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 junit.extensions.PA;
  15
  16 import org.testng.annotations.Test;
  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     PA.setValue(AlignmentSorter.class, "sortByFeatureCriteria", null);
  35
  36     AlignmentSorter.sortByFeature(null, null, 0, al.getWidth(), al,
  37             AlignmentSorter.FEATURE_SCORE);
  38     assertSame(al.getSequenceAt(0), seq1);
  39     assertSame(al.getSequenceAt(1), seq2);
  40     assertSame(al.getSequenceAt(2), seq3);
  41     assertSame(al.getSequenceAt(3), seq4);
  42
  43     /*
  44      * add score and non-score features
  45      * seq1 Cath(2.0) Pfam(4.0) average 3.0
  46      * seq2 Cath(2.5) Metal(NaN) average 2.5
  47      * seq3 KD(-4), KD(3.0) average -0.5
  48      * seq4 Helix(NaN) - should sort as if largest score
  49      */
  50     seq1.addSequenceFeature(
  51             new SequenceFeature("Cath", "", 2, 3, 2.0f, "g1"));
  52     seq1.addSequenceFeature(
  53             new SequenceFeature("Pfam", "", 4, 5, 4.0f, "g2"));
  54     seq2.addSequenceFeature(
  55             new SequenceFeature("Cath", "", 2, 3, 2.5f, "g3"));
  56     seq2.addSequenceFeature(
  57             new SequenceFeature("Metal", "", 2, 3, Float.NaN, "g4"));
  58     seq3.addSequenceFeature(new SequenceFeature("kD", "", 2, 3, -4f, "g5"));
  59     seq3.addSequenceFeature(
  60             new SequenceFeature("kD", "", 5, 6, 3.0f, "g6"));
  61     seq4.addSequenceFeature(
  62             new SequenceFeature("Helix", "", 2, 3, Float.NaN, "g7"));
  63
  64     /*
  65      * sort by ascending score, no filter on feature type or group
  66      * NB sort order for the same feature set (none) gets toggled, so descending
  67      */
  68     PA.setValue(AlignmentSorter.class, "sortByFeatureAscending", true);
  69     AlignmentSorter.sortByFeature(null, null, 0, al.getWidth(), al,
  70             AlignmentSorter.FEATURE_SCORE);
  71     assertSame(al.getSequenceAt(3), seq3); // -0.5
  72     assertSame(al.getSequenceAt(2), seq2); // 2.5
  73     assertSame(al.getSequenceAt(1), seq1); // 3.0
  74     assertSame(al.getSequenceAt(0), seq4); // maximum 'score'
  75
  76     /*
  77      * repeat sort toggles order - now ascending
  78      */
  79     AlignmentSorter.sortByFeature(null, null, 0, al.getWidth(), al,
  80             AlignmentSorter.FEATURE_SCORE);
  81     assertSame(al.getSequenceAt(0), seq3); // -0.5
  82     assertSame(al.getSequenceAt(1), seq2); // 2.5
  83     assertSame(al.getSequenceAt(2), seq1); // 3.0
  84     assertSame(al.getSequenceAt(3), seq4);
  85
  86     /*
  87      * specify features, excluding Pfam
  88      * seq1 average is now 2.0
  89      * next sort is ascending (not toggled) as for a different feature set
  90      */
  91     List<String> types = Arrays.asList(new String[] { "Cath", "kD" });
  92     AlignmentSorter.sortByFeature(types, null, 0, al.getWidth(), al,
  93             AlignmentSorter.FEATURE_SCORE);
  94     assertSame(al.getSequenceAt(0), seq3); // -0.5
  95     assertSame(al.getSequenceAt(1), seq1); // 2.0
  96     assertSame(al.getSequenceAt(2), seq2); // 2.5
  97     assertSame(al.getSequenceAt(3), seq4);
  98
  99     /*
 100      * specify groups, excluding g5 (kD -4 score)
 101      * seq3 average is now 3.0
 102      * next sort is ascending (not toggled) as for a different group spec
 103      */
 104     List<String> groups = Arrays
 105             .asList(new String[]
 106             { "g1", "g2", "g3", "g6" });
 107     AlignmentSorter.sortByFeature(types, groups, 0, al.getWidth(), al,
 108             AlignmentSorter.FEATURE_SCORE);
 109     assertSame(al.getSequenceAt(0), seq1); // 2.0
 110     assertSame(al.getSequenceAt(1), seq2); // 2.5
 111     assertSame(al.getSequenceAt(2), seq3); // 3.0
 112     assertSame(al.getSequenceAt(3), seq4);
 113
 114     /*
 115      * limit to columns 0-4, excluding 2nd feature of seq1 and seq3
 116      * seq1 is now 2.0, seq3 is now -4
 117      */
 118     // fails because seq1.findPosition(4) returns 4
 119     // although residue 4 is in column 5! - JAL-2544
 120     AlignmentSorter.sortByFeature(null, null, 0, 4, al,
 121             AlignmentSorter.FEATURE_SCORE);
 122     assertSame(al.getSequenceAt(0), seq3); // -4
 123     assertSame(al.getSequenceAt(1), seq1); // 2.0
 124     assertSame(al.getSequenceAt(2), seq2); // 2.5
 125     assertSame(al.getSequenceAt(3), seq4);
 126   }
 127
 128   @Test(groups = "Functional")
 129   public void testSortByFeature_density()
 130   {
 131     // TODO
 132   }
 133 }