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.assertFalse;
24 import static org.testng.AssertJUnit.assertSame;
25 import static org.testng.AssertJUnit.assertTrue;
27 import org.testng.Assert;
28 import org.testng.annotations.DataProvider;
29 import org.testng.annotations.Test;
31 public class IdentifyFileTest
34 @Test(groups = { "Functional" }, dataProvider = "identifyFiles")
35 public void testIdentify(String data, FileFormatI expectedFileType)
36 throws FileFormatException
38 DataSourceType protocol = DataSourceType.FILE;
39 IdentifyFile ider = new IdentifyFile();
40 FileFormatI actualFiletype = ider.identify(data, protocol);
41 Assert.assertSame(actualFiletype, expectedFileType,
42 "File identification Failed!");
46 * Additional tests for Jalview features file
48 * @throws FileFormatException
50 @Test(groups = "Functional")
51 public void testIdentify_featureFile() throws FileFormatException
53 IdentifyFile ider = new IdentifyFile();
56 * Jalview format with features only, no feature colours
58 String data = "Iron-sulfur (2Fe-2S)\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
59 + "Iron-phosphorus (2Fe-P)\tID_NOT_SPECIFIED\t2\t86\t87\tMETALLIC\n";
60 assertSame(FileFormat.Features,
61 ider.identify(data, DataSourceType.PASTE));
64 * Jalview feature colour followed by GFF format feature data
66 data = "METAL\tcc9900\n" + "GFF\n"
67 + "FER_CAPAA\tuniprot\tMETAL\t44\t45\t4.0\t.\t.\n";
68 assertSame(FileFormat.Features,
69 ider.identify(data, DataSourceType.PASTE));
72 * Feature with '<' in the name (JAL-2098)
74 data = "kD < 3\tred\n" + "Low kD\tFER_CAPAA\t-1\t39\t39\tkD < 3\n";
75 assertSame(FileFormat.Features,
76 ider.identify(data, DataSourceType.PASTE));
79 @DataProvider(name = "identifyFiles")
80 public Object[][] IdentifyFileDP()
82 return new Object[][] {
83 { "examples/example.json", FileFormat.Json },
84 { "examples/plantfdx.fa", FileFormat.Fasta },
85 { "examples/dna_interleaved.phy", FileFormat.Phylip },
86 { "examples/2GIS.pdb", FileFormat.PDB },
87 { "examples/rf00031_folded.stk", FileFormat.Stockholm },
88 { "examples/testdata/test.rnaml", FileFormat.Rnaml },
89 { "examples/testdata/test.aln", FileFormat.Clustal },
90 { "examples/testdata/test.pfam", FileFormat.Pfam },
91 { "examples/testdata/test.msf", FileFormat.MSF },
92 { "examples/testdata/test.pir", FileFormat.PIR },
93 { "examples/testdata/test.html", FileFormat.Html },
94 { "examples/testdata/test.pileup", FileFormat.Pileup },
95 { "examples/testdata/test.blc", FileFormat.BLC },
96 { "examples/exampleFeatures.txt", FileFormat.Features },
97 { "examples/testdata/simpleGff3.gff", FileFormat.Features },
98 { "examples/testdata/test.jvp", FileFormat.Jalview },
99 { "examples/testdata/test.cif", FileFormat.MMCif },
101 "examples/testdata/cullpdb_pc25_res3.0_R0.3_d150729_chains9361.fasta.15316",
104 // { "examples/testdata/test.amsa", "AMSA" },
105 // { "examples/test.jnet", "JnetFile" },
109 @Test(groups = "Functional")
110 public void testLooksLikeFeatureData()
112 IdentifyFile id = new IdentifyFile();
113 assertFalse(id.looksLikeFeatureData(null));
114 assertFalse(id.looksLikeFeatureData(""));
116 assertFalse(id.looksLikeFeatureData("1 \t 2 \t 3 \t 4 \t 5"));
119 .looksLikeFeatureData("Seq1\tlocal\tHelix\t2456\t2462\tss"));
121 assertTrue(id.looksLikeFeatureData("Helix\tSeq1\t-1\t2456\t2462\tss"));
122 // non-numeric start column:
123 assertFalse(id.looksLikeFeatureData("Helix\tSeq1\t-1\t.\t2462\tss"));
124 // non-numeric start column:
125 assertFalse(id.looksLikeFeatureData("Helix\tSeq1\t-1\t2456\t.\tss"));