/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview 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 General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.bin;
-import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
import jalview.io.AppletFormatAdapter;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
import jalview.io.FileParse;
+import jalview.io.IdentifyFile;
import java.applet.Applet;
import java.io.InputStream;
*
* @return void
*/
+ @Override
public void init()
{
this.setSize(300, 200);
.println("Specify a resource to read on the file parameter");
return;
}
- String protocol = null;
+ DataSourceType protocol = null;
try
{
System.out.println("Loading thread started with:\n>>file\n" + file
+ (rtn ? "" : "not") + " located by classloader.");
if (rtn)
{
- protocol = AppletFormatAdapter.CLASSLOADER;
+ protocol = DataSourceType.CLASSLOADER;
}
} catch (Exception ex)
{
- System.out.println("Exception checking resources: " + file + " "
- + ex);
+ System.out.println(
+ "Exception checking resources: " + file + " " + ex);
}
if (file.indexOf("://") > -1)
{
- protocol = AppletFormatAdapter.URL;
+ protocol = DataSourceType.URL;
}
else
{
// skipping codebase prepend check.
- protocol = AppletFormatAdapter.FILE;
+ protocol = DataSourceType.FILE;
}
System.out.println("Trying to get contents of resource:");
+ " cannot be read with protocol==" + protocol);
return;
}
- String format = getParameter("format");
- if (format == null || format.length() == 0)
+ FileFormatI format = FileFormats.getInstance()
+ .forName(getParameter("format"));
+ if (format == null)
{
- format = new jalview.io.IdentifyFile().Identify(file, protocol);
+ format = new IdentifyFile().identify(file, protocol);
System.out.println("Format is " + format);
}
else
{
System.out.println("User specified Format is " + format);
}
- Alignment al = null;
+ AlignmentI al = null;
try
{
al = new AppletFormatAdapter().readFile(file, protocol, format);
}
if (al != null)
{
- System.out.println(new AppletFormatAdapter().formatSequences(
- "FASTA", al, false));
+ System.out.println(new AppletFormatAdapter()
+ .formatSequences(FileFormat.Fasta, al, false));
}
} catch (Exception e)
{