JAL-2541 fix to initSeqFrom (and minor code tidy); more tests for

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

diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
index e55e507..739ef5d 100644 (file)
--- a/test/jalview/datamodel/SequenceTest.java
+++ b/test/jalview/datamodel/SequenceTest.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -23,12 +23,14 @@ 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;
 import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
 
 import jalview.datamodel.PDBEntry.Type;
+import jalview.gui.JvOptionPane;
 import jalview.util.MapList;
 
 import java.io.File;
@@ -37,12 +39,23 @@ 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;
 import org.testng.annotations.Test;
 
 public class SequenceTest
 {
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   Sequence seq;
 
   @BeforeMethod(alwaysRun = true)
@@ -275,19 +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" })