test/jalview/controller/AlignViewControllerTest.java

   1 package jalview.controller;
   2
   3 import static org.testng.AssertJUnit.assertEquals;
   4 import static org.testng.AssertJUnit.assertTrue;
   5
   6 import jalview.datamodel.Sequence;
   7 import jalview.datamodel.SequenceFeature;
   8 import jalview.datamodel.SequenceGroup;
   9 import jalview.datamodel.SequenceI;
  10
  11 import java.util.BitSet;
  12
  13 import org.testng.annotations.Test;
  14
  15 public class AlignViewControllerTest
  16 {
  17   @Test(groups = "Functional")
  18   public void testFindColumnsWithFeature()
  19   {
  20     SequenceI seq1 = new Sequence("seq1", "aMMMaaaaaaaaaaaaaaaa");
  21     SequenceI seq2 = new Sequence("seq2", "aaaMMMMMMMaaaaaaaaaa");
  22     SequenceI seq3 = new Sequence("seq3", "aaaaaaaaaaMMMMMaaaaa");
  23     SequenceI seq4 = new Sequence("seq3", "aaaaaaaaaaaaaaaaaaaa");
  24
  25     /*
  26      * features start/end are base 1
  27      */
  28     seq1.addSequenceFeature(new SequenceFeature("Metal", "desc", 2, 4, 0f,
  29             null));
  30     seq1.addSequenceFeature(new SequenceFeature("Helix", "desc", 1, 15, 0f,
  31             null));
  32     seq2.addSequenceFeature(new SequenceFeature("Metal", "desc", 4, 10, 0f,
  33             null));
  34     seq3.addSequenceFeature(new SequenceFeature("Metal", "desc", 11, 15,
  35             0f, null));
  36
  37     /*
  38      * select the first three columns --> Metal in seq1 2-3
  39      */
  40     SequenceGroup sg = new SequenceGroup();
  41     sg.setStartRes(0); // base 0
  42     sg.setEndRes(2);
  43     sg.addSequence(seq1, false);
  44     sg.addSequence(seq2, false);
  45     sg.addSequence(seq3, false);
  46     sg.addSequence(seq4, false);
  47
  48     BitSet bs = new BitSet();
  49     int seqCount = AlignViewController.findColumnsWithFeature("Metal", sg,
  50             bs);
  51     assertEquals(1, seqCount);
  52     assertEquals(2, bs.cardinality());
  53     assertTrue(bs.get(1));
  54     assertTrue(bs.get(2));
  55
  56     /*
  57      * select the first four columns: Metal in seq1 2:4, seq2 4:4
  58      */
  59     sg.setEndRes(3);
  60     bs.clear();
  61     seqCount = AlignViewController.findColumnsWithFeature("Metal", sg,
  62             bs);
  63     assertEquals(2, seqCount);
  64     assertEquals(3, bs.cardinality());
  65     assertTrue(bs.get(1));
  66     assertTrue(bs.get(2));
  67     assertTrue(bs.get(3));
  68
  69     /*
  70      * select column 11: Metal in seq3 only
  71      */
  72     sg.setStartRes(10);
  73     sg.setEndRes(10);
  74     bs.clear();
  75     seqCount = AlignViewController.findColumnsWithFeature("Metal", sg, bs);
  76     assertEquals(1, seqCount);
  77     assertEquals(1, bs.cardinality());
  78     assertTrue(bs.get(10));
  79
  80     /*
  81      * select columns 16-20: no Metal feature
  82      */
  83     sg.setStartRes(15);
  84     sg.setEndRes(19);
  85     bs.clear();
  86     seqCount = AlignViewController.findColumnsWithFeature("Metal", sg, bs);
  87     assertEquals(0, seqCount);
  88     assertEquals(0, bs.cardinality());
  89
  90     /*
  91      * look for a feature that isn't there
  92      */
  93     sg.setStartRes(0);
  94     sg.setEndRes(19);
  95     bs.clear();
  96     seqCount = AlignViewController.findColumnsWithFeature("Pfam", sg, bs);
  97     assertEquals(0, seqCount);
  98     assertEquals(0, bs.cardinality());
  99   }
 100 }