Merge branch 'releases/Release_2_10_4_Branch_merged_JAL-2759' into releases/Release_2...

[jalview.git] / test / jalview / datamodel / SequenceTest.java

diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
index a084a8e..5a14514 100644 (file)
--- a/test/jalview/datamodel/SequenceTest.java
+++ b/test/jalview/datamodel/SequenceTest.java
@@ -28,6 +28,7 @@ import static org.testng.AssertJUnit.assertNull;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 
+import jalview.analysis.AlignmentGenerator;
 import jalview.commands.EditCommand;
 import jalview.commands.EditCommand.Action;
 import jalview.datamodel.PDBEntry.Type;
@@ -38,16 +39,17 @@ import java.io.File;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.BitSet;
+import java.util.Iterator;
 import java.util.List;
 import java.util.Vector;
 
-import junit.extensions.PA;
-
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
+import junit.extensions.PA;
+
 public class SequenceTest
 {
 
@@ -799,7 +801,7 @@ public class SequenceTest
     Assert.assertEquals(pdbe1a,
             sq.getDatasetSequence().getPDBEntry("1PDB"),
             "PDB Entry '1PDB' not found on dataset sequence via getPDBEntry.");
-    ArrayList<Annotation> annotsList = new ArrayList<Annotation>();
+    ArrayList<Annotation> annotsList = new ArrayList<>();
     System.out.println(">>>>>> " + sq.getSequenceAsString().length());
     annotsList.add(new Annotation("A", "A", 'X', 0.1f));
     annotsList.add(new Annotation("A", "A", 'X', 0.1f));
@@ -1674,6 +1676,20 @@ public class SequenceTest
   }
 
   @Test(groups = { "Functional" })
+  public void testGapBitset()
+  {
+    SequenceI sq = new Sequence("test/8-13", "-ABC---DE-F--");
+    BitSet bs = sq.gapBitset();
+    BitSet expected = new BitSet();
+    expected.set(0);
+    expected.set(4, 7);
+    expected.set(9);
+    expected.set(11, 13);
+
+    assertTrue(bs.equals(expected));
+
+  }
+
   public void testFindFeatures_largeEndPos()
   {
     /*
@@ -1881,4 +1897,162 @@ public class SequenceTest
     assertEquals(8, sq.getDatasetSequence().getStart());
     assertEquals(9, sq.getDatasetSequence().getEnd());
   }
+
+  /**
+   * Test the code used to locate the reference sequence ruler origin
+   */
+  @Test(groups = { "Functional" })
+  public void testLocateVisibleStartofSequence()
+  {
+    // create random alignment
+    AlignmentGenerator gen = new AlignmentGenerator(false);
+    AlignmentI al = gen.generate(50, 20, 123, 5, 5);
+
+    HiddenColumns cs = al.getHiddenColumns();
+    ColumnSelection colsel = new ColumnSelection();
+
+    SequenceI seq = new Sequence("RefSeq", "-A-SD-ASD--E---");
+    assertEquals(2, seq.findIndex(seq.getStart()));
+
+    // no hidden columns
+    assertEquals(seq.findIndex(seq.getStart()) - 1,
+            seq.firstResidueOutsideIterator(cs.iterator()));
+
+    // hidden column on gap after end of sequence - should not affect bounds
+    colsel.hideSelectedColumns(13, al.getHiddenColumns());
+    assertEquals(seq.findIndex(seq.getStart()) - 1,
+            seq.firstResidueOutsideIterator(cs.iterator()));
+
+    cs.revealAllHiddenColumns(colsel);
+    // hidden column on gap before beginning of sequence - should vis bounds by
+    // one
+    colsel.hideSelectedColumns(0, al.getHiddenColumns());
+    assertEquals(seq.findIndex(seq.getStart()) - 2,
+            cs.absoluteToVisibleColumn(
+                    seq.firstResidueOutsideIterator(cs.iterator())));
+
+    cs.revealAllHiddenColumns(colsel);
+    // hide columns around most of sequence - leave one residue remaining
+    cs.hideColumns(1, 3);
+    cs.hideColumns(6, 11);
+
+    Iterator<int[]> it = cs.getVisContigsIterator(0, 6, false);
+
+    assertEquals("-D", seq.getSequenceStringFromIterator(it));
+    // cs.getVisibleSequenceStrings(0, 5, new SequenceI[]
+    // { seq })[0]);
+
+    assertEquals(4, seq.firstResidueOutsideIterator(cs.iterator()));
+    cs.revealAllHiddenColumns(colsel);
+
+    // hide whole sequence - should just get location of hidden region
+    // containing sequence
+    cs.hideColumns(1, 11);
+    assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator()));
+
+    cs.revealAllHiddenColumns(colsel);
+    cs.hideColumns(0, 15);
+    assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator()));
+
+    SequenceI seq2 = new Sequence("RefSeq2", "-------A-SD-ASD--E---");
+
+    cs.revealAllHiddenColumns(colsel);
+    cs.hideColumns(7, 17);
+    assertEquals(0, seq2.firstResidueOutsideIterator(cs.iterator()));
+
+    cs.revealAllHiddenColumns(colsel);
+    cs.hideColumns(3, 17);
+    assertEquals(0, seq2.firstResidueOutsideIterator(cs.iterator()));
+
+    cs.revealAllHiddenColumns(colsel);
+    cs.hideColumns(3, 19);
+    assertEquals(0, seq2.firstResidueOutsideIterator(cs.iterator()));
+
+    cs.revealAllHiddenColumns(colsel);
+    cs.hideColumns(0, 0);
+    assertEquals(1, seq.firstResidueOutsideIterator(cs.iterator()));
+
+    cs.revealAllHiddenColumns(colsel);
+    cs.hideColumns(0, 1);
+    assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator()));
+
+    cs.revealAllHiddenColumns(colsel);
+    cs.hideColumns(0, 2);
+    assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator()));
+
+    cs.revealAllHiddenColumns(colsel);
+    cs.hideColumns(1, 1);
+    assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator()));
+
+    cs.revealAllHiddenColumns(colsel);
+    cs.hideColumns(1, 2);
+    assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator()));
+
+    cs.revealAllHiddenColumns(colsel);
+    cs.hideColumns(1, 3);
+    assertEquals(4, seq.firstResidueOutsideIterator(cs.iterator()));
+
+    cs.revealAllHiddenColumns(colsel);
+    cs.hideColumns(0, 2);
+    cs.hideColumns(5, 6);
+    assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator()));
+
+    cs.revealAllHiddenColumns(colsel);
+    cs.hideColumns(0, 2);
+    cs.hideColumns(5, 6);
+    cs.hideColumns(9, 10);
+    assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator()));
+
+    cs.revealAllHiddenColumns(colsel);
+    cs.hideColumns(0, 2);
+    cs.hideColumns(7, 11);
+    assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator()));
+
+    cs.revealAllHiddenColumns(colsel);
+    cs.hideColumns(2, 4);
+    cs.hideColumns(7, 11);
+    assertEquals(1, seq.firstResidueOutsideIterator(cs.iterator()));
+
+    cs.revealAllHiddenColumns(colsel);
+    cs.hideColumns(2, 4);
+    cs.hideColumns(7, 12);
+    assertEquals(1, seq.firstResidueOutsideIterator(cs.iterator()));
+
+    cs.revealAllHiddenColumns(colsel);
+    cs.hideColumns(1, 11);
+    assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator()));
+
+    cs.revealAllHiddenColumns(colsel);
+    cs.hideColumns(0, 12);
+    assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator()));
+
+    cs.revealAllHiddenColumns(colsel);
+    cs.hideColumns(0, 4);
+    cs.hideColumns(6, 12);
+    assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator()));
+
+    cs.revealAllHiddenColumns(colsel);
+    cs.hideColumns(0, 1);
+    cs.hideColumns(3, 12);
+    assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator()));
+
+    cs.revealAllHiddenColumns(colsel);
+    cs.hideColumns(3, 14);
+    cs.hideColumns(17, 19);
+    assertEquals(0, seq2.firstResidueOutsideIterator(cs.iterator()));
+
+    cs.revealAllHiddenColumns(colsel);
+    cs.hideColumns(3, 7);
+    cs.hideColumns(9, 14);
+    cs.hideColumns(17, 19);
+    assertEquals(0, seq2.firstResidueOutsideIterator(cs.iterator()));
+
+    cs.revealAllHiddenColumns(colsel);
+    cs.hideColumns(0, 1);
+    cs.hideColumns(3, 4);
+    cs.hideColumns(6, 8);
+    cs.hideColumns(10, 12);
+    assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator()));
+
+  }
 }