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