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 testIdentify(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   /**
  44    * Additional tests for (a) Jalview features file with no colour
  45    * specifications (old style 'groups' file) and (b) Jalview features file with
  46    * embedded GFF
  47    */
  48   @Test(groups = "Functional")
  49   public void testIdentify_featureFile()
  50   {
  51     IdentifyFile ider = new IdentifyFile();
  52
  53     // Jalview format with features only, no feature colours
  54     String data = "Iron-sulfur (2Fe-2S)\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
  55             + "Iron-phosphorus (2Fe-P)\tID_NOT_SPECIFIED\t2\t86\t87\tMETALLIC\n";
  56     Assert.assertEquals(IdentifyFile.FeaturesFile, ider.identify(data, AppletFormatAdapter.PASTE));
  57
  58     // Jalview feature colour followed by GFF format feature data
  59     data = "METAL\tcc9900\n" + "GFF\n"
  60             + "FER_CAPAA\tuniprot\tMETAL\t44\t45\t4.0\t.\t.\n";
  61     Assert.assertEquals(IdentifyFile.FeaturesFile,
  62             ider.identify(data, AppletFormatAdapter.PASTE));
  63   }
  64
  65   @DataProvider(name = "identifyFiles")
  66   public Object[][] IdentifyFileDP()
  67   {
  68     return new Object[][] {
  69         { "examples/example.json", "JSON" },
  70         { "examples/plantfdx.fa", "FASTA" },
  71         { "examples/dna_interleaved.phy", "PHYLIP" },
  72         { "examples/2GIS.pdb", "PDB" },
  73         { "examples/rf00031_folded.stk", "STH" },
  74         { "examples/testdata/test.rnaml", "RNAML" },
  75         { "examples/testdata/test.aln", "CLUSTAL" },
  76         { "examples/testdata/test.pfam", "PFAM" },
  77         { "examples/testdata/test.msf", "MSF" },
  78         { "examples/testdata/test.pir", "PIR" },
  79         { "examples/testdata/test.html", "HTML" },
  80         { "examples/testdata/test.pileup", "PileUp" },
  81         { "examples/testdata/test.blc", "BLC" },
  82         { "examples/exampleFeatures.txt", IdentifyFile.FeaturesFile },
  83         { "examples/testdata/simplegff3.gff", IdentifyFile.FeaturesFile },
  84         { "examples/testdata/test.jvp", "Jalview" },
  85         {
  86             "examples/testdata/cullpdb_pc25_res3.0_R0.3_d150729_chains9361.fasta.15316",
  87             "FASTA" },
  88
  89     // { "examples/testdata/test.amsa", "AMSA" },
  90     // { "examples/test.jnet", "JnetFile" },
  91     };
  92   }
  93
  94   @Test(groups = "Functional")
  95   public void testLooksLikeFeatureData()
  96   {
  97     IdentifyFile id = new IdentifyFile();
  98     assertFalse(id.looksLikeFeatureData(null));
  99     assertFalse(id.looksLikeFeatureData(""));
 100     // too few columns:
 101     assertFalse(id.looksLikeFeatureData("1 \t 2 \t 3 \t 4 \t 5"));
 102     // GFF format:
 103     assertTrue(id
 104             .looksLikeFeatureData("Seq1\tlocal\tHelix\t2456\t2462\tss"));
 105     // Jalview format:
 106     assertTrue(id.looksLikeFeatureData("Helix\tSeq1\t-1\t2456\t2462\tss"));
 107     // non-numeric start column:
 108     assertFalse(id.looksLikeFeatureData("Helix\tSeq1\t-1\t.\t2462\tss"));
 109     // non-numeric start column:
 110     assertFalse(id.looksLikeFeatureData("Helix\tSeq1\t-1\t2456\t.\tss"));
 111   }
 112 }