test/jalview/analysis/AlignmentSorterTest.java

   1 package jalview.analysis;
   2
   3 import static org.testng.Assert.assertSame;
   4
   5 import jalview.datamodel.Alignment;
   6 import jalview.datamodel.AlignmentI;
   7 import jalview.datamodel.Sequence;
   8 import jalview.datamodel.SequenceFeature;
   9 import jalview.datamodel.SequenceI;
  10
  11 import java.util.Arrays;
  12 import java.util.List;
  13
  14 import org.testng.annotations.Test;
  15
  16 import junit.extensions.PA;
  17
  18 public class AlignmentSorterTest
  19 {
  20   @Test(groups = "Functional")
  21   public void testSortByFeature_score()
  22   {
  23     SequenceI seq1 = new Sequence("Seq1", "ABC--D-EFGHIJ");
  24     SequenceI seq2 = new Sequence("Seq2", "ABCDEFGHIJ");
  25     SequenceI seq3 = new Sequence("Seq3", "ABCDE-FGHIJ");
  26     SequenceI seq4 = new Sequence("Seq4", "ABCDEFGHIJ");
  27     SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 };
  28     AlignmentI al = new Alignment(seqs);
  29     al.setDataset(null);
  30
  31     /*
  32      * sort with no score features does nothing
  33      */
  34     AlignmentSorter sorter = (AlignmentSorter) PA
  35             .invokeMethod(AlignmentSorter.class, "getInstance()",
  36                     new Object[] {});
  37     PA.setValue(sorter, "sortByFeatureCriteria", null);
  38
  39     AlignmentSorter.sortByFeature(null, null, 0, al.getWidth(), al,
  40             AlignmentSorter.FEATURE_SCORE);
  41     assertSame(al.getSequenceAt(0), seq1);
  42     assertSame(al.getSequenceAt(1), seq2);
  43     assertSame(al.getSequenceAt(2), seq3);
  44     assertSame(al.getSequenceAt(3), seq4);
  45
  46     /*
  47      * add score and non-score features
  48      * seq1 Cath(2.0) Pfam(4.0) average 3.0
  49      * seq2 Cath(2.5) Metal(NaN) average 2.5
  50      * seq3 KD(-4), KD(3.0) average -0.5
  51      * seq4 Helix(NaN) - should sort as if largest score
  52      */
  53     seq1.addSequenceFeature(new SequenceFeature("Cath", "", 2, 3, 2.0f,
  54             "g1"));
  55     seq1.addSequenceFeature(new SequenceFeature("Pfam", "", 4, 5, 4.0f,
  56             "g2"));
  57     seq2.addSequenceFeature(new SequenceFeature("Cath", "", 2, 3, 2.5f,
  58             "g3"));
  59     seq2.addSequenceFeature(new SequenceFeature("Metal", "", 2, 3,
  60             Float.NaN, "g4"));
  61     seq3.addSequenceFeature(new SequenceFeature("kD", "", 2, 3, -4f, "g5"));
  62     seq3.addSequenceFeature(new SequenceFeature("kD", "", 5, 6, 3.0f, "g6"));
  63     seq4.addSequenceFeature(new SequenceFeature("Helix", "", 2, 3,
  64             Float.NaN, "g7"));
  65
  66     /*
  67      * sort by ascending score, no filter on feature type or group
  68      * NB sort order for the same feature set (none) gets toggled, so descending
  69      */
  70     PA.setValue(sorter, "sortByFeatureAscending", true);
  71     AlignmentSorter.sortByFeature(null, null, 0, al.getWidth(), al,
  72             AlignmentSorter.FEATURE_SCORE);
  73     assertSame(al.getSequenceAt(3), seq3); // -0.5
  74     assertSame(al.getSequenceAt(2), seq2); // 2.5
  75     assertSame(al.getSequenceAt(1), seq1); // 3.0
  76     assertSame(al.getSequenceAt(0), seq4); // maximum 'score'
  77
  78     /*
  79      * repeat sort toggles order - now ascending
  80      */
  81     AlignmentSorter.sortByFeature(null, null, 0, al.getWidth(), al,
  82             AlignmentSorter.FEATURE_SCORE);
  83     assertSame(al.getSequenceAt(0), seq3); // -0.5
  84     assertSame(al.getSequenceAt(1), seq2); // 2.5
  85     assertSame(al.getSequenceAt(2), seq1); // 3.0
  86     assertSame(al.getSequenceAt(3), seq4);
  87
  88     /*
  89      * specify features, excluding Pfam
  90      * seq1 average is now 2.0
  91      * next sort is ascending (not toggled) as for a different feature set
  92      */
  93     List<String> types = Arrays.asList(new String[] { "Cath", "kD" });
  94     AlignmentSorter.sortByFeature(types, null, 0, al.getWidth(), al,
  95             AlignmentSorter.FEATURE_SCORE);
  96     assertSame(al.getSequenceAt(0), seq3); // -0.5
  97     assertSame(al.getSequenceAt(1), seq1); // 2.0
  98     assertSame(al.getSequenceAt(2), seq2); // 2.5
  99     assertSame(al.getSequenceAt(3), seq4);
 100
 101     /*
 102      * specify groups, excluding g5 (kD -4 score)
 103      * seq3 average is now 3.0
 104      * next sort is ascending (not toggled) as for a different group spec
 105      */
 106     List<String> groups = Arrays.asList(new String[] { "g1", "g2", "g3",
 107         "g6" });
 108     AlignmentSorter.sortByFeature(types, groups, 0, al.getWidth(), al,
 109             AlignmentSorter.FEATURE_SCORE);
 110     assertSame(al.getSequenceAt(0), seq1); // 2.0
 111     assertSame(al.getSequenceAt(1), seq2); // 2.5
 112     assertSame(al.getSequenceAt(2), seq3); // 3.0
 113     assertSame(al.getSequenceAt(3), seq4);
 114
 115     /*
 116      * limit to columns 0-4, excluding 2nd feature of seq1 and seq3
 117      * seq1 is now 2.0, seq3 is now -4
 118      */
 119     // fails because seq1.findPosition(4) returns 4
 120     // although residue 4 is in column 5! - JAL-2544
 121     AlignmentSorter.sortByFeature(null, null, 0, 4, al,
 122             AlignmentSorter.FEATURE_SCORE);
 123     assertSame(al.getSequenceAt(0), seq3); // -4
 124     assertSame(al.getSequenceAt(1), seq1); // 2.0
 125     assertSame(al.getSequenceAt(2), seq2); // 2.5
 126     assertSame(al.getSequenceAt(3), seq4);
 127   }
 128
 129   @Test(groups = "Functional")
 130   public void testSortByFeature_density()
 131   {
 132     // TODO
 133   }
 134 }