Java tutorial
/* PDFWriter.java * Author: Nina Jeliazkova * Date: Feb 2, 2008 * Revision: 0.1 * * Copyright (C) 2005-2008 Nina Jeliazkova * * Contact: nina@acad.bg * * 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., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. * */ package ambit.io; import java.awt.Color; import java.awt.Dimension; import java.awt.image.BufferedImage; import java.io.IOException; import java.io.OutputStream; import java.io.Writer; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.interfaces.IChemFile; import org.openscience.cdk.interfaces.IChemObject; import org.openscience.cdk.interfaces.IMolecule; import org.openscience.cdk.interfaces.ISetOfMolecules; import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.tools.DataFeatures; import ambit.ui.data.CompoundImageTools; import com.lowagie.text.Document; import com.lowagie.text.Image; import com.lowagie.text.PageSize; import com.lowagie.text.Paragraph; import com.lowagie.text.pdf.PdfPCell; import com.lowagie.text.pdf.PdfPTable; import com.lowagie.text.pdf.PdfWriter; /** * Exporting set of structures as PDF file. * @author Nina Jeliazkova nina@acad.bg * <b>Modified</b> Feb 2, 2008 */ public class PDFWriter extends FileWithHeaderWriter { protected Document pdfDoc = null; protected PdfWriter pdfWriter; protected PdfPTable table; protected CompoundImageTools imageTools; protected Dimension cell = new Dimension(200, 200); /** * */ public PDFWriter(OutputStream outputStream) throws CDKException { super(); setWriter(outputStream); imageTools = new CompoundImageTools(cell); } /* (non-Javadoc) * @see org.openscience.cdk.io.IChemObjectWriter#setWriter(java.io.Writer) */ public void setWriter(Writer arg0) throws CDKException { throw new CDKException("Not supported!"); } /* (non-Javadoc) * @see org.openscience.cdk.io.IChemObjectWriter#setWriter(java.io.OutputStream) */ public void setWriter(OutputStream out) throws CDKException { pdfDoc = new Document(PageSize.A4, 80, 50, 30, 65); try { pdfWriter = PdfWriter.getInstance(pdfDoc, out); //writer.setViewerPreferences(PdfWriter.HideMenubar| PdfWriter.HideToolbar); pdfWriter.setViewerPreferences(PdfWriter.PageModeUseThumbs | PdfWriter.PageModeUseOutlines); pdfDoc.addCreationDate(); pdfDoc.addCreator(getClass().getName()); pdfDoc.addKeywords("structures"); pdfDoc.addTitle("structures"); pdfDoc.addSubject(""); pdfDoc.addAuthor("AMBIT"); pdfDoc.open(); /* pdfDoc.add(new Paragraph(method.getTitle())); pdfDoc.add(new Paragraph(method.getExplanation())); pdfDoc.add(new Paragraph()); */ table = new PdfPTable(new float[] { 3f, 5f }); table.setWidthPercentage(100); } catch (Exception x) { throw new CDKException(x.getMessage()); } } /* (non-Javadoc) * @see org.openscience.cdk.io.IChemObjectWriter#write(org.openscience.cdk.interfaces.IChemObject) */ public void write(IChemObject object) throws CDKException { if (object instanceof ISetOfMolecules) { writeSetOfMolecules((ISetOfMolecules) object); } else if (object instanceof IMolecule) { writeMolecule((IMolecule) object); } else { throw new CDKException("Only supported is writing of ChemFile and Molecule objects."); } } /* (non-Javadoc) * @see org.openscience.cdk.io.IChemObjectIO#accepts(java.lang.Class) */ public boolean accepts(Class classObject) { Class[] interfaces = classObject.getInterfaces(); for (int i = 0; i < interfaces.length; i++) { if (IChemFile.class.equals(interfaces[i])) return true; if (ISetOfMolecules.class.equals(interfaces[i])) return true; } return false; } public int getSupportedDataFeatures() { return DataFeatures.HAS_GRAPH_REPRESENTATION; } /* (non-Javadoc) * @see org.openscience.cdk.io.IChemObjectIO#close() */ public void close() throws IOException { try { pdfDoc.add(table); } catch (Exception x) { x.printStackTrace(); } pdfDoc.close(); } /* (non-Javadoc) * @see org.openscience.cdk.io.IChemObjectIO#getFormat() */ public IResourceFormat getFormat() { // TODO Auto-generated method stub return null; } @Override protected void writeHeader() throws IOException { PdfPCell cell = new PdfPCell(new Paragraph("Structure")); cell.setBackgroundColor(Color.white); table.addCell(cell); cell = new PdfPCell(new Paragraph("Properties")); cell.setBackgroundColor(Color.white); table.addCell(cell); } public void writeSetOfMolecules(ISetOfMolecules som) { for (int i = 0; i < som.getMoleculeCount(); i++) { try { writeMolecule(som.getMolecule(i)); } catch (Exception exc) { } } } public void writeMolecule(IMolecule molecule) { Object value; try { //give it a chance to create a header just before the first write if (!writingStarted) { if (header == null) setHeader(molecule.getProperties()); writeHeader(); writingStarted = true; } Paragraph p = new Paragraph(""); String s; for (int i = 0; i < header.size(); i++) { StringBuffer b = new StringBuffer(); b.append(header.getList().get(i)); b.append(" = "); value = molecule.getProperty(header.getList().get(i)); if (i == smilesIndex) { if (value == null) //no SMILES available try { value = ""; //sg.createSMILES(molecule); } catch (Exception x) { logger.error("Error while createSMILES\t", x.getMessage()); value = ""; } } if (value != null) { if (value instanceof Number) { s = value.toString(); } else { s = value.toString(); } b.append(s); p.add(new Paragraph(b.toString())); } } BufferedImage image = imageTools.getImage(molecule); image.flush(); Image png_struc = Image.getInstance(image, Color.white); png_struc.setAlignment(Image.LEFT); png_struc.scalePercent(100); PdfPCell cell = new PdfPCell(); cell.setMinimumHeight(cell.height()); cell.addElement(png_struc); table.addCell(cell); cell = new PdfPCell(p); cell.setBackgroundColor(Color.white); table.addCell(cell); } catch (Exception x) { logger.error("ERROR while writing Molecule: ", x.getMessage()); logger.debug(x); x.printStackTrace(); } } }