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.
21 package jalview.io.gff;
23 import static org.testng.AssertJUnit.assertNull;
24 import static org.testng.AssertJUnit.assertSame;
25 import static org.testng.AssertJUnit.assertTrue;
27 import org.testng.annotations.Test;
29 public class GffHelperFactoryTest
32 @Test(groups = "Functional")
33 public void testGetHelper()
35 assertNull(GffHelperFactory.getHelper(null));
37 String tabRegex = "\\t";
40 * column 3 = 'similarity' indicates exonerate GFF alignment data
42 String gff = "submitted\taffine:local\tsimilarity\t20\t30\t99\t+\t.\t";
43 // no attributes (column 9 data):
44 assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof Gff2Helper);
46 // attributes set but unhandled featureGroup - get generic handler
47 gff = "submitted\taffine:local\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
48 assertSame(GffHelperFactory.getHelper(gff.split(tabRegex)).getClass(),
51 // handled featureGroup (exonerate model) values
52 gff = "submitted\texonerate:protein2dna:local\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
53 assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
55 gff = "submitted\tprotein2genome\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
56 assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
58 gff = "submitted\tcoding2coding\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
59 assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
61 gff = "submitted\tcoding2genome\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
62 assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
64 gff = "submitted\tcdna2genome\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
65 assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
67 gff = "submitted\tgenome2genome\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
68 assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
70 // not case-sensitive:
71 gff = "submitted\tgenome2genome\tSIMILARITY\t20\t30\t99\t+\t.\tID=$1";
72 assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
75 * InterProScan has 'protein_match' in column 3
77 gff = "Submitted\tPANTHER\tprotein_match\t1\t1174\t0.0\t+\t.\tName=PTHR32154";
78 assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof InterProScanHelper);
81 * nothing specific - return the generic GFF3 class if Name=Value is present in col9
83 gff = "nothing\tinteresting\there\t20\t30\t99\t+\t.\tID=1";
84 GffHelperI helper = GffHelperFactory.getHelper(gff.split(tabRegex));
85 assertSame(helper.getClass(), Gff3Helper.class);
87 // return the generic GFF2 class if "Name Value" is present in col9
88 gff = "nothing\tinteresting\there\t20\t30\t99\t+\t.\tID 1";
89 helper = GffHelperFactory.getHelper(gff.split(tabRegex));
90 assertSame(helper.getClass(), Gff2Helper.class);