-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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.
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
public static void tearDownAfterClass() throws Exception
{
}
+ // TODO: make a better/more comprehensive test harness for identify/io
+
final static File ALIGN_FILE = new File("test/jalview/io/test_gz_fasta.gz");
final static File NOTGZALIGN_FILE = new File("test/jalview/io/test_gz_fasta_notgz.gz");
+ final static File STARS_FA_FILE1 = new File("test/jalview/io/test_fasta_stars.fa");
+ final static File STARS_FA_FILE2 = new File("test/jalview/io/test_fasta_stars2.fa");
- private void assertValidFasta(String src, FileParse fp)
+ private void assertValidFormat(String fmt, String src, FileParse fp)
{
assertTrue("Couldn't resolve "+src+" as a valid file",fp.isValid());
String type = new IdentifyFile().Identify(fp);
- assertTrue("Gzipped data from '"+src+"' identified as '"+type+"'",type.equalsIgnoreCase("FASTA"));
+ assertTrue("Data from '"+src+"' Expected to be '"+fmt+"' identified as '"+type+"'",type.equalsIgnoreCase(fmt));
+ }
+ @Test
+ public void testStarsInFasta1() throws IOException
+ {
+ String uri;
+ FileParse fp = new FileParse(uri=STARS_FA_FILE1.getAbsoluteFile().toString(),AppletFormatAdapter.FILE);
+ assertValidFormat("FASTA", uri, fp);
+ }
+ @Test
+ public void testStarsInFasta2() throws IOException
+ {
+ String uri;
+ FileParse fp = new FileParse(uri=STARS_FA_FILE2.getAbsoluteFile().toString(),AppletFormatAdapter.FILE);
+ assertValidFormat("FASTA", uri, fp);
}
@Test
public void testGzipIo() throws IOException
{
String uri;
FileParse fp = new FileParse(uri=ALIGN_FILE.getAbsoluteFile().toURI().toString(),AppletFormatAdapter.URL);
- assertValidFasta(uri, fp);
+ assertValidFormat("FASTA", uri, fp);
}
@Test
{
String filepath;
FileParse fp = new FileParse(filepath=ALIGN_FILE.getAbsoluteFile().toString(), AppletFormatAdapter.FILE);
- assertValidFasta(filepath, fp);
+ assertValidFormat("FASTA",filepath, fp);
}
@Test
public void testNonGzipURLIO() throws IOException
{
String uri;
FileParse fp = new FileParse(uri=NOTGZALIGN_FILE.getAbsoluteFile().toURI().toString(),AppletFormatAdapter.URL);
- assertValidFasta(uri, fp);
+ assertValidFormat("FASTA",uri, fp);
}
@Test
public void testNonGziplocalFileIO() throws IOException
{
String filepath;
FileParse fp = new FileParse(filepath=NOTGZALIGN_FILE.getAbsoluteFile().toString(), AppletFormatAdapter.FILE);
- assertValidFasta(filepath, fp);
+ assertValidFormat("FASTA",filepath, fp);
}
}