JAL-3364 align split frame sequence panels with wrapped view scale left
[jalview.git] / test / jalview / io / gff / GffHelperFactoryTest.java
1 /*
2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
4  * 
5  * This file is part of Jalview.
6  * 
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.
11  *  
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.
16  * 
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.
20  */
21 package jalview.io.gff;
22
23 import static org.testng.AssertJUnit.assertNull;
24 import static org.testng.AssertJUnit.assertSame;
25 import static org.testng.AssertJUnit.assertTrue;
26
27 import jalview.gui.JvOptionPane;
28
29 import org.testng.annotations.BeforeClass;
30 import org.testng.annotations.Test;
31
32 public class GffHelperFactoryTest
33 {
34
35   @BeforeClass(alwaysRun = true)
36   public void setUpJvOptionPane()
37   {
38     JvOptionPane.setInteractiveMode(false);
39     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
40   }
41
42   @Test(groups = "Functional")
43   public void testGetHelper()
44   {
45     assertNull(GffHelperFactory.getHelper(null));
46
47     String tabRegex = "\\t";
48
49     /*
50      * column 3 = 'similarity' indicates exonerate GFF alignment data
51      */
52     String gff = "submitted\taffine:local\tsimilarity\t20\t30\t99\t+\t.\t";
53     // no attributes (column 9 data):
54     assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof Gff2Helper);
55
56     // attributes set but unhandled featureGroup - get generic handler
57     gff = "submitted\taffine:local\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
58     assertSame(GffHelperFactory.getHelper(gff.split(tabRegex)).getClass(),
59             Gff3Helper.class);
60
61     // handled featureGroup (exonerate model) values
62     gff = "submitted\texonerate:protein2dna:local\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
63     assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
64
65     gff = "submitted\tprotein2genome\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
66     assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
67
68     gff = "submitted\tcoding2coding\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
69     assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
70
71     gff = "submitted\tcoding2genome\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
72     assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
73
74     gff = "submitted\tcdna2genome\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
75     assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
76
77     gff = "submitted\tgenome2genome\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
78     assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
79
80     // not case-sensitive:
81     gff = "submitted\tgenome2genome\tSIMILARITY\t20\t30\t99\t+\t.\tID=$1";
82     assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
83
84     /*
85      * InterProScan has 'protein_match' in column 3
86      */
87     gff = "Submitted\tPANTHER\tprotein_match\t1\t1174\t0.0\t+\t.\tName=PTHR32154";
88     assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof InterProScanHelper);
89
90     /*
91      * nothing specific - return the generic GFF3 class if Name=Value is present in col9
92      */
93     gff = "nothing\tinteresting\there\t20\t30\t99\t+\t.\tID=1";
94     GffHelperI helper = GffHelperFactory.getHelper(gff.split(tabRegex));
95     assertSame(helper.getClass(), Gff3Helper.class);
96
97     // return the generic GFF2 class if "Name Value" is present in col9
98     gff = "nothing\tinteresting\there\t20\t30\t99\t+\t.\tID 1";
99     helper = GffHelperFactory.getHelper(gff.split(tabRegex));
100     assertSame(helper.getClass(), Gff2Helper.class);
101   }
102 }