test/jalview/io/gff/GffHelperFactoryTest.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.gff;
  22
  23 import static org.testng.AssertJUnit.assertNull;
  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.annotations.BeforeClass;
  30 import org.testng.annotations.Test;
  31
  32 public class GffHelperFactoryTest
  33 {
  34
  35   @BeforeClass(alwaysRun = true)
  36   public void setUpJvOptionPane()
  37   {
  38     JvOptionPane.setInteractiveMode(false);
  39     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  40   }
  41
  42   @Test(groups = "Functional")
  43   public void testGetHelper()
  44   {
  45     assertNull(GffHelperFactory.getHelper(null));
  46
  47     String tabRegex = "\\t";
  48
  49     /*
  50      * column 3 = 'similarity' indicates exonerate GFF alignment data
  51      */
  52     String gff = "submitted\taffine:local\tsimilarity\t20\t30\t99\t+\t.\t";
  53     // no attributes (column 9 data):
  54     assertTrue(GffHelperFactory
  55             .getHelper(gff.split(tabRegex)) instanceof Gff2Helper);
  56
  57     // attributes set but unhandled featureGroup - get generic handler
  58     gff = "submitted\taffine:local\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
  59     assertSame(GffHelperFactory.getHelper(gff.split(tabRegex)).getClass(),
  60             Gff3Helper.class);
  61
  62     // handled featureGroup (exonerate model) values
  63     gff = "submitted\texonerate:protein2dna:local\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
  64     assertTrue(GffHelperFactory
  65             .getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
  66
  67     gff = "submitted\tprotein2genome\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
  68     assertTrue(GffHelperFactory
  69             .getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
  70
  71     gff = "submitted\tcoding2coding\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
  72     assertTrue(GffHelperFactory
  73             .getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
  74
  75     gff = "submitted\tcoding2genome\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
  76     assertTrue(GffHelperFactory
  77             .getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
  78
  79     gff = "submitted\tcdna2genome\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
  80     assertTrue(GffHelperFactory
  81             .getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
  82
  83     gff = "submitted\tgenome2genome\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
  84     assertTrue(GffHelperFactory
  85             .getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
  86
  87     // not case-sensitive:
  88     gff = "submitted\tgenome2genome\tSIMILARITY\t20\t30\t99\t+\t.\tID=$1";
  89     assertTrue(GffHelperFactory
  90             .getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
  91
  92     /*
  93      * InterProScan has 'protein_match' in column 3
  94      */
  95     gff = "Submitted\tPANTHER\tprotein_match\t1\t1174\t0.0\t+\t.\tName=PTHR32154";
  96     assertTrue(GffHelperFactory
  97             .getHelper(gff.split(tabRegex)) instanceof InterProScanHelper);
  98
  99     /*
 100      * nothing specific - return the generic GFF3 class if Name=Value is present in col9
 101      */
 102     gff = "nothing\tinteresting\there\t20\t30\t99\t+\t.\tID=1";
 103     GffHelperI helper = GffHelperFactory.getHelper(gff.split(tabRegex));
 104     assertSame(helper.getClass(), Gff3Helper.class);
 105
 106     // return the generic GFF2 class if "Name Value" is present in col9
 107     gff = "nothing\tinteresting\there\t20\t30\t99\t+\t.\tID 1";
 108     helper = GffHelperFactory.getHelper(gff.split(tabRegex));
 109     assertSame(helper.getClass(), Gff2Helper.class);
 110   }
 111 }