X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FSequenceTest.java;h=d7e720e8887eefde157e763eadf65cb78a958650;hb=b9d3d1f71c6a8aee09cd23e1303b062cbe43a239;hp=08e6f7d057e4852f2eb1f647cabc23386fcc3d9c;hpb=5f4e1e4c330b045e9c8bce28ee132a0fca3834d8;p=jalview.git

diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
index 08e6f7d..d7e720e 100644
--- a/test/jalview/datamodel/SequenceTest.java
+++ b/test/jalview/datamodel/SequenceTest.java
@@ -23,6 +23,7 @@ package jalview.datamodel;
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertNotSame;
 import static org.testng.AssertJUnit.assertNull;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
@@ -38,6 +39,8 @@ import java.util.Arrays;
 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;
@@ -285,19 +288,129 @@ public class SequenceTest
   @Test(groups = { "Functional" })
   public void testDeleteChars()
   {
+    /*
+     * internal delete
+     */
     SequenceI sq = new Sequence("test", "ABCDEF");
+    assertNull(PA.getValue(sq, "datasetSequence"));
     assertEquals(1, sq.getStart());
     assertEquals(6, sq.getEnd());
     sq.deleteChars(2, 3);
     assertEquals("ABDEF", sq.getSequenceAsString());
     assertEquals(1, sq.getStart());
     assertEquals(5, sq.getEnd());
+    assertNull(PA.getValue(sq, "datasetSequence"));
 
+    /*
+     * delete at start
+     */
     sq = new Sequence("test", "ABCDEF");
     sq.deleteChars(0, 2);
     assertEquals("CDEF", sq.getSequenceAsString());
     assertEquals(3, sq.getStart());
     assertEquals(6, sq.getEnd());
+    assertNull(PA.getValue(sq, "datasetSequence"));
+
+    /*
+     * delete at end
+     */
+    sq = new Sequence("test", "ABCDEF");
+    sq.deleteChars(4, 6);
+    assertEquals("ABCD", sq.getSequenceAsString());
+    assertEquals(1, sq.getStart());
+    assertEquals(4, sq.getEnd());
+    assertNull(PA.getValue(sq, "datasetSequence"));
+  }
+
+  @Test(groups = { "Functional" })
+  public void testDeleteChars_withDbRefsAndFeatures()
+  {
+    /*
+     * internal delete - new dataset sequence created
+     * gets a copy of any dbrefs
+     */
+    SequenceI sq = new Sequence("test", "ABCDEF");
+    sq.createDatasetSequence();
+    DBRefEntry dbr1 = new DBRefEntry("Uniprot", "0", "a123");
+    sq.addDBRef(dbr1);
+    Object ds = PA.getValue(sq, "datasetSequence");
+    assertNotNull(ds);
+    assertEquals(1, sq.getStart());
+    assertEquals(6, sq.getEnd());
+    sq.deleteChars(2, 3);
+    assertEquals("ABDEF", sq.getSequenceAsString());
+    assertEquals(1, sq.getStart());
+    assertEquals(5, sq.getEnd());
+    Object newDs = PA.getValue(sq, "datasetSequence");
+    assertNotNull(newDs);
+    assertNotSame(ds, newDs);
+    assertNotNull(sq.getDBRefs());
+    assertEquals(1, sq.getDBRefs().length);
+    assertNotSame(dbr1, sq.getDBRefs()[0]);
+    assertEquals(dbr1, sq.getDBRefs()[0]);
+
+    /*
+     * internal delete with sequence features
+     * (failure case for JAL-2541)
+     */
+    sq = new Sequence("test", "ABCDEF");
+    sq.createDatasetSequence();
+    SequenceFeature sf1 = new SequenceFeature("Cath", "desc", 2, 4, 2f,
+            "CathGroup");
+    sq.addSequenceFeature(sf1);
+    ds = PA.getValue(sq, "datasetSequence");
+    assertNotNull(ds);
+    assertEquals(1, sq.getStart());
+    assertEquals(6, sq.getEnd());
+    sq.deleteChars(2, 4);
+    assertEquals("ABEF", sq.getSequenceAsString());
+    assertEquals(1, sq.getStart());
+    assertEquals(4, sq.getEnd());
+    newDs = PA.getValue(sq, "datasetSequence");
+    assertNotNull(newDs);
+    assertNotSame(ds, newDs);
+    SequenceFeature[] sfs = sq.getSequenceFeatures();
+    assertNotNull(sfs);
+    assertEquals(1, sfs.length);
+    assertNotSame(sf1, sfs[0]);
+    assertEquals(sf1, sfs[0]);
+
+    /*
+     * delete at start - no new dataset sequence created
+     * any sequence features remain as before
+     */
+    sq = new Sequence("test", "ABCDEF");
+    sq.createDatasetSequence();
+    ds = PA.getValue(sq, "datasetSequence");
+    sf1 = new SequenceFeature("Cath", "desc", 2, 4, 2f, "CathGroup");
+    sq.addSequenceFeature(sf1);
+    sq.deleteChars(0, 2);
+    assertEquals("CDEF", sq.getSequenceAsString());
+    assertEquals(3, sq.getStart());
+    assertEquals(6, sq.getEnd());
+    assertSame(ds, PA.getValue(sq, "datasetSequence"));
+    sfs = sq.getSequenceFeatures();
+    assertNotNull(sfs);
+    assertEquals(1, sfs.length);
+    assertSame(sf1, sfs[0]);
+
+    /*
+     * delete at end - no new dataset sequence created
+     * any dbrefs remain as before
+     */
+    sq = new Sequence("test", "ABCDEF");
+    sq.createDatasetSequence();
+    ds = PA.getValue(sq, "datasetSequence");
+    dbr1 = new DBRefEntry("Uniprot", "0", "a123");
+    sq.addDBRef(dbr1);
+    sq.deleteChars(4, 6);
+    assertEquals("ABCD", sq.getSequenceAsString());
+    assertEquals(1, sq.getStart());
+    assertEquals(4, sq.getEnd());
+    assertSame(ds, PA.getValue(sq, "datasetSequence"));
+    assertNotNull(sq.getDBRefs());
+    assertEquals(1, sq.getDBRefs().length);
+    assertSame(dbr1, sq.getDBRefs()[0]);
   }
 
   @Test(groups = { "Functional" })
@@ -340,7 +453,7 @@ public class SequenceTest
     /*
      * SequenceFeature on sequence
      */
-    SequenceFeature sf = new SequenceFeature();
+    SequenceFeature sf = new SequenceFeature("Cath", "desc", 2, 4, 2f, null);
     sq.addSequenceFeature(sf);
     SequenceFeature[] sfs = sq.getSequenceFeatures();
     assertEquals(1, sfs.length);
@@ -353,7 +466,8 @@ public class SequenceTest
      * Note JAL-2046: spurious: we have no use case for this at the moment.
      * This test also buggy - as sf2.equals(sf), no new feature is added
      */
-    SequenceFeature sf2 = new SequenceFeature();
+    SequenceFeature sf2 = new SequenceFeature("Cath", "desc", 2, 4, 2f,
+            null);
     sq.getDatasetSequence().addSequenceFeature(sf2);
     sfs = sq.getSequenceFeatures();
     assertEquals(1, sfs.length);
@@ -435,11 +549,26 @@ public class SequenceTest
   public void testCreateDatasetSequence()
   {
     SequenceI sq = new Sequence("my", "ASDASD");
+    sq.addSequenceFeature(new SequenceFeature("type", "desc", 1, 10, 1f,
+            "group"));
+    sq.addDBRef(new DBRefEntry("source", "version", "accession"));
     assertNull(sq.getDatasetSequence());
+    assertNotNull(PA.getValue(sq, "sequenceFeatures")); // to be removed!
+    assertNotNull(PA.getValue(sq, "sequenceFeatureStore"));
+    assertNotNull(PA.getValue(sq, "dbrefs"));
+
     SequenceI rds = sq.createDatasetSequence();
     assertNotNull(rds);
     assertNull(rds.getDatasetSequence());
-    assertEquals(sq.getDatasetSequence(), rds);
+    assertSame(sq.getDatasetSequence(), rds);
+
+    // sequence features and dbrefs transferred to dataset sequence
+    assertNull(PA.getValue(sq, "sequenceFeatures"));
+    assertNull(PA.getValue(sq, "sequenceFeatureStore"));
+    assertNull(PA.getValue(sq, "dbrefs"));
+    assertNotNull(PA.getValue(rds, "sequenceFeatures"));
+    assertNotNull(PA.getValue(rds, "sequenceFeatureStore"));
+    assertNotNull(PA.getValue(rds, "dbrefs"));
   }
 
   /**
@@ -711,6 +840,36 @@ public class SequenceTest
     assertEquals(' ', sq.getCharAt(-1));
   }
 
+  @Test(groups = { "Functional" })
+  public void testAddSequenceFeatures()
+  {
+    SequenceI sq = new Sequence("", "abcde");
+    // type may not be null
+    assertFalse(sq.addSequenceFeature(new SequenceFeature(null, "desc", 4,
+            8, 0f, null)));
+    assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 4,
+            8, 0f, null)));
+    // can't add a duplicate feature
+    assertFalse(sq.addSequenceFeature(new SequenceFeature("Cath", "desc",
+            4, 8, 0f, null)));
+    // can add a different feature
+    assertTrue(sq.addSequenceFeature(new SequenceFeature("Scop", "desc", 4,
+            8, 0f, null))); // different type
+    assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath",
+            "description", 4, 8, 0f, null)));// different description
+    assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 3,
+            8, 0f, null))); // different start position
+    assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 4,
+            9, 0f, null))); // different end position
+    assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 4,
+            8, 1f, null))); // different score
+    assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 4,
+            8, Float.NaN, null))); // score NaN
+    assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 4,
+            8, 0f, "Metal"))); // different group
+    assertEquals(8, sq.getFeatures().getAllFeatures().size());
+  }
+
   /**
    * Tests for adding (or updating) dbrefs
    *