X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FSequenceTest.java;h=03c4a96025a0a44623acf71f04c9827954553568;hb=b052502c048abfd6981bdad47d1582e8663804e1;hp=a66a33115d12988afab7158f6dd19c89d9eb8f51;hpb=d1dcf07f3a505db364405c4f4c901219213c8f25;p=jalview.git

diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
index a66a331..03c4a96 100644
--- a/test/jalview/datamodel/SequenceTest.java
+++ b/test/jalview/datamodel/SequenceTest.java
@@ -30,10 +30,12 @@ import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
 
 import jalview.datamodel.PDBEntry.Type;
 
+import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
 import java.util.Vector;
 
+import org.testng.Assert;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
@@ -336,6 +338,10 @@ public class SequenceTest
      * sequence. Test shows no infinite loop results.
      */
     sq.getDatasetSequence().setSequenceFeatures(null);
+    /**
+     * is there a usecase for this ? setDatasetSequence should throw an error if
+     * this actually occurs.
+     */
     sq.getDatasetSequence().setDatasetSequence(sq); // loop!
     assertNull(sq.getSequenceFeatures());
   }
@@ -393,7 +399,71 @@ public class SequenceTest
     sq.setStart(3);
     sq.setEnd(4);
 
+    sq.setDescription("Test sequence description..");
+    sq.setVamsasId("TestVamsasId");
+    sq.setSourceDBRef(new DBRefEntry("PDB", "version0", "1TST"));
+
+    sq.addDBRef(new DBRefEntry("PDB", "version1", "1Tst"));
+    sq.addDBRef(new DBRefEntry("PDB", "version2", "2Tst"));
+    sq.addDBRef(new DBRefEntry("PDB", "version3", "3Tst"));
+    sq.addDBRef(new DBRefEntry("PDB", "version4", "4Tst"));
+
+    sq.addPDBId(new PDBEntry("1PDB", "A", Type.PDB, "filePath/test1"));
+    sq.addPDBId(new PDBEntry("1PDB", "B", Type.PDB, "filePath/test1"));
+    sq.addPDBId(new PDBEntry("2PDB", "A", Type.MMCIF, "filePath/test2"));
+    sq.addPDBId(new PDBEntry("2PDB", "B", Type.MMCIF, "filePath/test2"));
+
+    sq.getDatasetSequence().addDBRef(
+            new DBRefEntry("PDB", "version1", "1Tst"));
+    sq.getDatasetSequence().addDBRef(
+            new DBRefEntry("PDB", "version2", "2Tst"));
+    sq.getDatasetSequence().addDBRef(
+            new DBRefEntry("PDB", "version3", "3Tst"));
+    sq.getDatasetSequence().addDBRef(
+            new DBRefEntry("PDB", "version4", "4Tst"));
+
+    sq.getDatasetSequence().addPDBId(
+            new PDBEntry("1PDB", "A", Type.PDB, "filePath/test1"));
+    sq.getDatasetSequence().addPDBId(
+            new PDBEntry("1PDB", "B", Type.PDB, "filePath/test1"));
+    sq.getDatasetSequence().addPDBId(
+            new PDBEntry("2PDB", "A", Type.MMCIF, "filePath/test2"));
+    sq.getDatasetSequence().addPDBId(
+            new PDBEntry("2PDB", "B", Type.MMCIF, "filePath/test2"));
+
+    ArrayList<Annotation> annotsList = new ArrayList<Annotation>();
+    System.out.println(">>>>>> " + sq.getSequenceAsString().length());
+    annotsList.add(new Annotation("A", "A", 'X', 0.1f));
+    annotsList.add(new Annotation("A", "A", 'X', 0.1f));
+    Annotation[] annots = annotsList.toArray(new Annotation[0]);
+    sq.addAlignmentAnnotation(new AlignmentAnnotation("Test annot",
+            "Test annot description", annots));
+    sq.getDatasetSequence().addAlignmentAnnotation(
+            new AlignmentAnnotation("Test annot", "Test annot description",
+                    annots));
+    Assert.assertEquals(sq.getDescription(), "Test sequence description..");
+    Assert.assertEquals(sq.getDBRefs().length, 4);
+    Assert.assertEquals(sq.getAllPDBEntries().size(), 4);
+    Assert.assertNotNull(sq.getAnnotation());
+    Assert.assertEquals(sq.getAnnotation()[0].annotations.length, 2);
+    Assert.assertEquals(sq.getDatasetSequence().getDBRefs().length, 4);
+    Assert.assertEquals(sq.getDatasetSequence().getAllPDBEntries().size(),
+            4);
+    Assert.assertNotNull(sq.getDatasetSequence().getAnnotation());
+
     Sequence derived = (Sequence) sq.deriveSequence();
+
+    Assert.assertEquals(derived.getDescription(),
+            "Test sequence description..");
+    Assert.assertEquals(derived.getDBRefs().length, 4);
+    Assert.assertEquals(derived.getAllPDBEntries().size(), 4);
+    Assert.assertNotNull(derived.getAnnotation());
+    Assert.assertEquals(derived.getAnnotation()[0].annotations.length, 2);
+    Assert.assertEquals(derived.getDatasetSequence().getDBRefs().length, 4);
+    Assert.assertEquals(derived.getDatasetSequence().getAllPDBEntries()
+            .size(), 4);
+    Assert.assertNotNull(derived.getDatasetSequence().getAnnotation());
+
     assertEquals("CD", derived.getSequenceAsString());
     assertSame(sq.getDatasetSequence(), derived.getDatasetSequence());