JAL-3210 Barebones gradle/buildship/eclipse. See README

[jalview.git] / test / jalview / analysis / AlignmentSorterTest.java

diff --git a/test/jalview/analysis/AlignmentSorterTest.java b/test/jalview/analysis/AlignmentSorterTest.java
deleted file mode 100644 (file)
index 090ae1a..0000000
--- a/test/jalview/analysis/AlignmentSorterTest.java
+++ /dev/null
@@ -1,134 +0,0 @@
-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 org.testng.annotations.Test;
-
-import junit.extensions.PA;
-
-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
-     */
-    AlignmentSorter sorter = (AlignmentSorter) PA
-            .invokeMethod(AlignmentSorter.class, "getInstance()",
-                    new Object[] {});
-    PA.setValue(sorter, "sortByFeatureCriteria", 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) gets toggled, so descending
-     */
-    PA.setValue(sorter, "sortByFeatureAscending", 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! - JAL-2544
-    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
-  }
-}