataModel.getMoleculeFrequency(), tmpFragmentDataModel.getMoleculePercentage());
    }
    tmpWriter.close();
}

Example 4 with FragmentDataModel

use of de.unijena.cheminf.mortar.model.data.FragmentDataModel in project MORTAR by FelixBaensch.

the class Exporter method createItemizationTabCsvFile.

// </editor-fold>
// 
// <editor-fold desc="private methods" defaultstate="collapsed">
/**
 * Exports the fragmentation results as they are displayed on the itemization tab as a CSV file.
 *
 * @param aMoleculeDataModelList a list of MoleculeDataModel instances to export along with their fragments
 * @param aFragmentationName     fragmentation name to retrieve the specific set of fragments from the molecule data models
 * @param aSeparator             the separator for the csv file
 * @throws FileNotFoundException
 * @author Betül Sevindik
 */
private void createItemizationTabCsvFile(File aCsvFile, List<MoleculeDataModel> aMoleculeDataModelList, String aFragmentationName, String aSeparator) throws FileNotFoundException {
    if (aCsvFile == null || aMoleculeDataModelList == null || aFragmentationName == null) {
        return;
    }
    PrintWriter tmpWriter = new PrintWriter(aCsvFile.getPath());
    StringBuilder tmpCsvHeader = new StringBuilder();
    tmpCsvHeader.append(Message.get("Exporter.itemsTab.csvHeader.moleculeName") + aSeparator + Message.get("Exporter.itemsTab.csvHeader.smilesOfStructure") + aSeparator + Message.get("Exporter.itemsTab.csvHeader.smilesOfFragmentsAndFrequency") + "\n");
    tmpWriter.write(tmpCsvHeader.toString());
    for (MoleculeDataModel tmpMoleculeDataModel : aMoleculeDataModelList) {
        if (Thread.currentThread().isInterrupted()) {
            return;
        }
        tmpWriter.printf("%s" + aSeparator + "%s", tmpMoleculeDataModel.getName(), tmpMoleculeDataModel.getUniqueSmiles());
        if (!tmpMoleculeDataModel.hasMoleculeUndergoneSpecificFragmentation(aFragmentationName)) {
            continue;
        }
        List<FragmentDataModel> tmpFragmentList = tmpMoleculeDataModel.getFragmentsOfSpecificAlgorithm(aFragmentationName);
        for (FragmentDataModel tmpFragmentDataModel : tmpFragmentList) {
            if (Thread.currentThread().isInterrupted() || !tmpMoleculeDataModel.hasMoleculeUndergoneSpecificFragmentation(aFragmentationName)) {
                return;
            }
            tmpWriter.append(aSeparator);
            tmpWriter.printf("%s" + aSeparator + "%s", tmpFragmentDataModel.getUniqueSmiles(), tmpMoleculeDataModel.getFragmentFrequencyOfSpecificAlgorithm(aFragmentationName).get(tmpFragmentDataModel.getUniqueSmiles()).toString());
        }
        tmpWriter.append("\n");
    }
    tmpWriter.close();
}

Example 5 with FragmentDataModel

use of de.unijena.cheminf.mortar.model.data.FragmentDataModel in project MORTAR by FelixBaensch.

the class Exporter method createItemizationTabPdfFile.

// 
/**
 * Exports the fragmentation results as they are displayed on the itemization tab as a PDF file. Opens a file chooser
 * dialog for the user to determine a directory and file for the exported data.
 *
 * @param aFragmentDataModelListSize size of list of FragmentDataModel instances to export
 * @param aMoleculeDataModelList     a list MoleculeDataModel needed for the fragmentation report at the head of the exported document
 * @param aFragmentationName         fragmentation name to retrieve the specific set of fragments from the molecule data models
 * @throws FileNotFoundException
 * @throws DocumentException
 * @author Betül Sevindik
 */
private List<String> createItemizationTabPdfFile(File aPdfFile, int aFragmentDataModelListSize, ObservableList<MoleculeDataModel> aMoleculeDataModelList, String aFragmentationName) throws FileNotFoundException, DocumentException {
    if (aPdfFile == null || aFragmentDataModelListSize == 0 || aMoleculeDataModelList == null || aMoleculeDataModelList.size() == 0 || aFragmentationName == null || aFragmentationName.isEmpty()) {
        return null;
    }
    List<String> tmpFailedExportFragments = new LinkedList<>();
    this.document = new Document(PageSize.A4);
    PdfWriter.getInstance(this.document, new FileOutputStream(aPdfFile.getPath()));
    this.document.open();
    // creates the pdf table
    Chunk tmpItemizationTabHeader = new Chunk(Message.get("Exporter.itemsTab.pdfCellHeader.header"), FontFactory.getFont(FontFactory.TIMES_ROMAN, 18, Font.UNDERLINE));
    Paragraph tmpSpace = new Paragraph(" ");
    this.document.add(tmpItemizationTabHeader);
    this.document.add(tmpSpace);
    this.document.add(this.createHeaderTable(aFragmentDataModelListSize, aMoleculeDataModelList.size(), aFragmentationName));
    this.document.add(tmpSpace);
    for (MoleculeDataModel tmpMoleculeDataModel : aMoleculeDataModelList) {
        if (Thread.currentThread().isInterrupted()) {
            return null;
        }
        PdfPTable tmpTable = new PdfPTable(2);
        PdfPTable tmpFragmentTable = new PdfPTable(1);
        tmpTable.setWidths(new int[] { 40, 80 });
        PdfPCell tmpNameCell = new PdfPCell(new Paragraph(Message.get("Exporter.itemsTab.pdfCellHeader.name"), this.fontFactory));
        tmpNameCell.setFixedHeight(55f);
        PdfPCell tmpStructureCell = new PdfPCell(new Paragraph(Message.get("Exporter.itemsTab.pdfCellHeader.structure"), this.fontFactory));
        tmpStructureCell.setFixedHeight(120f);
        tmpTable.addCell(tmpNameCell);
        String tmpName = tmpMoleculeDataModel.getName();
        tmpTable.addCell(tmpName);
        tmpTable.addCell(tmpStructureCell);
        // Image of molecule
        IAtomContainer tmpMoleculeStructure;
        try {
            tmpMoleculeStructure = tmpMoleculeDataModel.getAtomContainer();
        } catch (CDKException anException) {
            Exporter.LOGGER.getLogger(MoleculeDataModel.class.getName()).log(Level.SEVERE, anException.toString() + "_" + tmpMoleculeDataModel.getName(), anException);
            tmpFailedExportFragments.add(tmpMoleculeDataModel.getUniqueSmiles());
            continue;
        }
        PdfPCell tmpMoleculeStructureCell = new PdfPCell();
        tmpMoleculeStructureCell.setFixedHeight(120f);
        javafx.scene.image.Image tmpMoleculeImage = DepictionUtil.depictImageWithZoom(tmpMoleculeStructure, 3.0);
        BufferedImage tmpBufferedImageOfMolecule = SwingFXUtils.fromFXImage(tmpMoleculeImage, null);
        Image tmpMolecule = this.getITextImage(tmpBufferedImageOfMolecule);
        tmpMoleculeStructureCell.addElement(tmpMolecule);
        tmpTable.addCell(tmpMoleculeStructureCell);
        PdfPCell tmpCellOfFragment = new PdfPCell(new Paragraph(Message.get("Exporter.itemsTab.pdfCellHeader.fragments"), this.fontFactory));
        tmpCellOfFragment.setHorizontalAlignment(Element.ALIGN_CENTER);
        tmpFragmentTable.addCell(tmpCellOfFragment);
        this.document.add(tmpTable);
        this.document.add(tmpFragmentTable);
        if (!tmpMoleculeDataModel.hasMoleculeUndergoneSpecificFragmentation(aFragmentationName)) {
            continue;
        }
        List<FragmentDataModel> tmpFragmentList = tmpMoleculeDataModel.getFragmentsOfSpecificAlgorithm(aFragmentationName);
        PdfPTable tmpFragmentationTable2 = new PdfPTable(3);
        for (int tmpFragmentNumber = 0; tmpFragmentNumber < tmpFragmentList.size(); ) {
            if (Thread.currentThread().isInterrupted()) {
                return null;
            }
            // magic number, see line 487 (loop below): "for (; tmpImagesNumbers < 3; tmpImagesNumbers++){"
            ArrayList<PdfPCell> tmpCell = new ArrayList<PdfPCell>(3);
            int tmpImagesNumbers = 0;
            for (; tmpImagesNumbers < 3; tmpImagesNumbers++) {
                if (Thread.currentThread().isInterrupted()) {
                    return null;
                }
                if (tmpFragmentNumber >= tmpFragmentList.size()) {
                    break;
                }
                FragmentDataModel tmpFragmentDatModel = tmpFragmentList.get(tmpFragmentNumber);
                IAtomContainer tmpFragmentStructure;
                try {
                    tmpFragmentStructure = tmpFragmentDatModel.getAtomContainer();
                } catch (CDKException anException) {
                    Exporter.LOGGER.getLogger(MoleculeDataModel.class.getName()).log(Level.SEVERE, anException.toString() + "_" + tmpFragmentDatModel.getName(), anException);
                    tmpFailedExportFragments.add(tmpFragmentDatModel.getUniqueSmiles());
                    continue;
                }
                if (!tmpMoleculeDataModel.hasMoleculeUndergoneSpecificFragmentation(aFragmentationName)) {
                    continue;
                }
                String tmpFrequency = tmpMoleculeDataModel.getFragmentFrequencyOfSpecificAlgorithm(aFragmentationName).get(tmpFragmentDatModel.getUniqueSmiles()).toString();
                javafx.scene.image.Image tmpFragmentImage = DepictionUtil.depictImageWithText(tmpFragmentStructure, 3.0, BasicDefinitions.DEFAULT_IMAGE_WIDTH_DEFAULT, BasicDefinitions.DEFAULT_IMAGE_HEIGHT_DEFAULT, tmpFrequency);
                BufferedImage tmpBufferedImageOfFragment = SwingFXUtils.fromFXImage(tmpFragmentImage, null);
                Image tmpFragment = this.getITextImage(tmpBufferedImageOfFragment);
                PdfPCell cell = new PdfPCell();
                cell.addElement(tmpFragment);
                tmpCell.add(cell);
                tmpFragmentNumber++;
            }
            for (int tmpCellIterator = 0; tmpCellIterator < 3; tmpCellIterator++) {
                if (Thread.currentThread().isInterrupted()) {
                    return null;
                }
                if (tmpCellIterator < tmpImagesNumbers) {
                    tmpFragmentationTable2.addCell(tmpCell.get(tmpCellIterator));
                } else {
                    tmpFragmentationTable2.addCell(new Paragraph(""));
                }
            }
        }
        this.document.add(tmpFragmentationTable2);
        this.document.newPage();
    }
    this.document.close();
    return tmpFailedExportFragments;
}