X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FSequenceTest.java;h=a084a8e61cfbb19500fd6f7f8a6c7b16a06cabe5;hb=406881e2d77e85afa29c580abcc94e5b20fd9bb0;hp=23e8cf709eff21671b2ff3a55f63723bd241a34b;hpb=98558735e9208afa98bb155bd5350ad0a680ca24;p=jalview.git

diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
index 23e8cf7..a084a8e 100644
--- a/test/jalview/datamodel/SequenceTest.java
+++ b/test/jalview/datamodel/SequenceTest.java
@@ -1704,4 +1704,181 @@ public class SequenceTest
     found = sq.findFeatures(10, 11);
     assertEquals(0, found.size());
   }
+
+  @Test(groups = { "Functional" })
+  public void testSetName()
+  {
+    SequenceI sq = new Sequence("test", "-ABC---DE-F--");
+    assertEquals("test", sq.getName());
+    assertEquals(1, sq.getStart());
+    assertEquals(6, sq.getEnd());
+
+    sq.setName("testing");
+    assertEquals("testing", sq.getName());
+
+    sq.setName("test/8-10");
+    assertEquals("test", sq.getName());
+    assertEquals(8, sq.getStart());
+    assertEquals(13, sq.getEnd()); // note end is recomputed
+
+    sq.setName("testing/7-99");
+    assertEquals("testing", sq.getName());
+    assertEquals(7, sq.getStart());
+    assertEquals(99, sq.getEnd()); // end may be beyond physical end
+
+    sq.setName("/2-3");
+    assertEquals("", sq.getName());
+    assertEquals(2, sq.getStart());
+    assertEquals(7, sq.getEnd());
+
+    sq.setName("test/"); // invalid
+    assertEquals("test/", sq.getName());
+    assertEquals(2, sq.getStart());
+    assertEquals(7, sq.getEnd());
+
+    sq.setName("test/6-13/7-99");
+    assertEquals("test/6-13", sq.getName());
+    assertEquals(7, sq.getStart());
+    assertEquals(99, sq.getEnd());
+
+    sq.setName("test/0-5"); // 0 is invalid - ignored
+    assertEquals("test/0-5", sq.getName());
+    assertEquals(7, sq.getStart());
+    assertEquals(99, sq.getEnd());
+
+    sq.setName("test/a-5"); // a is invalid - ignored
+    assertEquals("test/a-5", sq.getName());
+    assertEquals(7, sq.getStart());
+    assertEquals(99, sq.getEnd());
+
+    sq.setName("test/6-5"); // start > end is invalid - ignored
+    assertEquals("test/6-5", sq.getName());
+    assertEquals(7, sq.getStart());
+    assertEquals(99, sq.getEnd());
+
+    sq.setName("test/5"); // invalid - ignored
+    assertEquals("test/5", sq.getName());
+    assertEquals(7, sq.getStart());
+    assertEquals(99, sq.getEnd());
+
+    sq.setName("test/-5"); // invalid - ignored
+    assertEquals("test/-5", sq.getName());
+    assertEquals(7, sq.getStart());
+    assertEquals(99, sq.getEnd());
+
+    sq.setName("test/5-"); // invalid - ignored
+    assertEquals("test/5-", sq.getName());
+    assertEquals(7, sq.getStart());
+    assertEquals(99, sq.getEnd());
+
+    sq.setName("test/5-6-7"); // invalid - ignored
+    assertEquals("test/5-6-7", sq.getName());
+    assertEquals(7, sq.getStart());
+    assertEquals(99, sq.getEnd());
+
+    sq.setName(null); // invalid, gets converted to space
+    assertEquals("", sq.getName());
+    assertEquals(7, sq.getStart());
+    assertEquals(99, sq.getEnd());
+  }
+
+  @Test(groups = { "Functional" })
+  public void testCheckValidRange()
+  {
+    Sequence sq = new Sequence("test/7-12", "-ABC---DE-F--");
+    assertEquals(7, sq.getStart());
+    assertEquals(12, sq.getEnd());
+
+    /*
+     * checkValidRange ensures end is at least the last residue position
+     */
+    PA.setValue(sq, "end", 2);
+    sq.checkValidRange();
+    assertEquals(12, sq.getEnd());
+
+    /*
+     * end may be beyond the last residue position
+     */
+    PA.setValue(sq, "end", 22);
+    sq.checkValidRange();
+    assertEquals(22, sq.getEnd());
+  }
+
+  @Test(groups = { "Functional" })
+  public void testDeleteChars_withGaps()
+  {
+    /*
+     * delete gaps only
+     */
+    SequenceI sq = new Sequence("test/8-10", "A-B-C");
+    sq.createDatasetSequence();
+    assertEquals("ABC", sq.getDatasetSequence().getSequenceAsString());
+    sq.deleteChars(1, 2); // delete first gap
+    assertEquals("AB-C", sq.getSequenceAsString());
+    assertEquals(8, sq.getStart());
+    assertEquals(10, sq.getEnd());
+    assertEquals("ABC", sq.getDatasetSequence().getSequenceAsString());
+
+    /*
+     * delete gaps and residues at start (no new dataset sequence)
+     */
+    sq = new Sequence("test/8-10", "A-B-C");
+    sq.createDatasetSequence();
+    sq.deleteChars(0, 3); // delete A-B
+    assertEquals("-C", sq.getSequenceAsString());
+    assertEquals(10, sq.getStart());
+    assertEquals(10, sq.getEnd());
+    assertEquals("ABC", sq.getDatasetSequence().getSequenceAsString());
+
+    /*
+     * delete gaps and residues at end (no new dataset sequence)
+     */
+    sq = new Sequence("test/8-10", "A-B-C");
+    sq.createDatasetSequence();
+    sq.deleteChars(2, 5); // delete B-C
+    assertEquals("A-", sq.getSequenceAsString());
+    assertEquals(8, sq.getStart());
+    assertEquals(8, sq.getEnd());
+    assertEquals("ABC", sq.getDatasetSequence().getSequenceAsString());
+
+    /*
+     * delete gaps and residues internally (new dataset sequence)
+     * first delete from gap to residue
+     */
+    sq = new Sequence("test/8-10", "A-B-C");
+    sq.createDatasetSequence();
+    sq.deleteChars(1, 3); // delete -B
+    assertEquals("A-C", sq.getSequenceAsString());
+    assertEquals(8, sq.getStart());
+    assertEquals(9, sq.getEnd());
+    assertEquals("AC", sq.getDatasetSequence().getSequenceAsString());
+    assertEquals(8, sq.getDatasetSequence().getStart());
+    assertEquals(9, sq.getDatasetSequence().getEnd());
+
+    /*
+     * internal delete from gap to gap
+     */
+    sq = new Sequence("test/8-10", "A-B-C");
+    sq.createDatasetSequence();
+    sq.deleteChars(1, 4); // delete -B-
+    assertEquals("AC", sq.getSequenceAsString());
+    assertEquals(8, sq.getStart());
+    assertEquals(9, sq.getEnd());
+    assertEquals("AC", sq.getDatasetSequence().getSequenceAsString());
+    assertEquals(8, sq.getDatasetSequence().getStart());
+    assertEquals(9, sq.getDatasetSequence().getEnd());
+
+    /*
+     * internal delete from residue to residue
+     */
+    sq = new Sequence("test/8-10", "A-B-C");
+    sq.createDatasetSequence();
+    sq.deleteChars(2, 3); // delete B
+    assertEquals("A--C", sq.getSequenceAsString());
+    assertEquals(8, sq.getStart());
+    assertEquals(9, sq.getEnd());
+    assertEquals("AC", sq.getDatasetSequence().getSequenceAsString());
+    assertEquals(8, sq.getDatasetSequence().getStart());
+    assertEquals(9, sq.getDatasetSequence().getEnd());
+  }
 }