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.assertTrue;
  25
  26 import org.testng.Assert;
  27 import org.testng.annotations.DataProvider;
  28 import org.testng.annotations.Test;
  29
  30 public class IdentifyFileTest
  31 {
  32
  33   @Test(groups = { "Functional" }, dataProvider = "identifyFiles")
  34   public void Identify(String data, String expectedFileType)
  35   {
  36     String protocol = AppletFormatAdapter.FILE;
  37     IdentifyFile ider = new IdentifyFile();
  38     String actualFiletype = ider.identify(data, protocol);
  39     Assert.assertEquals(actualFiletype, expectedFileType,
  40             "File identification Failed!");
  41   }
  42
  43   @DataProvider(name = "identifyFiles")
  44   public Object[][] IdentifyFileDP()
  45   {
  46     return new Object[][] {
  47         { "examples/example.json", "JSON" },
  48         { "examples/plantfdx.fa", "FASTA" },
  49         { "examples/dna_interleaved.phy", "PHYLIP" },
  50         { "examples/2GIS.pdb", "PDB" },
  51         { "examples/rf00031_folded.stk", "STH" },
  52         { "examples/testdata/test.rnaml", "RNAML" },
  53         { "examples/testdata/test.aln", "CLUSTAL" },
  54         { "examples/testdata/test.pfam", "PFAM" },
  55         { "examples/testdata/test.msf", "MSF" },
  56         { "examples/testdata/test.pir", "PIR" },
  57         { "examples/testdata/test.html", "HTML" },
  58         { "examples/testdata/test.pileup", "PileUp" },
  59         { "examples/testdata/test.blc", "BLC" },
  60         { "examples/exampleFeatures.txt", IdentifyFile.FeaturesFile },
  61         { "examples/testdata/simplegff3.gff", IdentifyFile.FeaturesFile },
  62         { "examples/testdata/exampleFeaturesMixed.gff",
  63             IdentifyFile.FeaturesFile },
  64         { "examples/testdata/test.jvp", "Jalview" },
  65         {
  66             "examples/testdata/cullpdb_pc25_res3.0_R0.3_d150729_chains9361.fasta.15316",
  67             "FASTA" },
  68
  69     // { "examples/testdata/test.amsa", "AMSA" },
  70     // { "examples/test.jnet", "JnetFile" },
  71     };
  72   }
  73
  74   @Test(groups = "Functional")
  75   public void testLooksLikeFeatureData()
  76   {
  77     IdentifyFile id = new IdentifyFile();
  78     assertFalse(id.looksLikeFeatureData(null));
  79     assertFalse(id.looksLikeFeatureData(""));
  80     // too few columns:
  81     assertFalse(id.looksLikeFeatureData("1 \t 2 \t 3 \t 4 \t 5"));
  82     // GFF format:
  83     assertTrue(id
  84             .looksLikeFeatureData("Seq1\tlocal\tHelix\t2456\t2462\tss"));
  85     // Jalview format:
  86     assertTrue(id.looksLikeFeatureData("Helix\tSeq1\t-1\t2456\t2462\tss"));
  87     // non-numeric start column:
  88     assertFalse(id.looksLikeFeatureData("Helix\tSeq1\t-1\t.\t2462\tss"));
  89     // non-numeric start column:
  90     assertFalse(id.looksLikeFeatureData("Helix\tSeq1\t-1\t2456\t.\tss"));
  91   }
  92 }