2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ 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.testng.AssertJUnit.assertNotNull;
24 import static org.testng.AssertJUnit.assertTrue;
26 import jalview.datamodel.AlignmentI;
27 import jalview.datamodel.ColumnSelection;
28 import jalview.io.AnnotationFile.ViewDef;
31 import java.util.Hashtable;
33 import org.testng.Assert;
34 import org.testng.annotations.Test;
36 public class AnnotationFileIOTest
39 static String TestFiles[][] =
41 { "Test example annotation import/export", "examples/uniref50.fa",
42 "examples/testdata/example_annot_file.jva" },
43 { "Test multiple combine annotation statements import/export",
44 "examples/uniref50.fa",
45 "examples/testdata/test_combine_annot.jva" },
47 "Test multiple combine annotation statements with sequence_ref import/export",
48 "examples/uniref50.fa", "examples/testdata/uniref50_iupred.jva" },
50 "Test group only annotation file parsing results in parser indicating annotation was parsed",
51 "examples/uniref50.fa", "examples/testdata/test_grpannot.jva" },
52 { "Test hiding/showing of insertions on sequence_ref",
53 "examples/uniref50.fa", "examples/testdata/uniref50_seqref.jva" } };
55 @Test(groups ={ "Functional" })
56 public void exampleAnnotationFileIO() throws Exception
58 for (String[] testPair : TestFiles)
60 testAnnotationFileIO(testPair[0], new File(testPair[1]), new File(
65 public static AlignmentI readAlignmentFile(File f)
67 System.out.println("Reading file: " + f);
68 String ff = f.getPath();
71 FormatAdapter rf = new FormatAdapter();
73 AlignmentI al = rf.readFile(ff, AppletFormatAdapter.FILE,
74 new IdentifyFile().Identify(ff, AppletFormatAdapter.FILE));
76 // make sure dataset is initialised ? not sure about this
77 for (int i = 0; i < al.getSequencesArray().length; ++i)
79 al.getSequenceAt(i).setDatasetSequence(
80 al.getSequenceAt(i).createDatasetSequence());
82 assertNotNull("Couldn't read supplied alignment data.", al);
88 Assert.fail("Couln't read the alignment in file '" + f.toString() + "'");
93 * test alignment data in given file can be imported, exported and reimported
97 * - source datafile (IdentifyFile.identify() should work with it)
99 * - label for IO class used to write and read back in the data from
103 // @Test(groups ={ "Functional" })
104 public static void testAnnotationFileIO(String testname, File f,
107 System.out.println("Test: " + testname + "\nReading annotation file '"
108 + annotFile + "' onto : " + f);
109 String af = annotFile.getPath();
112 AlignmentI al = readAlignmentFile(f);
113 ColumnSelection cs = new ColumnSelection();
117 + "\nAlignment was not annotated - annotation file not imported.",
118 new AnnotationFile().readAnnotationFile(al, cs, af,
119 FormatAdapter.FILE));
121 AnnotationFile aff = new AnnotationFile();
122 ViewDef v = aff.new ViewDef(null, al.getHiddenSequences(), cs,
124 String anfileout = new AnnotationFile().printAnnotations(
125 al.getAlignmentAnnotation(), al.getGroups(),
126 al.getProperties(), null, al, v);
130 + "\nAlignment annotation file was not regenerated. Null string",
135 + "\nAlignment annotation file was not regenerated. Empty string",
136 anfileout.length() > "JALVIEW_ANNOTATION".length());
138 System.out.println("Output annotation file:\n" + anfileout
141 AlignmentI al_new = readAlignmentFile(f);
145 + "\nregenerated annotation file did not annotate alignment.",
146 new AnnotationFile().readAnnotationFile(al_new, anfileout,
147 FormatAdapter.PASTE));
149 // test for consistency in io
150 StockholmFileTest.testAlignmentEquivalence(al, al_new, false);
152 } catch (Exception e)
158 + "\nCouldn't complete Annotation file roundtrip input/output/input test for '"