org.openscience.cdk.applications.taverna.renderer.DrawPDF.java Source code

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Here is the source code for org.openscience.cdk.applications.taverna.renderer.DrawPDF.java

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/*
 * Copyright (C) 2010 by Andreas Truszkowski <ATruszkowski@gmx.de>
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public License
 * as published by the Free Software Foundation; either version 2.1
 * of the License, or (at your option) any later version.
 * All we ask is that proper credit is given for our work, which includes
 * - but is not limited to - adding the above copyright notice to the beginning
 * of your source code files, and to any copyright notice that you may distribute
 * with programs based on this work.
 * 
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU Lesser General Public License for more details.
 * 
 * You should have received a copy of the GNU Lesser General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 */
package org.openscience.cdk.applications.taverna.renderer;

import java.awt.Toolkit;
import java.awt.geom.Rectangle2D;
import java.awt.image.BufferedImage;
import java.io.File;
import java.io.FileOutputStream;
import java.util.List;
import java.util.Map.Entry;

import org.openscience.cdk.Reaction;
import org.openscience.cdk.geometry.GeometryTools;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IReaction;
import org.openscience.cdk.tools.manipulator.ReactionManipulator;
import org.openscience.jchempaint.renderer.BoundsCalculator;

import com.itextpdf.text.Document;
import com.itextpdf.text.Element;
import com.itextpdf.text.Font;
import com.itextpdf.text.FontFactory;
import com.itextpdf.text.Image;
import com.itextpdf.text.Paragraph;
import com.itextpdf.text.pdf.PdfPCell;
import com.itextpdf.text.pdf.PdfPTable;
import com.itextpdf.text.pdf.PdfWriter;

/**
 * Class for creating PDFs containing images of reactions or molecules.
 * 
 * @author Andreas Truszkowski
 * 
 */
@SuppressWarnings("unused")
// TODO
public class DrawPDF {
    private static int width = 300;
    private static int height = 300;
    private static double scale = 0.9;
    private static int ncol = 1;
    private static int nrow = 3;

    public static void drawMoleculesAsPDF(List<IAtomContainer> molecules, File file) throws Exception {
        Document pdf = new Document();
        PdfWriter writer = PdfWriter.getInstance(pdf, new FileOutputStream(file));
        pdf.open();
        Paragraph para = new Paragraph();
        Font font = FontFactory.getFont(FontFactory.HELVETICA, 24);
        para.setFont(font);
        para.setAlignment(Element.ALIGN_CENTER);
        para.add("CDK-Taverna 2.0");
        pdf.add(para);
        para = new Paragraph();
        font = FontFactory.getFont(FontFactory.HELVETICA, 12);
        para.setFont(font);
        para.setAlignment(Element.ALIGN_CENTER);
        para.add("The open-source chemo-/bioinformatics workflow solution\n\n\n");
        pdf.add(para);
        PdfPTable table = new PdfPTable(ncol);
        for (IAtomContainer molecule : molecules) {
            PdfPCell cell = new PdfPCell();
            cell.disableBorderSide(PdfPCell.BOTTOM | PdfPCell.LEFT | PdfPCell.RIGHT | PdfPCell.TOP);
            BufferedImage image = Draw2DStructure.drawMolecule(molecule, (int) pdf.getPageSize().getWidth(), height,
                    0.95);
            java.awt.Image awtImage = Toolkit.getDefaultToolkit().createImage(image.getSource());
            cell.addElement(Image.getInstance(awtImage, null));
            table.addCell(cell);
            cell = new PdfPCell();
            cell.disableBorderSide(PdfPCell.LEFT | PdfPCell.RIGHT | PdfPCell.TOP);
            para = new Paragraph();
            font = FontFactory.getFont(FontFactory.HELVETICA, 12);
            para.setFont(font);
            para.add("\n");
            for (Entry<Object, Object> entry : molecule.getProperties().entrySet()) {
                try {
                    String key = String.valueOf(entry.getKey());
                    String value = String.valueOf(entry.getValue());
                    para.add(key + ":\n" + value + "\n\n");
                } catch (Exception e) {
                    // Not a String entry --> skip
                }
            }
            cell.addElement(para);
            table.addCell(cell);
        }
        pdf.add(table);
        pdf.close();
    }

    public static void drawReactionAsPDF(List<Reaction> reactions, File file) throws Exception {
        Document pdf = new Document();
        PdfWriter writer = PdfWriter.getInstance(pdf, new FileOutputStream(file));
        pdf.open();
        PdfPTable table = new PdfPTable(1);
        int reactionWitdh = width * (reactions.get(0).getReactantCount() + reactions.get(0).getProductCount() + 1);
        if (reactionWitdh > width * 5) {
            reactionWitdh = width * 5;
        }
        for (IReaction reaction : reactions) {
            // shift the molecules not to overlap
            // TODO remove here
            Rectangle2D usedBounds = null;
            usedBounds = null;
            for (IAtomContainer container : ReactionManipulator.getAllAtomContainers(reaction)) {
                // now move it so that they don't overlap
                Rectangle2D bounds = BoundsCalculator.calculateBounds(container);
                if (usedBounds != null) {
                    double bondLength = GeometryTools.getBondLengthAverage(container);
                    Rectangle2D shiftedBounds = GeometryTools.shiftContainer(container, bounds, usedBounds,
                            bondLength);
                    usedBounds = usedBounds.createUnion(shiftedBounds);
                } else {
                    usedBounds = bounds;
                }
            }
            PdfPCell cell = new PdfPCell();
            BufferedImage image = Draw2DStructure.drawReaction(reaction, reactionWitdh, height);
            java.awt.Image awtImage = Toolkit.getDefaultToolkit().createImage(image.getSource());
            cell.addElement(Image.getInstance(awtImage, null));
            table.addCell(cell);
        }
        pdf.add(table);
        pdf.close();
    }
}