File contents

import java.awt.Color;
import java.awt.Dimension;
import java.awt.Font;
import java.awt.Graphics2D;
import java.awt.geom.Point2D;
import java.awt.geom.Rectangle2D;
import java.awt.image.BufferedImage;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;

import javax.imageio.ImageIO;
import javax.swing.JFrame;

import metabolic.MolFigure;
import canvas.AbstractComponent;
import canvas.DrawPane;
import canvas.LineStroke;
import canvas.View;
import draw2d.MOLformat;
import draw2d.SmilesFormat;

public class MolPanel extends DrawPane
	{
		MolFigure mf = null;

		public MolPanel()
			{
				super(null, null);
			}

		/**
		 * Read a SMILES format into this molecular panel.
		 * 
		 * @param id
		 *          ... String id for the molecule data. This
		 *          value can be null.
		 * @param smiles
		 *          ... SMILES description of the molecule
		 */
		public void read(String id, String smiles)
			{
				SmilesFormat sf = new SmilesFormat(smiles);
				init(id, sf.toMOLformat());
			}

		/**
		 * Read a MOL format into this molecular panel.
		 * 
		 * @param id
		 *          ... String id for the molecule data. This
		 *          value can be null.
		 * @param smiles
		 *          ... MOL description of the molecule
		 */
		public void read(String id, MOLformat mol)
			{
				init(id, mol);
			}

		private void init(String id, MOLformat mol)
			{
				mf = new MolFigure(id, mol);
				mf
						.initialization(this, new Point2D.Float(0, 0),
								20);
				mf.setRectBound();
				newDraw(id, true);
				getLayer().addNew(mf, new Point2D.Float(5, 5), 0);
				Dimension d = getPictureSize();
				setPaperSize(d);
				super.repaint();
			}

		static private void printHelp()
			{
				System.out
						.println("java -jar MolFigure.jar [options] [MOL files (.mol)]");
				System.out.println("OPTIONS");
				System.out
						.println(" -z  ... specify size (e.g. -s 200)");
				System.out
						.println(" -s  ... specify scale (5-50, default is 15)");
				System.out
						.println(" -f  ... specify fontsize (default is 7)");
				System.out
						.println(" -l  ... specify line width (1-7, default is 1)");
				System.out
						.println(" -o  ... specify output directory");
				System.out
						.println(" -p  ... output PNG format instead of JPG");
				System.out.println(" -h  ... this help");
			}

		/**
		 * convert from the array of MOL filenames into JPG
		 * pictures
		 * 
		 * @param args
		 */
		static public void convertToJPGformat(String[] args)
			{
				searchPane.ViewerOptions drawOptions = new searchPane.ViewerOptions();
				DrawPane canvas = new DrawPane(null, null);

				String ext = "jpg";
				// Set molecular scaling. 5 is the smallest, 50 is
				// the largest
				float scale = 15;
				// This String value is the name of output directory
				String dir = "";
				int size = 0;
				int argi = 0;
				Font F = null;
				LineStroke ls = null;
				while ((argi < args.length)
						&& args[argi].startsWith("-"))
					{
						try
							{
								if (args[argi].length() < 2)
									throw new Exception("");
								else
									{
										if (args[argi].equals("-z"))
											{// size
												size = (int) Float
														.parseFloat(args[++argi]);
												argi++;
											}
										else if (args[argi].equals("-p"))
											{// output png
												ext = "png";
												argi++;
											}
										else if (args[argi].equals("-s"))
											{// scale
												scale = Float
														.parseFloat(args[++argi]);
												argi++;
											}
										else if (args[argi].equals("-o"))
											{// scale
												dir = args[++argi];
												argi++;
											}
										else if (args[argi].equals("-l"))
											{// linestroke
												int f = (int) Float
														.parseFloat(args[++argi]);
												if (f <= 0)
													f = 1;
												if (f > 7)
													f = 7;
												ls = LineStroke.getStroke(f, 0);
												argi++;
											}
										else if (args[argi].equals("-f"))
											{// output png
												int f = (int) Float
														.parseFloat(args[++argi]);
												F = new Font("Dialog", Font.PLAIN,
														f);
												argi++;
											}
										else
											throw new Exception("");
									}
							}
						catch (Exception e)
							{
								printHelp();
								System.exit(0);
							}
					}

				AbstractComponent.setDefaultTo(null, null, ls,
						null, F);
				for (int i = argi; i < args.length; i++)
					{
						try
							{
								draw2d.MOLformat mf = new draw2d.MOLformat();
								java.io.BufferedReader br = new java.io.BufferedReader(
										new FileReader(args[i]));
								mf.read(br);
								// Generate MolFigure from the filenames
								MolFigure mF = new MolFigure(args[i], mf);
								// Set the location of this figure at (0,0)
								mF.initialization(canvas,
										new Point2D.Float(0, 0), scale);
								// Set the picture size (different from scale)
								if (size != 0)
									mF.setRectBound(size, size);
								else
									mF.setRectBound();
								BufferedImage img;
								Graphics2D g;
								// Determine the image size
								Rectangle2D.Float R = mF.getBoundingBox();
								if (ext.equals("jpg"))
									{
										img = new BufferedImage((int) R.width,
												(int) R.height,
												BufferedImage.TYPE_INT_RGB);
										g = (Graphics2D) img.getGraphics();
										g.setColor(Color.white);
										g.fillRect(0, 0, (int) R.width,
												(int) R.height);
									}
								else
									{
										img = new BufferedImage((int) R.width,
												(int) R.height,
												BufferedImage.TYPE_INT_ARGB);
										g = (Graphics2D) img.getGraphics();
									}
								g.setRenderingHints(drawOptions
										.getRenderingHints());
								mF.draw(g, false);
								
								// Generate the output filename
								int slashPos = Math.max(0, args[i]
										.lastIndexOf("/") + 1);
								int suffxPos = Math.min(args[i]
										.lastIndexOf("."), args[i].length());
								String fname = args[i].substring(slashPos,
										suffxPos);
								// Inscribe filename into the picture
								// g.drawString(fname, 10, R.height - 10);
								fname = (dir.equals("") ? "" : (dir + "/"))
										+ fname + "." + ext;
								ImageIO.write(img, ext, new File(fname));
								g.dispose();
								System.out.println(fname);
							}
						catch (Exception e)
							{
								System.out.println("in processing file "
										+ args[i]);
								e.printStackTrace();
							}
					}
			}

		static public void main(String[] args)
			{
				util.MolMass.init();
				try
					{
						draw2d.MOLformat mf = new draw2d.MOLformat();
						java.io.BufferedReader br = new java.io.BufferedReader(
								new FileReader(args[0]));
						mf.read(br);
						
						 View.PreviewFrame f = new
						 View.PreviewFrame(); f.read("foo", new
						 MolFigure("foo", mf)); f.pack();
						 f.setVisible(true);

						 // If you want to use the standard JPanel to display
						 // a structure, use the following code instead.
						 
//						JFrame jf = new JFrame();
//						MolPanel mp = new MolPanel();
//						mp.prepareMenusForPopups();
//						mp.read("foo", mf);
//						jf.getContentPane().add(mp);
//						jf.pack();
//						jf.setVisible(true);
					}
				catch (IOException e)
					{
						e.printStackTrace();
					}
			}
	}