/*
* 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.
*
* 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.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertTrue;
import java.awt.Color;
import java.io.File;
import java.util.Hashtable;
import java.util.List;
import org.testng.Assert;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SequenceGroup;
import jalview.gui.AlignFrame;
import jalview.gui.JvOptionPane;
import jalview.io.AnnotationFile.ViewDef;
public class AnnotationFileIOTest
{
@BeforeClass(alwaysRun = true)
public void setUpJvOptionPane()
{
JvOptionPane.setInteractiveMode(false);
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
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 hiding/showing of insertions on sequence_ref",
"examples/uniref50.fa",
"examples/testdata/uniref50_seqref.jva" } };
@Test(groups = { "Functional" })
public void exampleAnnotationFileIO() throws Exception
{
for (String[] testPair : TestFiles)
{
testAnnotationFileIO(testPair[0], new File(testPair[1]),
new File(testPair[2]));
}
}
protected AlignmentI readAlignmentFile(File f)
{
System.out.println("Reading file: " + f);
String ff = f.getPath();
try
{
FormatAdapter rf = new FormatAdapter();
AlignmentI al = rf.readFile(ff, DataSourceType.FILE,
new IdentifyFile().identify(ff, DataSourceType.FILE));
// make sure dataset is initialised ? not sure about this
for (int i = 0; i < al.getSequencesArray().length; ++i)
{
al.getSequenceAt(i).createDatasetSequence();
}
assertNotNull("Couldn't read supplied alignment data.", al);
return al;
} catch (Exception e)
{
e.printStackTrace();
}
Assert.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
*/
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);
HiddenColumns cs = new HiddenColumns();
assertTrue("Test " + testname
+ "\nAlignment was not annotated - annotation file not imported.",
new AnnotationFile().readAnnotationFile(al, cs, af,
DataSourceType.FILE));
AnnotationFile aff = new AnnotationFile();
// ViewDef is not used by Jalview
ViewDef v = aff.new ViewDef(null, al.getHiddenSequences(), cs,
new Hashtable());
String anfileout = new AnnotationFile().printAnnotations(
al.getAlignmentAnnotation(), al.getGroups(),
al.getProperties(), null, al, v);
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<Seq1\nQRSIL\n>Seq2\nFTHND\n>Seq3\nRPVSL\n",
DataSourceType.PASTE);
long t2 = System.currentTimeMillis();
System.err.println("t0: " + (t2 - t1));
// seq1 and seq3 are in distinct groups both named Group1
String annotationFile = "JALVIEW_ANNOTATION\nSEQUENCE_GROUP\tGroup1\t*\t*\t1\n"
+ "SEQUENCE_GROUP\tGroup2\t*\t*\t2\n"
+ "SEQUENCE_GROUP\tGroup1\t*\t*\t3\n"
+ "PROPERTIES\tGroup1\toutlineColour=blue\tidColour=red\n";
new AnnotationFile().annotateAlignmentView(af.getViewport(),
annotationFile, DataSourceType.PASTE);
AlignmentI al = af.getViewport().getAlignment();
List groups = al.getGroups();
assertEquals(3, groups.size());
SequenceGroup sg = groups.get(0);
assertEquals("Group1", sg.getName());
assertTrue(sg.contains(al.getSequenceAt(0)));
assertEquals(Color.BLUE, sg.getOutlineColour());
assertEquals(Color.RED, sg.getIdColour());
sg = groups.get(1);
assertEquals("Group2", sg.getName());
assertTrue(sg.contains(al.getSequenceAt(1)));
/*
* the bug fix: a second group of the same name is also given properties
*/
sg = groups.get(2);
assertEquals("Group1", sg.getName());
assertTrue(sg.contains(al.getSequenceAt(2)));
assertEquals(Color.BLUE, sg.getOutlineColour());
assertEquals(Color.RED, sg.getIdColour());
}
}