2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
3 * Copyright (C) 2014 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 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
17 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 import static org.junit.Assert.assertNotNull;
22 import static org.junit.Assert.assertTrue;
23 import static org.junit.Assert.fail;
24 import jalview.datamodel.AlignmentI;
28 import org.junit.Test;
30 public class AnnotationFileIOTest
33 static String TestFiles[][] =
35 { "Test example annotation import/export", "examples/uniref50.fa",
36 "examples/testdata/example_annot_file.jva" },
37 { "Test multiple combine annotation statements import/export",
38 "examples/uniref50.fa",
39 "examples/testdata/test_combine_annot.jva" },
41 "Test multiple combine annotation statements with sequence_ref import/export",
42 "examples/uniref50.fa", "examples/testdata/uniref50_iupred.jva" },
44 "Test group only annotation file parsing results in parser indicating annotation was parsed",
45 "examples/uniref50.fa", "examples/testdata/test_grpannot.jva" } };
48 public void exampleAnnotationFileIO() throws Exception
50 for (String[] testPair:TestFiles)
52 testAnnotationFileIO(testPair[0], new File(testPair[1]), new File(testPair[2]));
56 public static AlignmentI readAlignmentFile(File f)
58 System.out.println("Reading file: " + f);
59 String ff = f.getPath();
62 FormatAdapter rf = new FormatAdapter();
64 AlignmentI al = rf.readFile(ff, AppletFormatAdapter.FILE,
65 new IdentifyFile().Identify(ff, AppletFormatAdapter.FILE));
67 // make sure dataset is initialised ? not sure about this
68 for (int i = 0; i < al.getSequencesArray().length; ++i)
70 al.getSequenceAt(i).setDatasetSequence(al.getSequenceAt(i).createDatasetSequence());
72 assertNotNull("Couldn't read supplied alignment data.", al);
78 fail("Couln't read the alignment in file '"+f.toString()+"'");
82 * test alignment data in given file can be imported, exported and reimported
86 * - source datafile (IdentifyFile.identify() should work with it)
88 * - label for IO class used to write and read back in the data from
91 public static void testAnnotationFileIO(String testname, File f, File annotFile)
93 System.out.println("Test: "+testname+"\nReading annotation file '"+annotFile+"' onto : " + f);
94 String af = annotFile.getPath();
97 AlignmentI al = readAlignmentFile(f);
99 assertTrue("Test "+testname+"\nAlignment was not annotated - annotation file not imported.",new AnnotationFile().readAnnotationFile(al, af, FormatAdapter.FILE));
101 String anfileout = new AnnotationFile().printAnnotations(al.getAlignmentAnnotation(), al.getGroups(), al.getProperties());
102 assertTrue("Test "+testname+"\nAlignment annotation file was not regenerated. Null string",anfileout!=null);
103 assertTrue("Test "+testname+"\nAlignment annotation file was not regenerated. Empty string",anfileout.length()>"JALVIEW_ANNOTATION".length());
105 System.out.println("Output annotation file:\n"+anfileout+"\n<<EOF\n");
107 AlignmentI al_new = readAlignmentFile(f);
108 assertTrue("Test "+testname+"\nregenerated annotation file did not annotate alignment.",new AnnotationFile().readAnnotationFile(al_new, anfileout, FormatAdapter.PASTE));
110 // test for consistency in io
111 StockholmFileTest.testAlignmentEquivalence(al, al_new);
113 } catch (Exception e)
117 fail("Test "+testname+"\nCouldn't complete Annotation file roundtrip input/output/input test for '"+annotFile+"'.");