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.assertEquals;
  24 import static org.testng.AssertJUnit.assertFalse;
  25 import static org.testng.AssertJUnit.assertTrue;
  26
  27 import org.testng.Assert;
  28 import org.testng.annotations.DataProvider;
  29 import org.testng.annotations.Test;
  30
  31 public class IdentifyFileTest
  32 {
  33
  34   @Test(groups = { "Functional" }, dataProvider = "identifyFiles")
  35   public void testIdentify(String data, String expectedFileType)
  36           throws FileFormatException
  37   {
  38     DataSourceType protocol = DataSourceType.FILE;
  39     IdentifyFile ider = new IdentifyFile();
  40     String actualFiletype = ider.identify(data, protocol).toString();
  41     Assert.assertEquals(actualFiletype, expectedFileType,
  42             "File identification Failed!");
  43   }
  44
  45   /**
  46    * Additional tests for Jalview features file
  47    *
  48    * @throws FileFormatException
  49    */
  50   @Test(groups = "Functional")
  51   public void testIdentify_featureFile() throws FileFormatException
  52   {
  53     IdentifyFile ider = new IdentifyFile();
  54
  55     /*
  56      * Jalview format with features only, no feature colours
  57      */
  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     assertEquals(IdentifyFile.FeaturesFile,
  61             ider.identify(data, DataSourceType.PASTE));
  62
  63     /*
  64      * Jalview feature colour followed by GFF format feature data
  65      */
  66     data = "METAL\tcc9900\n" + "GFF\n"
  67             + "FER_CAPAA\tuniprot\tMETAL\t44\t45\t4.0\t.\t.\n";
  68     assertEquals(IdentifyFile.FeaturesFile,
  69             ider.identify(data, DataSourceType.PASTE));
  70
  71     /*
  72      * Feature with '<' in the name (JAL-2098)
  73      */
  74     data = "kD < 3\tred\n" + "Low kD\tFER_CAPAA\t-1\t39\t39\tkD < 3\n";
  75     assertEquals(IdentifyFile.FeaturesFile,
  76             ider.identify(data, DataSourceType.PASTE));
  77   }
  78
  79   @DataProvider(name = "identifyFiles")
  80   public Object[][] IdentifyFileDP()
  81   {
  82     return new Object[][] {
  83         { "examples/example.json", "JSON" },
  84         { "examples/plantfdx.fa", "FASTA" },
  85         { "examples/dna_interleaved.phy", "PHYLIP" },
  86         { "examples/2GIS.pdb", "PDB" },
  87         { "examples/rf00031_folded.stk", "STH" },
  88         { "examples/testdata/test.rnaml", "RNAML" },
  89         { "examples/testdata/test.aln", "CLUSTAL" },
  90         { "examples/testdata/test.pfam", "PFAM" },
  91         { "examples/testdata/test.msf", "MSF" },
  92         { "examples/testdata/test.pir", "PIR" },
  93         { "examples/testdata/test.html", "HTML" },
  94         { "examples/testdata/test.pileup", "PileUp" },
  95         { "examples/testdata/test.blc", "BLC" },
  96         { "examples/exampleFeatures.txt", IdentifyFile.FeaturesFile },
  97         { "examples/testdata/simpleGff3.gff", IdentifyFile.FeaturesFile },
  98         { "examples/testdata/test.jvp", "Jalview" },
  99         { "examples/testdata/test.cif", "mmCIF" },
 100         {
 101             "examples/testdata/cullpdb_pc25_res3.0_R0.3_d150729_chains9361.fasta.15316",
 102             "FASTA" },
 103
 104     // { "examples/testdata/test.amsa", "AMSA" },
 105     // { "examples/test.jnet", "JnetFile" },
 106     };
 107   }
 108
 109   @Test(groups = "Functional")
 110   public void testLooksLikeFeatureData()
 111   {
 112     IdentifyFile id = new IdentifyFile();
 113     assertFalse(id.looksLikeFeatureData(null));
 114     assertFalse(id.looksLikeFeatureData(""));
 115     // too few columns:
 116     assertFalse(id.looksLikeFeatureData("1 \t 2 \t 3 \t 4 \t 5"));
 117     // GFF format:
 118     assertTrue(id
 119             .looksLikeFeatureData("Seq1\tlocal\tHelix\t2456\t2462\tss"));
 120     // Jalview format:
 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"));
 126   }
 127 }