2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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19 package jalview.bin;
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21 import jalview.appletgui.AlignFrame;
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23 import jalview.datamodel.*;
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25 import jalview.io.*;
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27 import java.applet.*;
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30 import java.awt.event.*;
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31 import jalview.appletgui.TreePanel;
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35 * Jalview Applet. Runs in Java 1.18 runtime
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38 * @version $Revision$
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40 public class JalviewLite extends Applet
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42 static int lastFrameX = 200;
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43 static int lastFrameY = 200;
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44 boolean fileFound = true;
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45 String file = "No file";
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46 Button launcher = new Button("Start Jalview");
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48 AlignFrame currentAlignFrame;
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52 * init method for Jalview Applet
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59 String param = getParameter("RGB");
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65 r = Integer.parseInt(param.substring(0, 2), 16);
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66 g = Integer.parseInt(param.substring(2, 4), 16);
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67 b = Integer.parseInt(param.substring(4, 6), 16);
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69 catch (Exception ex)
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77 param = getParameter("label");
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79 launcher.setLabel(param);
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81 this.setBackground(new Color(r, g, b));
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84 param = getParameter("features");
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87 if(param.indexOf("://")==-1)
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88 param = getCodeBase() + param;
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90 final String featuresFile = param;
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92 file = getParameter("file");
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93 final JalviewLite applet = this;
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97 if(file.indexOf("://")==-1)
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98 file = getCodeBase() + file;
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100 launcher.addActionListener(new java.awt.event.ActionListener()
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102 public void actionPerformed(ActionEvent e)
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104 String format = jalview.io.IdentifyFile.Identify(file,
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106 LoadingThread loader = new LoadingThread(file,
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123 public static void main(String [] args)
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127 System.out.println("\nUsage: java -jar jalviewApplet.jar fileName\n");
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131 String format = jalview.io.IdentifyFile.Identify(args[0],"File");
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132 SequenceI[] sequences = new AppletFormatAdapter().readFile(args[0], "File", format);
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134 if ( (sequences != null) && (sequences.length > 0))
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136 AlignFrame af = new AlignFrame(new Alignment(sequences), null, args[0]);
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137 af.statusBar.setText("Successfully loaded file " + args[0]);
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143 * Initialises and displays a new java.awt.Frame
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145 * @param frame java.awt.Frame to be displayed
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146 * @param title title of new frame
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147 * @param width width if new frame
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148 * @param height height of new frame
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150 public static void addFrame(final Frame frame, String title, int width,
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153 frame.setLocation(lastFrameX, lastFrameY);
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156 frame.setSize(width, height);
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157 frame.setTitle(title);
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158 frame.addWindowListener(new WindowAdapter()
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160 public void windowClosing(WindowEvent e)
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167 frame.setVisible(true);
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170 public String getAlignment(String format)
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172 return getAlignment(format, "true");
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175 public String getAlignment(String format, String suffix)
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179 boolean seqlimits = suffix.equalsIgnoreCase("true");
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181 String reply = new AppletFormatAdapter().formatSequences(format,
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182 currentAlignFrame.viewport.getAlignment().getSequences(), seqlimits);
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185 catch (Exception ex)
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186 {ex.printStackTrace();
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187 return "Error retrieving alignment in " + format + " format. ";
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193 * This paints the background surrounding the "Launch Jalview button"
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195 * <br>If file given in parameter not found, displays error message
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197 * @param g graphics context
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199 public void paint(Graphics g)
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203 g.setColor(new Color(200, 200, 200));
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204 g.setColor(Color.cyan);
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205 g.fillRect(0, 0, getSize().width, getSize().height);
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206 g.setColor(Color.red);
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207 g.drawString("Jalview can't open file", 5, 15);
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208 g.drawString("\"" + file + "\"", 5, 30);
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212 class LoadingThread extends Thread
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217 String featuresFile;
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218 JalviewLite applet;
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220 public LoadingThread(String file,
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224 JalviewLite applet)
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227 this.protocol = protocol;
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228 this.format = format;
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229 featuresFile = features;
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230 this.applet = applet;
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235 SequenceI[] sequences = null;
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236 sequences = new AppletFormatAdapter().readFile(file, protocol, format);
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238 if ((sequences != null) && (sequences.length > 0))
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240 currentAlignFrame = new AlignFrame(new Alignment(sequences),
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242 currentAlignFrame.statusBar.setText("Successfully loaded file " + file);
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244 if(featuresFile!=null)
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245 currentAlignFrame.parseFeaturesFile(featuresFile);
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247 String treeFile = applet.getParameter("treeFile");
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248 if (treeFile != null)
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252 jalview.io.NewickFile fin = new jalview.io.NewickFile(applet.
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253 getCodeBase() + treeFile, "URL");
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256 if (fin.getTree() != null)
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258 TreePanel tp = null;
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259 tp = new TreePanel(currentAlignFrame.viewport,
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260 currentAlignFrame.viewport.getAlignment().getSequences(),
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261 fin, "FromFile", applet.getCodeBase() + treeFile);
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262 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
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263 currentAlignFrame.addTreeMenuItem(tp, treeFile);
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266 catch (Exception ex)
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268 ex.printStackTrace();
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273 String pdbfile = applet.getParameter("PDBFILE");
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276 if(pdbfile.indexOf("://")==-1)
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277 pdbfile = getCodeBase() + pdbfile;
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279 String sequence = applet.getParameter("PDBSEQ");
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283 new MCview.AppletPDBViewer(pdbfile, "URL",
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284 (Sequence)currentAlignFrame.getAlignViewport().getAlignment().findName(sequence),
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285 currentAlignFrame.getSeqcanvas());
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