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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34 * Jalview Applet. Runs in Java 1.18 runtime
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37 * @version $Revision$
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39 public class JalviewLite extends Applet
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41 static int lastFrameX = 200;
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42 static int lastFrameY = 200;
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43 static Applet applet;
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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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49 * init method for Jalview Applet
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58 String param = getParameter("RGB");
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64 r = Integer.parseInt(param.substring(0, 2), 16);
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65 g = Integer.parseInt(param.substring(2, 4), 16);
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66 b = Integer.parseInt(param.substring(4, 6), 16);
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68 catch (Exception ex)
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76 this.setBackground(new Color(r, g, b));
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78 file = getParameter("file");
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83 file = applet.getCodeBase() + file;
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84 launcher.addActionListener(new java.awt.event.ActionListener()
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86 public void actionPerformed(ActionEvent e)
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88 String format = jalview.io.IdentifyFile.Identify(file,
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90 LoadFile(file, "URL", format);
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102 * Displays the given URL in a new browser window
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104 * @param url URL to display in browser window.
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105 * <br>New window will be named "HELP_WINDOW"
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107 public static void showURL(String url)
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109 showURL(url, "HELP");
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112 public static void showURL(String url, String target)
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116 applet.getAppletContext().showDocument(new java.net.URL(url),
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119 catch (Exception ex)
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121 ex.printStackTrace();
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127 * Starts a new LoadingThread for loading an alignment file
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129 * @param file file name including full path to file
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130 * @param protocol file or URL or paste
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131 * @param format Fasta, Clustal, PFAM, MSF, PIR, BLC, Jalview
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133 public void LoadFile(String file, String protocol, String format)
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135 LoadingThread loader = new LoadingThread(file, protocol, format, this);
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140 * Initialises and displays a new java.awt.Frame
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142 * @param frame java.awt.Frame to be displayed
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143 * @param title title of new frame
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144 * @param width width if new frame
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145 * @param height height of new frame
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147 public static void addFrame(final Frame frame, String title, int width,
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150 frame.setLocation(lastFrameX, lastFrameY);
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153 frame.setSize(width, height);
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154 frame.setTitle(title);
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155 frame.addWindowListener(new WindowAdapter()
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157 public void windowClosing(WindowEvent e)
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162 frame.setVisible(true);
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166 * This paints the background surrounding the "Launch Jalview button"
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168 * <br>If file given in parameter not found, displays error message
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170 * @param g graphics context
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172 public void paint(Graphics g)
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176 g.setColor(new Color(200, 200, 200));
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177 g.setColor(Color.cyan);
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178 g.fillRect(0, 0, getSize().width, getSize().height);
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179 g.setColor(Color.red);
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180 g.drawString("Jalview can't open file", 5, 15);
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181 g.drawString("\"" + file + "\"", 5, 30);
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185 class LoadingThread extends Thread
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190 JalviewLite jlapplet;
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192 public LoadingThread(String file, String protocol, String format,
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193 JalviewLite applet)
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196 this.protocol = protocol;
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197 this.format = format;
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198 this.jlapplet = applet;
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203 SequenceI[] sequences = null;
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204 sequences = FormatAdapter.readFile(file, protocol, format);
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206 if ((sequences != null) && (sequences.length > 0))
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208 AlignFrame af = new AlignFrame(new Alignment(sequences),
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210 addFrame(af, file, AlignFrame.NEW_WINDOW_WIDTH,
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211 AlignFrame.NEW_WINDOW_HEIGHT);
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212 af.statusBar.setText("Successfully loaded file " + file);
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