2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
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
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import static org.junit.Assert.assertNotNull;
24 import static org.junit.Assert.assertTrue;
25 import static org.junit.Assert.fail;
26 import jalview.datamodel.AlignmentI;
30 import org.junit.Test;
32 public class AnnotationFileIOTest
35 static String TestFiles[][] =
37 { "Test example annotation import/export", "examples/uniref50.fa",
38 "examples/testdata/example_annot_file.jva" },
39 { "Test multiple combine annotation statements import/export",
40 "examples/uniref50.fa",
41 "examples/testdata/test_combine_annot.jva" },
43 "Test multiple combine annotation statements with sequence_ref import/export",
44 "examples/uniref50.fa", "examples/testdata/uniref50_iupred.jva" },
46 "Test group only annotation file parsing results in parser indicating annotation was parsed",
47 "examples/uniref50.fa", "examples/testdata/test_grpannot.jva" } };
50 public void exampleAnnotationFileIO() throws Exception
52 for (String[] testPair : TestFiles)
54 testAnnotationFileIO(testPair[0], new File(testPair[1]), new File(
59 public static AlignmentI readAlignmentFile(File f)
61 System.out.println("Reading file: " + f);
62 String ff = f.getPath();
65 FormatAdapter rf = new FormatAdapter();
67 AlignmentI al = rf.readFile(ff, AppletFormatAdapter.FILE,
68 new IdentifyFile().Identify(ff, AppletFormatAdapter.FILE));
70 // make sure dataset is initialised ? not sure about this
71 for (int i = 0; i < al.getSequencesArray().length; ++i)
73 al.getSequenceAt(i).setDatasetSequence(
74 al.getSequenceAt(i).createDatasetSequence());
76 assertNotNull("Couldn't read supplied alignment data.", al);
82 fail("Couln't read the alignment in file '" + f.toString() + "'");
87 * test alignment data in given file can be imported, exported and reimported
91 * - source datafile (IdentifyFile.identify() should work with it)
93 * - label for IO class used to write and read back in the data from
96 public static void testAnnotationFileIO(String testname, File f,
99 System.out.println("Test: " + testname + "\nReading annotation file '"
100 + annotFile + "' onto : " + f);
101 String af = annotFile.getPath();
104 AlignmentI al = readAlignmentFile(f);
109 + "\nAlignment was not annotated - annotation file not imported.",
110 new AnnotationFile().readAnnotationFile(al, af,
111 FormatAdapter.FILE));
113 String anfileout = new AnnotationFile().printAnnotations(
114 al.getAlignmentAnnotation(), al.getGroups(),
119 + "\nAlignment annotation file was not regenerated. Null string",
124 + "\nAlignment annotation file was not regenerated. Empty string",
125 anfileout.length() > "JALVIEW_ANNOTATION".length());
127 System.out.println("Output annotation file:\n" + anfileout
130 AlignmentI al_new = readAlignmentFile(f);
134 + "\nregenerated annotation file did not annotate alignment.",
135 new AnnotationFile().readAnnotationFile(al_new, anfileout,
136 FormatAdapter.PASTE));
138 // test for consistency in io
139 StockholmFileTest.testAlignmentEquivalence(al, al_new);
141 } catch (Exception e)
147 + "\nCouldn't complete Annotation file roundtrip input/output/input test for '"