JAL-2505 unit test for sort by feature density, Javadoc

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index e9fb335..cc4c469 100755 (executable)
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -33,7 +33,6 @@ import jalview.util.MessageManager;
 import jalview.util.QuickSort;
 
 import java.util.ArrayList;
-import java.util.Arrays;
 import java.util.List;
 
 /**
@@ -703,6 +702,26 @@ public class AlignmentSorter
     return false;
   }
 
+  /**
+   * Sort sequences by feature score or density, optionally restricted by
+   * feature types, feature groups, or alignment start/end positions.
+   * <p>
+   * If the sort is repeated for the same combination of types and groups, sort
+   * order is reversed.
+   * 
+   * @param featureLabels
+   *          a list of feature types to include (or null for all)
+   * @param groupLabels
+   *          a list of feature groups to include (or null for all)
+   * @param start
+   *          start column position to include (base zero)
+   * @param stop
+   *          end column position to include (base zero)
+   * @param alignment
+   *          the alignment to be sorted
+   * @param method
+   *          either "average_score" or "density" ("text" not yet implemented)
+   */
   public static void sortByFeature(List<String> featureLabels,
           List<String> groupLabels, int start, int stop,
           AlignmentI alignment, String method)

diff --git a/test/jalview/analysis/AlignmentSorterTest.java b/test/jalview/analysis/AlignmentSorterTest.java
new file mode 100644 (file)
index 0000000..0255f66
--- /dev/null
+++ b/test/jalview/analysis/AlignmentSorterTest.java
@@ -0,0 +1,131 @@
+package jalview.analysis;
+
+import static org.testng.Assert.assertSame;
+
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+
+import java.util.Arrays;
+import java.util.List;
+
+import junit.extensions.PA;
+
+import org.testng.annotations.Test;
+
+public class AlignmentSorterTest
+{
+  @Test(groups = "Functional")
+  public void testSortByFeature_score()
+  {
+    SequenceI seq1 = new Sequence("Seq1", "ABC--D-EFGHIJ");
+    SequenceI seq2 = new Sequence("Seq2", "ABCDEFGHIJ");
+    SequenceI seq3 = new Sequence("Seq3", "ABCDE-FGHIJ");
+    SequenceI seq4 = new Sequence("Seq4", "ABCDEFGHIJ");
+    SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 };
+    AlignmentI al = new Alignment(seqs);
+    al.setDataset(null);
+
+    /*
+     * sort with no score features does nothing
+     */
+    PA.setValue(AlignmentSorter.class, "lastSortByFeatureScore", null);
+
+    AlignmentSorter.sortByFeature(null, null, 0, al.getWidth(), al,
+            AlignmentSorter.FEATURE_SCORE);
+    assertSame(al.getSequenceAt(0), seq1);
+    assertSame(al.getSequenceAt(1), seq2);
+    assertSame(al.getSequenceAt(2), seq3);
+    assertSame(al.getSequenceAt(3), seq4);
+
+    /*
+     * add score and non-score features
+     * seq1 Cath(2.0) Pfam(4.0) average 3.0
+     * seq2 Cath(2.5) Metal(NaN) average 2.5
+     * seq3 KD(-4), KD(3.0) average -0.5
+     * seq4 Helix(NaN) - should sort as if largest score
+     */
+    seq1.addSequenceFeature(new SequenceFeature("Cath", "", 2, 3, 2.0f,
+            "g1"));
+    seq1.addSequenceFeature(new SequenceFeature("Pfam", "", 4, 5, 4.0f,
+            "g2"));
+    seq2.addSequenceFeature(new SequenceFeature("Cath", "", 2, 3, 2.5f,
+            "g3"));
+    seq2.addSequenceFeature(new SequenceFeature("Metal", "", 2, 3,
+            Float.NaN, "g4"));
+    seq3.addSequenceFeature(new SequenceFeature("kD", "", 2, 3, -4f, "g5"));
+    seq3.addSequenceFeature(new SequenceFeature("kD", "", 5, 6, 3.0f, "g6"));
+    seq4.addSequenceFeature(new SequenceFeature("Helix", "", 2, 3,
+            Float.NaN, "g7"));
+
+    /*
+     * sort by ascending score, no filter on feature type or group
+     * NB sort order for the same feature set (none) is toggled so descending
+     */
+    PA.setValue(AlignmentSorter.class, "sortByFeatureScoreAscending", true);
+    AlignmentSorter.sortByFeature(null, null, 0, al.getWidth(), al,
+            AlignmentSorter.FEATURE_SCORE);
+    assertSame(al.getSequenceAt(3), seq3); // -0.5
+    assertSame(al.getSequenceAt(2), seq2); // 2.5
+    assertSame(al.getSequenceAt(1), seq1); // 3.0
+    assertSame(al.getSequenceAt(0), seq4); // maximum 'score'
+
+    /*
+     * repeat sort toggles order - now ascending
+     */
+    AlignmentSorter.sortByFeature(null, null, 0, al.getWidth(), al,
+            AlignmentSorter.FEATURE_SCORE);
+    assertSame(al.getSequenceAt(0), seq3); // -0.5
+    assertSame(al.getSequenceAt(1), seq2); // 2.5
+    assertSame(al.getSequenceAt(2), seq1); // 3.0
+    assertSame(al.getSequenceAt(3), seq4);
+
+    /*
+     * specify features, excluding Pfam
+     * seq1 average is now 2.0
+     * next sort is ascending (not toggled) as for a different feature set
+     */
+    List<String> types = Arrays.asList(new String[] { "Cath", "kD" });
+    AlignmentSorter.sortByFeature(types, null, 0, al.getWidth(), al,
+            AlignmentSorter.FEATURE_SCORE);
+    assertSame(al.getSequenceAt(0), seq3); // -0.5
+    assertSame(al.getSequenceAt(1), seq1); // 2.0
+    assertSame(al.getSequenceAt(2), seq2); // 2.5
+    assertSame(al.getSequenceAt(3), seq4);
+
+    /*
+     * specify groups, excluding g5 (kD -4 score)
+     * seq3 average is now 3.0
+     * next sort is ascending (not toggled) as for a different group spec
+     */
+    List<String> groups = Arrays.asList(new String[] { "g1", "g2", "g3",
+        "g6" });
+    AlignmentSorter.sortByFeature(types, groups, 0, al.getWidth(), al,
+            AlignmentSorter.FEATURE_SCORE);
+    assertSame(al.getSequenceAt(0), seq1); // 2.0
+    assertSame(al.getSequenceAt(1), seq2); // 2.5
+    assertSame(al.getSequenceAt(2), seq3); // 3.0
+    assertSame(al.getSequenceAt(3), seq4);
+
+    /*
+     * limit to columns 0-4, excluding 2nd feature of seq1 and seq3
+     * seq1 is now 2.0, seq3 is now -4
+     */
+    // fails because seq1.findPosition(4) returns 4
+    // although residue 4 is in column 5!
+    AlignmentSorter.sortByFeature(null, null, 0, 4, al,
+            AlignmentSorter.FEATURE_SCORE);
+    assertSame(al.getSequenceAt(0), seq3); // -4
+    assertSame(al.getSequenceAt(1), seq1); // 2.0
+    assertSame(al.getSequenceAt(2), seq2); // 2.5
+    assertSame(al.getSequenceAt(3), seq4);
+  }
+
+  @Test(groups = "Functional")
+  public void testSortByFeature_density()
+  {
+    // TODO
+  }
+}