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   /**
  45    * Test the method that checks for one sequence id starting with the other,
  46    * followed by an 'allowed' separator character
  47    */
  48   @Test(groups = "Functional")
  49   public void test_seqIdNameEquals()
  50   {
  51     SequenceIdMatcher sequenceIdMatcher = new SequenceIdMatcher(
  52             new SequenceI[] {});
  53
  54     /*
  55      * target name = matcher name + word separator...
  56      */
  57     SeqIdName testee = sequenceIdMatcher.new SeqIdName("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\""));
  70     assertTrue(testee.equals("A12345" + String.valueOf((char) 0x00A4)));
  71     assertTrue(testee.equals("A12345$a"));
  72     assertTrue(testee.equals("A12345%b"));
  73     assertTrue(testee.equals("A12345^cd"));
  74     assertTrue(testee.equals("A12345*efg"));
  75     assertTrue(testee.equals("A12345)^&!"));
  76     assertTrue(testee.equals("A12345}01&*"));
  77     assertTrue(testee.equals("A12345[A23456"));
  78     assertTrue(testee.equals("A12345@|Uniprot"));
  79     assertTrue(testee.equals("A12345'whatever you want here"));
  80     assertTrue(testee.equals("A12345,"));
  81     assertTrue(testee.equals("A12345?"));
  82     assertTrue(testee.equals("A12345_"));
  83     /*
  84      * case insensitive matching
  85      */
  86     assertTrue(testee.equals("a12345"));
  87
  88     /*
  89      * matcher name = target name + word separator...
  90      */
  91     testee = sequenceIdMatcher.new SeqIdName("A12345#");
  92     assertTrue(testee.equals("A12345"));
  93
  94     /*
  95      * case insensitive matching
  96      */
  97     assertTrue(testee.equals("a12345"));
  98
  99     /*
 100      * miscellaneous failing cases
 101      */
 102     testee = sequenceIdMatcher.new SeqIdName("A12345");
 103     assertFalse(testee.equals((Object) null));
 104     assertFalse(testee.equals(""));
 105     assertFalse(testee.equals("A12346|A12345"));
 106     /*
 107      * case insensitive matching
 108      */
 109     assertTrue(testee.equals("a12345"));
 110
 111     testee = sequenceIdMatcher.new SeqIdName("A12345?B23456");
 112     assertFalse(testee.equals("B23456"));
 113     assertFalse(testee.equals("A12345|"));
 114     assertFalse(testee.equals("A12345?"));
 115
 116     testee = sequenceIdMatcher.new SeqIdName("A12345<");
 117     assertFalse(testee.equals("A12345?"));
 118     assertTrue(testee.equals("A12345<")); // bug? inconsistent
 119     /*
 120      * case insensitive matching
 121      */
 122     assertTrue(testee.equals("a12345"));
 123
 124     testee = sequenceIdMatcher.new SeqIdName("UNIPROT|A12345");
 125     assertFalse(testee.equals("A12345"));
 126     assertFalse(testee.equals("UNIPROT|B98765"));
 127     assertFalse(testee.equals("UNIPROT|"));
 128     assertTrue(testee.equals("UNIPROT"));
 129   }
 130 }