/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
* 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 .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
import jalview.datamodel.AlignmentI;
import java.io.File;
import org.junit.Test;
public class AnnotationFileIOTest
{
static String TestFiles[][] =
{
{ "Test example annotation import/export", "examples/uniref50.fa",
"examples/testdata/example_annot_file.jva" },
{ "Test multiple combine annotation statements import/export",
"examples/uniref50.fa",
"examples/testdata/test_combine_annot.jva" },
{
"Test multiple combine annotation statements with sequence_ref import/export",
"examples/uniref50.fa", "examples/testdata/uniref50_iupred.jva" },
{
"Test group only annotation file parsing results in parser indicating annotation was parsed",
"examples/uniref50.fa", "examples/testdata/test_grpannot.jva" } };
@Test
public void exampleAnnotationFileIO() throws Exception
{
for (String[] testPair:TestFiles)
{
testAnnotationFileIO(testPair[0], new File(testPair[1]), new File(testPair[2]));
}
}
public static AlignmentI readAlignmentFile(File f)
{
System.out.println("Reading file: " + f);
String ff = f.getPath();
try
{
FormatAdapter rf = new FormatAdapter();
AlignmentI al = rf.readFile(ff, AppletFormatAdapter.FILE,
new IdentifyFile().Identify(ff, AppletFormatAdapter.FILE));
// make sure dataset is initialised ? not sure about this
for (int i = 0; i < al.getSequencesArray().length; ++i)
{
al.getSequenceAt(i).setDatasetSequence(al.getSequenceAt(i).createDatasetSequence());
}
assertNotNull("Couldn't read supplied alignment data.", al);
return al;
} catch (Exception e)
{
e.printStackTrace();
}
fail("Couln't read the alignment in file '"+f.toString()+"'");
return null;
}
/**
* test alignment data in given file can be imported, exported and reimported
* with no dataloss
*
* @param f
* - source datafile (IdentifyFile.identify() should work with it)
* @param ioformat
* - label for IO class used to write and read back in the data from
* f
*/
public static void testAnnotationFileIO(String testname, File f, File annotFile)
{
System.out.println("Test: "+testname+"\nReading annotation file '"+annotFile+"' onto : " + f);
String af = annotFile.getPath();
try
{
AlignmentI al = readAlignmentFile(f);
assertTrue("Test "+testname+"\nAlignment was not annotated - annotation file not imported.",new AnnotationFile().readAnnotationFile(al, af, FormatAdapter.FILE));
String anfileout = new AnnotationFile().printAnnotations(al.getAlignmentAnnotation(), al.getGroups(), al.getProperties());
assertTrue("Test "+testname+"\nAlignment annotation file was not regenerated. Null string",anfileout!=null);
assertTrue("Test "+testname+"\nAlignment annotation file was not regenerated. Empty string",anfileout.length()>"JALVIEW_ANNOTATION".length());
System.out.println("Output annotation file:\n"+anfileout+"\n<