2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.datamodel.AlignmentI;
24 import jalview.io.AppletFormatAdapter;
25 import jalview.io.DataSourceType;
26 import jalview.io.FileFormat;
27 import jalview.io.FileFormatI;
28 import jalview.io.FileParse;
29 import jalview.io.IdentifyFile;
31 import java.applet.Applet;
32 import java.io.InputStream;
34 public class JalviewLiteURLRetrieve extends Applet
37 private static final long serialVersionUID = 1L;
40 * This is the default constructor
42 public JalviewLiteURLRetrieve()
48 * This method initializes this
55 this.setSize(300, 200);
56 String file = getParameter("file");
60 .println("Specify a resource to read on the file parameter");
63 DataSourceType protocol = null;
66 System.out.println("Loading thread started with:\n>>file\n" + file
68 // This might throw a security exception in certain browsers
69 // Netscape Communicator for instance.
73 InputStream is = getClass().getResourceAsStream("/" + file);
79 System.err.println("Resource '" + file + "' was "
80 + (rtn ? "" : "not") + " located by classloader.");
83 protocol = DataSourceType.CLASSLOADER;
86 } catch (Exception ex)
88 System.out.println("Exception checking resources: " + file + " "
91 if (file.indexOf("://") > -1)
93 protocol = DataSourceType.URL;
97 // skipping codebase prepend check.
98 protocol = DataSourceType.FILE;
101 System.out.println("Trying to get contents of resource:");
102 FileParse fp = new FileParse(file, protocol);
106 while ((ln = fp.nextLine()) != null)
108 System.out.print(ln);
114 System.out.println("Resource at " + file
115 + " cannot be read with protocol==" + protocol);
118 FileFormatI format = FileFormat.valueOf(getParameter("format"));
121 format = new IdentifyFile().identify(file, protocol);
122 System.out.println("Format is " + format);
126 System.out.println("User specified Format is " + format);
128 AlignmentI al = null;
131 al = new AppletFormatAdapter().readFile(file, protocol, format);
132 } catch (java.io.IOException ex)
134 System.err.println("Failed to open the file.");
135 ex.printStackTrace();
139 System.out.println(new AppletFormatAdapter().formatSequences(
140 FileFormat.Fasta, al, false));
142 } catch (Exception e)
144 System.err.println("bailing out : Unexpected exception:");