test/jalview/analysis/SequenceIdMatcherTest.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.analysis;
  22
  23 import static org.testng.AssertJUnit.assertFalse;
  24 import static org.testng.AssertJUnit.assertTrue;
  25
  26 import jalview.analysis.SequenceIdMatcher.SeqIdName;
  27 import jalview.datamodel.SequenceI;
  28 import jalview.gui.JvOptionPane;
  29
  30 import org.testng.annotations.BeforeClass;
  31 import org.testng.annotations.Test;
  32
  33 public class SequenceIdMatcherTest
  34 {
  35
  36   @BeforeClass(alwaysRun = true)
  37   public void setUpJvOptionPane()
  38   {
  39     JvOptionPane.setInteractiveMode(false);
  40     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  41   }
  42
  43   /**
  44    * Test the method that checks for one sequence id starting with the other,
  45    * followed by an 'allowed' separator character
  46    */
  47   @Test(groups = "Functional")
  48   public void test_seqIdNameEquals()
  49   {
  50     SequenceIdMatcher sequenceIdMatcher = new SequenceIdMatcher(
  51             new SequenceI[] {});
  52
  53     /*
  54      * target name = matcher name + word separator...
  55      */
  56     SeqIdName testee = sequenceIdMatcher.new SeqIdName("A12345");
  57     assertTrue(testee.equals("A12345"));
  58     assertTrue(testee.equals("A12345~"));
  59     assertTrue(testee.equals("A12345."));
  60     assertTrue(testee.equals("A12345 "));
  61     assertTrue(testee.equals("A12345|"));
  62     assertTrue(testee.equals("A12345#"));
  63     assertTrue(testee.equals("A12345\\"));
  64     assertTrue(testee.equals("A12345/"));
  65     assertTrue(testee.equals("A12345<"));
  66     assertTrue(testee.equals("A12345>"));
  67     assertTrue(testee.equals("A12345!"));
  68     assertTrue(testee.equals("A12345\""));
  69     assertTrue(testee.equals("A12345" + String.valueOf((char) 0x00A4)));
  70     assertTrue(testee.equals("A12345$a"));
  71     assertTrue(testee.equals("A12345%b"));
  72     assertTrue(testee.equals("A12345^cd"));
  73     assertTrue(testee.equals("A12345*efg"));
  74     assertTrue(testee.equals("A12345)^&!"));
  75     assertTrue(testee.equals("A12345}01&*"));
  76     assertTrue(testee.equals("A12345[A23456"));
  77     assertTrue(testee.equals("A12345@|Uniprot"));
  78     assertTrue(testee.equals("A12345'whatever you want here"));
  79     assertTrue(testee.equals("A12345,"));
  80     assertTrue(testee.equals("A12345?"));
  81     assertTrue(testee.equals("A12345_"));
  82     /*
  83      * case insensitive matching
  84      */
  85     assertTrue(testee.equals("a12345"));
  86
  87     /*
  88      * matcher name = target name + word separator...
  89      */
  90     testee = sequenceIdMatcher.new SeqIdName("A12345#");
  91     assertTrue(testee.equals("A12345"));
  92
  93     /*
  94      * case insensitive matching
  95      */
  96     assertTrue(testee.equals("a12345"));
  97
  98     /*
  99      * miscellaneous failing cases
 100      */
 101     testee = sequenceIdMatcher.new SeqIdName("A12345");
 102     assertFalse(testee.equals((Object) null));
 103     assertFalse(testee.equals(""));
 104     assertFalse(testee.equals("A12346|A12345"));
 105     /*
 106      * case insensitive matching
 107      */
 108     assertTrue(testee.equals("a12345"));
 109
 110     testee = sequenceIdMatcher.new SeqIdName("A12345?B23456");
 111     assertFalse(testee.equals("B23456"));
 112     assertFalse(testee.equals("A12345|"));
 113     assertFalse(testee.equals("A12345?"));
 114
 115     testee = sequenceIdMatcher.new SeqIdName("A12345<");
 116     assertFalse(testee.equals("A12345?"));
 117     assertTrue(testee.equals("A12345<")); // bug? inconsistent
 118     /*
 119      * case insensitive matching
 120      */
 121     assertTrue(testee.equals("a12345"));
 122
 123     testee = sequenceIdMatcher.new SeqIdName("UNIPROT|A12345");
 124     assertFalse(testee.equals("A12345"));
 125     assertFalse(testee.equals("UNIPROT|B98765"));
 126     assertFalse(testee.equals("UNIPROT|"));
 127     assertTrue(testee.equals("UNIPROT"));
 128   }
 129 }