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 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, String expectedFileType)
  46   {
  47     String protocol = AppletFormatAdapter.FILE;
  48     IdentifyFile ider = new IdentifyFile();
  49     String actualFiletype = ider.identify(data, protocol);
  50     Assert.assertEquals(actualFiletype, expectedFileType,
  51             "File identification Failed!");
  52   }
  53
  54   /**
  55    * Additional tests for Jalview features file
  56    */
  57   @Test(groups = "Functional")
  58   public void testIdentify_featureFile()
  59   {
  60     IdentifyFile ider = new IdentifyFile();
  61
  62     /*
  63      * Jalview format with features only, no feature colours
  64      */
  65     String data = "Iron-sulfur (2Fe-2S)\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
  66             + "Iron-phosphorus (2Fe-P)\tID_NOT_SPECIFIED\t2\t86\t87\tMETALLIC\n";
  67     assertEquals(IdentifyFile.FeaturesFile,
  68             ider.identify(data, AppletFormatAdapter.PASTE));
  69
  70     /*
  71      * Jalview feature colour followed by GFF format feature data
  72      */
  73     data = "METAL\tcc9900\n" + "GFF\n"
  74             + "FER_CAPAA\tuniprot\tMETAL\t44\t45\t4.0\t.\t.\n";
  75     assertEquals(IdentifyFile.FeaturesFile,
  76             ider.identify(data, AppletFormatAdapter.PASTE));
  77
  78     /*
  79      * Feature with '<' in the name (JAL-2098)
  80      */
  81     data = "kD < 3\tred\n" + "Low kD\tFER_CAPAA\t-1\t39\t39\tkD < 3\n";
  82     assertEquals(IdentifyFile.FeaturesFile,
  83             ider.identify(data, AppletFormatAdapter.PASTE));
  84   }
  85
  86   @DataProvider(name = "identifyFiles")
  87   public Object[][] IdentifyFileDP()
  88   {
  89     return new Object[][] {
  90         { "examples/example.json", "JSON" },
  91         { "examples/plantfdx.fa", "FASTA" },
  92         { "examples/dna_interleaved.phy", "PHYLIP" },
  93         { "examples/2GIS.pdb", "PDB" },
  94         { "examples/rf00031_folded.stk", "STH" },
  95         { "examples/testdata/test.rnaml", "RNAML" },
  96         { "examples/testdata/test.aln", "CLUSTAL" },
  97         { "examples/testdata/test.pfam", "PFAM" },
  98         { "examples/testdata/test.msf", "MSF" },
  99         { "examples/testdata/test.pir", "PIR" },
 100         { "examples/testdata/test.html", "HTML" },
 101         { "examples/testdata/test.pileup", "PileUp" },
 102         { "examples/testdata/test.blc", "BLC" },
 103         { "examples/exampleFeatures.txt", IdentifyFile.FeaturesFile },
 104         { "examples/testdata/simpleGff3.gff", IdentifyFile.FeaturesFile },
 105         { "examples/testdata/test.jvp", "Jalview" },
 106         { "examples/testdata/test.cif", "mmCIF" },
 107         {
 108             "examples/testdata/cullpdb_pc25_res3.0_R0.3_d150729_chains9361.fasta.15316",
 109             "FASTA" },
 110
 111     // { "examples/testdata/test.amsa", "AMSA" },
 112     // { "examples/test.jnet", "JnetFile" },
 113     };
 114   }
 115
 116   @Test(groups = "Functional")
 117   public void testLooksLikeFeatureData()
 118   {
 119     IdentifyFile id = new IdentifyFile();
 120     assertFalse(id.looksLikeFeatureData(null));
 121     assertFalse(id.looksLikeFeatureData(""));
 122     // too few columns:
 123     assertFalse(id.looksLikeFeatureData("1 \t 2 \t 3 \t 4 \t 5"));
 124     // GFF format:
 125     assertTrue(id
 126             .looksLikeFeatureData("Seq1\tlocal\tHelix\t2456\t2462\tss"));
 127     // Jalview format:
 128     assertTrue(id.looksLikeFeatureData("Helix\tSeq1\t-1\t2456\t2462\tss"));
 129     // non-numeric start column:
 130     assertFalse(id.looksLikeFeatureData("Helix\tSeq1\t-1\t.\t2462\tss"));
 131     // non-numeric start column:
 132     assertFalse(id.looksLikeFeatureData("Helix\tSeq1\t-1\t2456\t.\tss"));
 133   }
 134 }