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

deleteChars

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index b0faf21..9994675 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -34,6 +34,8 @@ import java.util.Enumeration;
 import java.util.List;
 import java.util.Vector;
 
+import com.stevesoft.pat.Regex;
+
 import fr.orsay.lri.varna.models.rna.RNA;
 
 /**
@@ -45,6 +47,11 @@ import fr.orsay.lri.varna.models.rna.RNA;
  */
 public class Sequence extends ASequence implements SequenceI
 {
+  private static final Regex limitrx = new Regex(
+          "[/][0-9]{1,}[-][0-9]{1,}$");
+
+  private static final Regex endrx = new Regex("[0-9]{1,}$");
+
   SequenceI datasetSequence;
 
   String name;
@@ -124,11 +131,6 @@ public class Sequence extends ASequence implements SequenceI
     checkValidRange();
   }
 
-  com.stevesoft.pat.Regex limitrx = new com.stevesoft.pat.Regex(
-          "[/][0-9]{1,}[-][0-9]{1,}$");
-
-  com.stevesoft.pat.Regex endrx = new com.stevesoft.pat.Regex("[0-9]{1,}$");
-
   void parseId()
   {
     if (name == null)
@@ -230,23 +232,28 @@ public class Sequence extends ASequence implements SequenceI
   protected void initSeqFrom(SequenceI seq,
           AlignmentAnnotation[] alAnnotation)
   {
-    {
-      char[] oseq = seq.getSequence();
-      initSeqAndName(seq.getName(), Arrays.copyOf(oseq, oseq.length),
-              seq.getStart(), seq.getEnd());
-    }
+    char[] oseq = seq.getSequence();
+    initSeqAndName(seq.getName(), Arrays.copyOf(oseq, oseq.length),
+            seq.getStart(), seq.getEnd());
+
     description = seq.getDescription();
     if (seq != datasetSequence)
     {
       setDatasetSequence(seq.getDatasetSequence());
     }
-    if (datasetSequence == null && seq.getDBRefs() != null)
+    
+    /*
+     * only copy DBRefs and seqfeatures if we really are a dataset sequence
+     */
+    if (datasetSequence == null)
     {
-      // only copy DBRefs and seqfeatures if we really are a dataset sequence
-      DBRefEntry[] dbr = seq.getDBRefs();
-      for (int i = 0; i < dbr.length; i++)
+      if (seq.getDBRefs() != null)
       {
-        addDBRef(new DBRefEntry(dbr[i]));
+        DBRefEntry[] dbr = seq.getDBRefs();
+        for (int i = 0; i < dbr.length; i++)
+        {
+          addDBRef(new DBRefEntry(dbr[i]));
+        }
       }
       if (seq.getSequenceFeatures() != null)
       {
@@ -257,6 +264,7 @@ public class Sequence extends ASequence implements SequenceI
         }
       }
     }
+
     if (seq.getAnnotation() != null)
     {
       AlignmentAnnotation[] sqann = seq.getAnnotation();
@@ -1214,11 +1222,11 @@ public class Sequence extends ASequence implements SequenceI
       return null;
     }
 
-    Vector subset = new Vector();
-    Enumeration e = annotation.elements();
+    Vector<AlignmentAnnotation> subset = new Vector<AlignmentAnnotation>();
+    Enumeration<AlignmentAnnotation> e = annotation.elements();
     while (e.hasMoreElements())
     {
-      AlignmentAnnotation ann = (AlignmentAnnotation) e.nextElement();
+      AlignmentAnnotation ann = e.nextElement();
       if (ann.label != null && ann.label.equals(label))
       {
         subset.addElement(ann);
@@ -1233,7 +1241,7 @@ public class Sequence extends ASequence implements SequenceI
     e = subset.elements();
     while (e.hasMoreElements())
     {
-      anns[i++] = (AlignmentAnnotation) e.nextElement();
+      anns[i++] = e.nextElement();
     }
     subset.removeAllElements();
     return anns;
@@ -1304,10 +1312,10 @@ public class Sequence extends ASequence implements SequenceI
     // transfer PDB entries
     if (entry.getAllPDBEntries() != null)
     {
-      Enumeration e = entry.getAllPDBEntries().elements();
+      Enumeration<PDBEntry> e = entry.getAllPDBEntries().elements();
       while (e.hasMoreElements())
       {
-        PDBEntry pdb = (PDBEntry) e.nextElement();
+        PDBEntry pdb = e.nextElement();
         addPDBId(pdb);
       }
     }

diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
index 08e6f7d..739ef5d 100644 (file)
--- 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" })