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 }