JAL-1988 JAL-3130 New jlinked JRE in jalview_java2 with modules. Still needs jaxws...
[jalview.git] / test / jalview / io / IdentifyFileTest.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;
22
23 import static org.testng.AssertJUnit.assertFalse;
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.Assert;
30 import org.testng.annotations.BeforeClass;
31 import org.testng.annotations.DataProvider;
32 import org.testng.annotations.Test;
33
34 public class IdentifyFileTest
35 {
36
37   @BeforeClass(alwaysRun = true)
38   public void setUpJvOptionPane()
39   {
40     JvOptionPane.setInteractiveMode(false);
41     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
42   }
43
44   @Test(groups = { "Functional" }, dataProvider = "identifyFiles")
45   public void testIdentify(String data, FileFormatI expectedFileType)
46           throws FileFormatException
47   {
48     DataSourceType protocol = DataSourceType.FILE;
49     IdentifyFile ider = new IdentifyFile();
50     FileFormatI actualFiletype = ider.identify(data, protocol);
51     Assert.assertSame(actualFiletype, expectedFileType,
52             "File identification Failed!");
53   }
54
55   /**
56    * Additional tests for Jalview features file
57    * 
58    * @throws FileFormatException
59    */
60   @Test(groups = "Functional")
61   public void testIdentify_featureFile() throws FileFormatException
62   {
63     IdentifyFile ider = new IdentifyFile();
64
65     /*
66      * Jalview format with features only, no feature colours
67      */
68     String data = "Iron-sulfur (2Fe-2S)\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
69             + "Iron-phosphorus (2Fe-P)\tID_NOT_SPECIFIED\t2\t86\t87\tMETALLIC\n";
70     assertSame(FileFormat.Features,
71             ider.identify(data, DataSourceType.PASTE));
72
73     /*
74      * Jalview feature colour followed by GFF format feature data
75      */
76     data = "METAL\tcc9900\n" + "GFF\n"
77             + "FER_CAPAA\tuniprot\tMETAL\t44\t45\t4.0\t.\t.\n";
78     assertSame(FileFormat.Features,
79             ider.identify(data, DataSourceType.PASTE));
80
81     /*
82      * Feature with '<' in the name (JAL-2098)
83      */
84     data = "kD < 3\tred\n" + "Low kD\tFER_CAPAA\t-1\t39\t39\tkD < 3\n";
85     assertSame(FileFormat.Features,
86             ider.identify(data, DataSourceType.PASTE));
87   }
88
89   @DataProvider(name = "identifyFiles")
90   public Object[][] IdentifyFileDP()
91   {
92     return new Object[][] {
93         { "examples/example.json", FileFormat.Json },
94         { "examples/plantfdx.fa", FileFormat.Fasta },
95         { "examples/dna_interleaved.phy", FileFormat.Phylip },
96         { "examples/2GIS.pdb", FileFormat.PDB },
97         { "examples/rf00031_folded.stk", FileFormat.Stockholm },
98         { "examples/testdata/test.rnaml", FileFormat.Rnaml },
99         { "examples/testdata/test.aln", FileFormat.Clustal },
100         { "examples/testdata/test.pfam", FileFormat.Pfam },
101         { "examples/testdata/test.msf", FileFormat.MSF },
102         { "examples/testdata/test.pir", FileFormat.PIR },
103         { "examples/testdata/test.html", FileFormat.Html },
104         { "examples/testdata/test.pileup", FileFormat.Pileup },
105         { "examples/testdata/test.blc", FileFormat.BLC },
106         { "examples/exampleFeatures.txt", FileFormat.Features },
107         { "examples/testdata/simpleGff3.gff", FileFormat.Features },
108         { "examples/testdata/test.jvp", FileFormat.Jalview },
109         { "examples/testdata/test.cif", FileFormat.MMCif },
110         {
111             "examples/testdata/cullpdb_pc25_res3.0_R0.3_d150729_chains9361.fasta.15316",
112             FileFormat.Fasta },
113         { "resources/scoreModel/pam250.scm", FileFormat.ScoreMatrix },
114         { "resources/scoreModel/blosum80.scm", FileFormat.ScoreMatrix }
115     // { "examples/testdata/test.amsa", "AMSA" },
116     // { "examples/test.jnet", "JnetFile" },
117     };
118   }
119
120   @Test(groups = "Functional")
121   public void testLooksLikeFeatureData()
122   {
123     IdentifyFile id = new IdentifyFile();
124     assertFalse(id.looksLikeFeatureData(null));
125     assertFalse(id.looksLikeFeatureData(""));
126     // too few columns:
127     assertFalse(id.looksLikeFeatureData("1 \t 2 \t 3 \t 4 \t 5"));
128     // GFF format:
129     assertTrue(id
130             .looksLikeFeatureData("Seq1\tlocal\tHelix\t2456\t2462\tss"));
131     // Jalview format:
132     assertTrue(id.looksLikeFeatureData("Helix\tSeq1\t-1\t2456\t2462\tss"));
133     // non-numeric start column:
134     assertFalse(id.looksLikeFeatureData("Helix\tSeq1\t-1\t.\t2462\tss"));
135     // non-numeric start column:
136     assertFalse(id.looksLikeFeatureData("Helix\tSeq1\t-1\t2456\t.\tss"));
137   }
138 }