import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
+import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
import jalview.io.AppletFormatAdapter;
import jalview.io.FormatAdapter;
import jalview.util.MapList;
import java.util.Iterator;
import java.util.List;
+import org.testng.Assert;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
return a;
}
+ /**
+ * assert wrapper: tests all references in the given alignment are consistent
+ *
+ * @param alignment
+ */
+ public static void assertAlignmentDatasetRefs(AlignmentI alignment)
+ {
+ verifyAlignmentDatasetRefs(alignment, true, null);
+ }
+
+ /**
+ * assert wrapper: tests all references in the given alignment are consistent
+ *
+ * @param alignment
+ * @param message
+ * - prefixed to any assert failed messages
+ */
+ public static void assertAlignmentDatasetRefs(AlignmentI alignment,
+ String message)
+ {
+ verifyAlignmentDatasetRefs(alignment, true, message);
+ }
+
+ /**
+ * verify sequence and dataset references are properly contained within
+ * dataset
+ *
+ * @param alignment
+ * - the alignmentI object to verify (either alignment or dataset)
+ * @param raiseAssert
+ * - when set, testng assertions are raised.
+ * @param message
+ * - null or a string message to prepend to the assert failed messages.
+ * @return true if alignment references were in order, otherwise false.
+ */
+ public static boolean verifyAlignmentDatasetRefs(AlignmentI alignment,
+ boolean raiseAssert, String message)
+ {
+ if (message==null) { message = ""; }
+ if (alignment == null)
+ {
+ if (raiseAssert)
+ {
+ Assert.fail(message+"Alignment for verification was null.");
+ }
+ return false;
+ }
+ if (alignment.getDataset() != null)
+ {
+ AlignmentI dataset = alignment.getDataset();
+ // check all alignment sequences have their dataset within the dataset
+ for (SequenceI seq : alignment.getSequences())
+ {
+ SequenceI seqds = seq.getDatasetSequence();
+ if (seqds.getDatasetSequence() != null)
+ {
+ if (raiseAssert)
+ {
+ Assert.fail(message+" Alignment contained a sequence who's dataset sequence has a second dataset reference.");
+ }
+ return false;
+ }
+ if (dataset.findIndex(seqds) == -1)
+ {
+ if (raiseAssert)
+ {
+ Assert.fail(message+" Alignment contained a sequence who's dataset sequence was not in the dataset.");
+ }
+ return false;
+ }
+ }
+ return verifyAlignmentDatasetRefs(alignment.getDataset(), raiseAssert, message);
+ }
+ else
+ {
+ // verify all dataset sequences
+ for (SequenceI seqds : alignment.getSequences())
+ {
+ if (seqds.getDatasetSequence() != null)
+ {
+ if (raiseAssert)
+ {
+ Assert.fail(message+" Dataset contained a sequence with non-null dataset reference (ie not a dataset sequence!)");
+ }
+ return false;
+ }
+ if (seqds.getDBRefs() != null)
+ {
+ for (DBRefEntry dbr : seqds.getDBRefs())
+ {
+ if (dbr.getMap() != null)
+ {
+ SequenceI seqdbrmapto = dbr.getMap().getTo();
+ if (seqdbrmapto != null)
+ {
+ if (seqdbrmapto.getDatasetSequence() != null)
+ {
+ if (raiseAssert)
+ {
+ Assert.fail(message+" DBRefEntry for sequence in alignment had map to sequence which was not a dataset sequence");
+ }
+ return false;
+
+ }
+ if (alignment.findIndex(dbr.getMap().getTo()) == -1)
+ {
+ if (raiseAssert)
+ {
+ Assert.fail(message+" DBRefEntry for sequence in alignment had map to sequence not in dataset");
+ }
+ return false;
+ }
+ }
+ }
+ }
+ }
+ }
+ // finally, verify codonmappings involve only dataset sequences.
+ if (alignment.getCodonFrames() != null)
+ {
+ for (AlignedCodonFrame alc : alignment.getCodonFrames())
+ {
+ for (SequenceToSequenceMapping ssm : alc.getMappings())
+ {
+ if (ssm.getFromSeq().getDatasetSequence() != null)
+ {
+ if (raiseAssert)
+ {
+ Assert.fail(message+" CodonFrame-SSM-FromSeq is not a dataset sequence");
+ }
+ return false;
+ }
+ if (alignment.findIndex(ssm.getFromSeq()) == -1)
+ {
+
+ if (raiseAssert)
+ {
+ Assert.fail(message+" CodonFrame-SSM-FromSeq is not contained in dataset");
+ }
+ return false;
+ }
+ if (ssm.getMapping().getTo().getDatasetSequence() != null)
+ {
+ if (raiseAssert)
+ {
+ Assert.fail(message+" CodonFrame-SSM-Mapping-ToSeq is not a dataset sequence");
+ }
+ return false;
+ }
+ if (alignment.findIndex(ssm.getMapping().getTo()) == -1)
+ {
+
+ if (raiseAssert)
+ {
+ Assert.fail(message+" CodonFrame-SSM-Mapping-ToSeq is not contained in dataset");
+ }
+ return false;
+ }
+ }
+ }
+ }
+ }
+ return true; // all relationships verified!
+ }
+
+ /**
+ * call verifyAlignmentDatasetRefs with and without assertion raising enabled,
+ * to check expected pass/fail actually occurs in both conditions
+ *
+ * @param al
+ * @param expected
+ * @param msg
+ */
+ private void assertVerifyAlignment(AlignmentI al, boolean expected,
+ String msg)
+ {
+ if (expected)
+ {
+ try
+ {
+
+ Assert.assertTrue(verifyAlignmentDatasetRefs(al, true, null),
+ "Valid test alignment failed when raiseAsserts enabled:"
+ + msg);
+ } catch (AssertionError ae)
+ {
+ ae.printStackTrace();
+ Assert.fail(
+ "Valid test alignment raised assertion errors when raiseAsserts enabled: "
+ + msg, ae);
+ }
+ // also check validation passes with asserts disabled
+ Assert.assertTrue(verifyAlignmentDatasetRefs(al, false, null),
+ "Valid test alignment tested false when raiseAsserts disabled:"
+ + msg);
+ }
+ else
+ {
+ boolean assertRaised = false;
+ try
+ {
+ verifyAlignmentDatasetRefs(al, true, null);
+ } catch (AssertionError ae)
+ {
+ // expected behaviour
+ assertRaised = true;
+ }
+ if (!assertRaised)
+ {
+ Assert.fail("Invalid test alignment passed when raiseAsserts enabled:"
+ + msg);
+ }
+ // also check validation passes with asserts disabled
+ Assert.assertFalse(verifyAlignmentDatasetRefs(al, false, null),
+ "Invalid test alignment tested true when raiseAsserts disabled:"
+ + msg);
+ }
+ }
+ @Test(groups = { "Functional" })
+ public void testVerifyAlignmentDatasetRefs()
+ {
+ SequenceI sq1 = new Sequence("sq1", "ASFDD"), sq2 = new Sequence("sq2",
+ "TTTTTT");
+
+ // construct simple valid alignment dataset
+ Alignment al = new Alignment(new SequenceI[] {
+ sq1, sq2 });
+ // expect this to pass
+ assertVerifyAlignment(al, true, "Simple valid alignment didn't verify");
+
+ // check test for sequence->datasetSequence validity
+ sq1.setDatasetSequence(sq2);
+ assertVerifyAlignment(
+ al,
+ false,
+ "didn't detect dataset sequence with a dataset sequence reference.");
+
+ sq1.setDatasetSequence(null);
+ assertVerifyAlignment(
+ al,
+ true,
+ "didn't reinstate validity after nulling dataset sequence dataset reference");
+
+ // now create dataset and check again
+ al.createDatasetAlignment();
+ assertNotNull(al.getDataset());
+
+ assertVerifyAlignment(al, true,
+ "verify failed after createDatasetAlignment");
+
+ // create a dbref on sq1 with a sequence ref to sq2
+ DBRefEntry dbrs1tos2 = new DBRefEntry("UNIPROT", "1", "Q111111");
+ dbrs1tos2.setMap(new Mapping(sq2.getDatasetSequence(),
+ new int[] { 1, 5 }, new int[] { 2, 6 }, 1, 1));
+ sq1.getDatasetSequence().addDBRef(dbrs1tos2);
+ assertVerifyAlignment(al, true,
+ "verify failed after addition of valid DBRefEntry/map");
+ // now create a dbref on a new sequence which maps to another sequence
+ // outside of the dataset
+ SequenceI sqout = new Sequence("sqout", "ututututucagcagcag"), sqnew = new Sequence(
+ "sqnew", "EEERRR");
+ DBRefEntry sqnewsqout = new DBRefEntry("ENAFOO", "1", "R000001");
+ sqnewsqout.setMap(new Mapping(sqout, new int[] { 1, 6 }, new int[] { 1,
+ 18 }, 1, 3));
+ al.getDataset().addSequence(sqnew);
+
+ assertVerifyAlignment(al, true,
+ "verify failed after addition of new sequence to dataset");
+ // now start checking exception conditions
+ sqnew.addDBRef(sqnewsqout);
+ assertVerifyAlignment(
+ al,
+ false,
+ "verify passed when a dbref with map to sequence outside of dataset was added");
+ // make the verify pass by adding the outsider back in
+ al.getDataset().addSequence(sqout);
+ assertVerifyAlignment(al, true,
+ "verify should have passed after adding dbref->to sequence in to dataset");
+ // and now the same for a codon mapping...
+ SequenceI sqanotherout = new Sequence("sqanotherout",
+ "aggtutaggcagcagcag");
+
+ AlignedCodonFrame alc = new AlignedCodonFrame();
+ alc.addMap(sqanotherout, sqnew, new MapList(new int[] { 1, 6 },
+ new int[] { 1, 18 }, 3, 1));
+
+ al.addCodonFrame(alc);
+ Assert.assertEquals(al.getDataset().getCodonFrames().size(), 1);
+
+ assertVerifyAlignment(
+ al,
+ false,
+ "verify passed when alCodonFrame mapping to sequence outside of dataset was added");
+ // make the verify pass by adding the outsider back in
+ al.getDataset().addSequence(sqanotherout);
+ assertVerifyAlignment(
+ al,
+ true,
+ "verify should have passed once all sequences involved in alCodonFrame were added to dataset");
+ al.getDataset().addSequence(sqanotherout);
+ assertVerifyAlignment(al, false,
+ "verify should have failed when a sequence was added twice to the dataset");
+
+ }
/*
* Read in Stockholm format test data including secondary structure
* annotations.
*
* @throws IOException
*/
- @Test(groups = { "Functional" }, enabled = false)
+ @Test(groups = { "Functional" }, enabled = true)
// TODO review / update this test after redesign of alignAs method
public void testAlignAs_cdnaAsProtein() throws IOException
{
* Realign DNA; currently keeping existing gaps in introns only
*/
((Alignment) al1).alignAs(al2, false, true);
- assertEquals("ACG---GCUCCA------ACT", al1.getSequenceAt(0)
+ assertEquals("ACG---GCUCCA------ACT---", al1.getSequenceAt(0)
.getSequenceAsString());
assertEquals("---CGT---TAACGA---AGT---", al1.getSequenceAt(1)
.getSequenceAsString());
*
* @throws IOException
*/
- @Test(groups = { "Functional" }, enabled = false)
+ @Test(groups = { "Functional" }, enabled = true)
// TODO review / update this test after redesign of alignAs method
public void testAlignAs_cdnaAsProtein_singleSequence() throws IOException
{
acf.addMap(seqFrom, seqTo, ml);
}
+ /*
+ * not sure whether mappings 'belong' or protein or nucleotide
+ * alignment, so adding to both ;~)
+ */
alFrom.addCodonFrame(acf);
+ alTo.addCodonFrame(acf);
}
/**
// TODO should the copy constructor copy the dataset?
// or make a new one referring to the same dataset sequences??
assertNull(copy.getDataset());
+ // TODO test metadata is copied when AlignmentI is a dataset
+
// assertArrayEquals(copy.getDataset().getSequencesArray(), protein
// .getDataset().getSequencesArray());
}
// TODO promote this method to AlignmentI
((Alignment) protein).createDatasetAlignment();
- // TODO this method should return AlignmentI not Alignment !!
- Alignment ds = protein.getDataset();
+ AlignmentI ds = protein.getDataset();
// side-effect: dataset created on second sequence
assertNotNull(protein.getSequenceAt(1).getDatasetSequence());
assertTrue(ds.getCodonFrames().contains(acf));
}
+ /**
+ * tests the addition of *all* sequences referred to by a sequence being added
+ * to the dataset
+ */
+ @Test(groups = "Functional")
+ public void testCreateDatasetAlignmentWithMappedToSeqs()
+ {
+ // Alignment with two sequences, gapped.
+ SequenceI sq1 = new Sequence("sq1", "A--SDF");
+ SequenceI sq2 = new Sequence("sq2", "G--TRQ");
+
+ // cross-references to two more sequences.
+ DBRefEntry dbr = new DBRefEntry("SQ1", "", "sq3");
+ SequenceI sq3 = new Sequence("sq3", "VWANG");
+ dbr.setMap(new Mapping(sq3, new MapList(new int[] { 1, 4 }, new int[] {
+ 2, 5 }, 1, 1)));
+ sq1.addDBRef(dbr);
+
+ SequenceI sq4 = new Sequence("sq4", "ERKWI");
+ DBRefEntry dbr2 = new DBRefEntry("SQ2", "", "sq4");
+ dbr2.setMap(new Mapping(sq4, new MapList(new int[] { 1, 4 }, new int[] {
+ 2, 5 }, 1, 1)));
+ sq2.addDBRef(dbr2);
+ // and a 1:1 codonframe mapping between them.
+ AlignedCodonFrame alc = new AlignedCodonFrame();
+ alc.addMap(sq1, sq2, new MapList(new int[] { 1, 4 },
+ new int[] { 1, 4 }, 1, 1));
+
+ AlignmentI protein = new Alignment(new SequenceI[] { sq1, sq2 });
+
+ /*
+ * create the alignment dataset
+ * note this creates sequence datasets where missing
+ * as a side-effect (in this case, on seq2
+ */
+
+ // TODO promote this method to AlignmentI
+ ((Alignment) protein).createDatasetAlignment();
+
+ AlignmentI ds = protein.getDataset();
+
+ // should be 4 sequences in dataset - two materialised, and two propagated
+ // from dbref
+ assertEquals(4, ds.getHeight());
+ assertTrue(ds.getSequences().contains(sq1.getDatasetSequence()));
+ assertTrue(ds.getSequences().contains(sq2.getDatasetSequence()));
+ assertTrue(ds.getSequences().contains(sq3));
+ assertTrue(ds.getSequences().contains(sq4));
+ // Should have one codon frame mapping between sq1 and sq2 via dataset
+ // sequences
+ assertEquals(ds.getCodonFrame(sq1.getDatasetSequence()),
+ ds.getCodonFrame(sq2.getDatasetSequence()));
+ }
+
@Test(groups = "Functional")
public void testAddCodonFrame()
{
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