X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=test%2Fjalview%2Fdatamodel%2FSequenceTest.java;fp=test%2Fjalview%2Fdatamodel%2FSequenceTest.java;h=2a2d2ab7733b66fa9bbe21c6407eb72ec856a1ed;hb=e07fc11d5aaf4d1237d83e5f7ea0909dea09902e;hp=40476a0788240f0ddaa478914ca6eecfb8ba38f5;hpb=913c7db3eaf97959bcd34a7e96b64632b622edc8;p=jalview.git

diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
index 40476a0..2a2d2ab 100644
--- a/test/jalview/datamodel/SequenceTest.java
+++ b/test/jalview/datamodel/SequenceTest.java
@@ -5,6 +5,7 @@ import static org.junit.Assert.assertNull;
 import static org.junit.Assert.assertSame;
 import static org.junit.Assert.assertTrue;
 
+import java.util.Arrays;
 import java.util.List;
 
 import org.junit.Before;
@@ -135,4 +136,130 @@ public class SequenceTest
     assertSame(annotation2, anns[1]);
 
   }
+
+  @Test
+  public void testGetStartGetEnd()
+  {
+    SequenceI seq = new Sequence("test", "ABCDEF");
+    assertEquals(1, seq.getStart());
+    assertEquals(6, seq.getEnd());
+
+    seq = new Sequence("test", "--AB-C-DEF--");
+    assertEquals(1, seq.getStart());
+    assertEquals(6, seq.getEnd());
+
+    seq = new Sequence("test", "----");
+    assertEquals(1, seq.getStart());
+    assertEquals(0, seq.getEnd()); // ??
+  }
+
+  /**
+   * Tests for the method that returns an alignment column position (base 1) for
+   * a given sequence position (base 1).
+   */
+  @Test
+  public void testFindIndex()
+  {
+    SequenceI seq = new Sequence("test", "ABCDEF");
+    assertEquals(0, seq.findIndex(0));
+    assertEquals(1, seq.findIndex(1));
+    assertEquals(5, seq.findIndex(5));
+    assertEquals(6, seq.findIndex(6));
+    assertEquals(6, seq.findIndex(9));
+
+    seq = new Sequence("test", "-A--B-C-D-E-F--");
+    assertEquals(2, seq.findIndex(1));
+    assertEquals(5, seq.findIndex(2));
+    assertEquals(7, seq.findIndex(3));
+
+    // before start returns 0
+    assertEquals(0, seq.findIndex(0));
+    assertEquals(0, seq.findIndex(-1));
+
+    // beyond end returns last residue column
+    assertEquals(13, seq.findIndex(99));
+
+  }
+
+  /**
+   * Tests for the method that returns a dataset sequence position (base 1) for
+   * an aligned column position (base 0).
+   */
+  @Test
+  public void testFindPosition()
+  {
+    SequenceI seq = new Sequence("test", "ABCDEF");
+    assertEquals(1, seq.findPosition(0));
+    assertEquals(6, seq.findPosition(5));
+    // assertEquals(-1, seq.findPosition(6)); // fails
+
+    seq = new Sequence("test", "AB-C-D--");
+    assertEquals(1, seq.findPosition(0));
+    assertEquals(2, seq.findPosition(1));
+    // gap position 'finds' residue to the right (not the left as per javadoc)
+    assertEquals(3, seq.findPosition(2));
+    assertEquals(3, seq.findPosition(3));
+    assertEquals(4, seq.findPosition(4));
+    assertEquals(4, seq.findPosition(5));
+    // returns 1 more than sequence length if off the end ?!?
+    assertEquals(5, seq.findPosition(6));
+    assertEquals(5, seq.findPosition(7));
+
+    seq = new Sequence("test", "--AB-C-DEF--");
+    assertEquals(1, seq.findPosition(0));
+    assertEquals(1, seq.findPosition(1));
+    assertEquals(1, seq.findPosition(2));
+    assertEquals(2, seq.findPosition(3));
+    assertEquals(3, seq.findPosition(4));
+    assertEquals(3, seq.findPosition(5));
+    assertEquals(4, seq.findPosition(6));
+    assertEquals(4, seq.findPosition(7));
+    assertEquals(5, seq.findPosition(8));
+    assertEquals(6, seq.findPosition(9));
+    assertEquals(7, seq.findPosition(10));
+    assertEquals(7, seq.findPosition(11));
+  }
+
+  @Test
+  public void testDeleteChars()
+  {
+    SequenceI seq = new Sequence("test", "ABCDEF");
+    assertEquals(1, seq.getStart());
+    assertEquals(6, seq.getEnd());
+    seq.deleteChars(2, 3);
+    assertEquals("ABDEF", seq.getSequenceAsString());
+    assertEquals(1, seq.getStart());
+    assertEquals(5, seq.getEnd());
+
+    seq = new Sequence("test", "ABCDEF");
+    seq.deleteChars(0, 2);
+    assertEquals("CDEF", seq.getSequenceAsString());
+    assertEquals(3, seq.getStart());
+    assertEquals(6, seq.getEnd());
+  }
+
+  @Test
+  public void testInsertCharAt()
+  {
+    // non-static methods:
+    SequenceI seq = new Sequence("test", "ABCDEF");
+    seq.insertCharAt(0, 'z');
+    assertEquals("zABCDEF", seq.getSequenceAsString());
+    seq.insertCharAt(2, 2, 'x');
+    assertEquals("zAxxBCDEF", seq.getSequenceAsString());
+    
+    // for static method see StringUtilsTest
+  }
+
+  /**
+   * Test the method that returns an array of aligned sequence positions where
+   * the array index is the data sequence position (both base 0).
+   */
+  @Test
+  public void testGapMap()
+  {
+    SequenceI seq = new Sequence("test", "-A--B-CD-E--F-");
+    seq.createDatasetSequence();
+    assertEquals("[1, 4, 6, 7, 9, 12]", Arrays.toString(seq.gapMap()));
+  }
 }