+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
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.assertNull;
+import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
-import jalview.io.AppletFormatAdapter;
-import jalview.io.FormatAdapter;
-import jalview.util.MapList;
-
import java.io.IOException;
+import java.util.Arrays;
import java.util.Iterator;
+import java.util.List;
+import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
+import jalview.analysis.AlignmentGenerator;
+import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
+import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FileFormatI;
+import jalview.io.FormatAdapter;
+import jalview.util.Comparison;
+import jalview.util.MapList;
+
/**
* Unit tests for Alignment datamodel.
*
*/
public class AlignmentTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
// @formatter:off
private static final String TEST_DATA =
"# STOCKHOLM 1.0\n" +
"//";
private static final String AA_SEQS_1 =
- ">Seq1Name\n" +
+ ">Seq1Name/5-8\n" +
"K-QY--L\n" +
- ">Seq2Name\n" +
+ ">Seq2Name/12-15\n" +
"-R-FP-W-\n";
private static final String CDNA_SEQS_1 =
- ">Seq1Name\n" +
+ ">Seq1Name/100-111\n" +
"AC-GG--CUC-CAA-CT\n" +
- ">Seq2Name\n" +
+ ">Seq2Name/200-211\n" +
"-CG-TTA--ACG---AAGT\n";
private static final String CDNA_SEQS_2 =
- ">Seq1Name\n" +
+ ">Seq1Name/50-61\n" +
"GCTCGUCGTACT\n" +
- ">Seq2Name\n" +
+ ">Seq2Name/60-71\n" +
"GGGTCAGGCAGT\n";
// @formatter:on
* @return
* @throws IOException
*/
- protected AlignmentI loadAlignment(final String data, String format)
+ protected AlignmentI loadAlignment(final String data, FileFormatI format)
throws IOException
{
- AlignmentI a = new FormatAdapter().readFile(data,
- AppletFormatAdapter.PASTE, format);
+ AlignmentI a = new FormatAdapter().readFile(data, DataSourceType.PASTE,
+ format);
a.setDataset(null);
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
+ {
+ int dsp = -1;
+ // verify all dataset sequences
+ for (SequenceI seqds : alignment.getSequences())
+ {
+ dsp++;
+ 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;
+ }
+ int foundp = alignment.findIndex(seqds);
+ if (foundp != dsp)
+ {
+ if (raiseAssert)
+ {
+ Assert.fail(message
+ + " Dataset sequence array contains a reference at "
+ + dsp + " to a sequence first seen at " + foundp + " ("
+ + seqds.toString() + ")");
+ }
+ 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 " + dbr
+ + " for sequence " + seqds
+ + " in alignment has 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");
+ al.getDataset().deleteSequence(sqanotherout);
+ assertVerifyAlignment(al, true,
+ "verify should have passed after duplicate entry for sequence was removed");
+ }
+
+ /**
+ * checks that the sequence data for an alignment's dataset is non-redundant.
+ * Fails if there are sequences with same id, sequence, start, and.
+ */
+
+ public static void assertDatasetIsNormalised(AlignmentI al)
+ {
+ assertDatasetIsNormalised(al, null);
+ }
+
+ /**
+ * checks that the sequence data for an alignment's dataset is non-redundant.
+ * Fails if there are sequences with same id, sequence, start, and.
+ *
+ * @param al
+ * - alignment to verify
+ * @param message
+ * - null or message prepended to exception message.
+ */
+ public static void assertDatasetIsNormalised(AlignmentI al,
+ String message)
+ {
+ if (al.getDataset() != null)
+ {
+ assertDatasetIsNormalised(al.getDataset(), message);
+ return;
+ }
+ /*
+ * look for pairs of sequences with same ID, start, end, and sequence
+ */
+ List<SequenceI> seqSet = al.getSequences();
+ for (int p = 0; p < seqSet.size(); p++)
+ {
+ SequenceI pSeq = seqSet.get(p);
+ for (int q = p + 1; q < seqSet.size(); q++)
+ {
+ SequenceI qSeq = seqSet.get(q);
+ if (pSeq.getStart() != qSeq.getStart())
+ {
+ continue;
+ }
+ if (pSeq.getEnd() != qSeq.getEnd())
+ {
+ continue;
+ }
+ if (!pSeq.getName().equals(qSeq.getName()))
+ {
+ continue;
+ }
+ if (!Arrays.equals(pSeq.getSequence(), qSeq.getSequence()))
+ {
+ continue;
+ }
+ Assert.fail((message == null ? "" : message + " :")
+ + "Found similar sequences at position " + p + " and " + q
+ + "\n" + pSeq.toString());
+ }
+ }
+ }
+
+ @Test(groups = { "Functional", "Asserts" })
+ public void testAssertDatasetIsNormalised()
+ {
+ Sequence sq1 = new Sequence("s1/1-4", "asdf");
+ Sequence sq1shift = new Sequence("s1/2-5", "asdf");
+ Sequence sq1seqd = new Sequence("s1/1-4", "asdt");
+ Sequence sq2 = new Sequence("s2/1-4", "asdf");
+ Sequence sq1dup = new Sequence("s1/1-4", "asdf");
+
+ Alignment al = new Alignment(new SequenceI[] { sq1 });
+ al.setDataset(null);
+
+ try
+ {
+ assertDatasetIsNormalised(al);
+ } catch (AssertionError ae)
+ {
+ Assert.fail("Single sequence should be valid normalised dataset.");
+ }
+ al.addSequence(sq2);
+ try
+ {
+ assertDatasetIsNormalised(al);
+ } catch (AssertionError ae)
+ {
+ Assert.fail(
+ "Two different sequences should be valid normalised dataset.");
+ }
+ /*
+ * now change sq2's name in the alignment. should still be valid
+ */
+ al.findName(sq2.getName()).setName("sq1");
+ try
+ {
+ assertDatasetIsNormalised(al);
+ } catch (AssertionError ae)
+ {
+ Assert.fail(
+ "Two different sequences in dataset, but same name in alignment, should be valid normalised dataset.");
+ }
+
+ al.addSequence(sq1seqd);
+ try
+ {
+ assertDatasetIsNormalised(al);
+ } catch (AssertionError ae)
+ {
+ Assert.fail(
+ "sq1 and sq1 with different sequence should be distinct.");
+ }
+
+ al.addSequence(sq1shift);
+ try
+ {
+ assertDatasetIsNormalised(al);
+ } catch (AssertionError ae)
+ {
+ Assert.fail(
+ "sq1 and sq1 with different start/end should be distinct.");
+ }
+ /*
+ * finally, the failure case
+ */
+ al.addSequence(sq1dup);
+ boolean ssertRaised = false;
+ try
+ {
+ assertDatasetIsNormalised(al);
+
+ } catch (AssertionError ae)
+ {
+ ssertRaised = true;
+ }
+ if (!ssertRaised)
+ {
+ Assert.fail("Expected identical sequence to raise exception.");
+ }
+ }
+
/*
* Read in Stockholm format test data including secondary structure
* annotations.
*/
- @BeforeMethod
+ @BeforeMethod(alwaysRun = true)
public void setUp() throws IOException
{
- al = loadAlignment(TEST_DATA, "STH");
+ al = loadAlignment(TEST_DATA, FileFormat.Stockholm);
int i = 0;
for (AlignmentAnnotation ann : al.getAlignmentAnnotation())
{
/**
* Test method that returns annotations that match on calcId.
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testFindAnnotation_byCalcId()
{
Iterable<AlignmentAnnotation> anns = al
AlignmentAnnotation ann = iter.next();
assertEquals("D.melanogaster.2", ann.sequenceRef.getName());
assertFalse(iter.hasNext());
+
+ // invalid id
+ anns = al.findAnnotation("CalcIdForD.melanogaster.?");
+ assertFalse(iter.hasNext());
+ anns = al.findAnnotation(null);
+ assertFalse(iter.hasNext());
+ }
+
+ /**
+ * Test method that returns annotations that match on reference sequence,
+ * label, or calcId.
+ */
+ @Test(groups = { "Functional" })
+ public void testFindAnnotations_bySeqLabelandorCalcId()
+ {
+ // TODO: finish testFindAnnotations_bySeqLabelandorCalcId test
+ /* Note - this is an incomplete test - need to check null or
+ * non-null [ matches, not matches ] behaviour for each of the three
+ * parameters..*/
+
+ // search for a single, unique calcId with wildcards on other params
+ Iterable<AlignmentAnnotation> anns = al.findAnnotations(null,
+ "CalcIdForD.melanogaster.2", null);
+ Iterator<AlignmentAnnotation> iter = anns.iterator();
+ assertTrue(iter.hasNext());
+ AlignmentAnnotation ann = iter.next();
+ assertEquals("D.melanogaster.2", ann.sequenceRef.getName());
+ assertFalse(iter.hasNext());
+
+ // save reference to test sequence reference parameter
+ SequenceI rseq = ann.sequenceRef;
+
+ // search for annotation associated with a single sequence
+ anns = al.findAnnotations(rseq, null, null);
+ iter = anns.iterator();
+ assertTrue(iter.hasNext());
+ ann = iter.next();
+ assertEquals("D.melanogaster.2", ann.sequenceRef.getName());
+ assertFalse(iter.hasNext());
+
+ // search for annotation with a non-existant calcId
+ anns = al.findAnnotations(null, "CalcIdForD.melanogaster.?", null);
+ iter = anns.iterator();
+ assertFalse(iter.hasNext());
+
+ // search for annotation with a particular label - expect three
+ anns = al.findAnnotations(null, null, "Secondary Structure");
+ iter = anns.iterator();
+ assertTrue(iter.hasNext());
+ iter.next();
+ assertTrue(iter.hasNext());
+ iter.next();
+ assertTrue(iter.hasNext());
+ iter.next();
+ // third found.. so
+ assertFalse(iter.hasNext());
+
+ // search for annotation on one sequence with a particular label - expect
+ // one
+ SequenceI sqfound;
+ anns = al.findAnnotations(sqfound = al.getSequenceAt(1), null,
+ "Secondary Structure");
+ iter = anns.iterator();
+ assertTrue(iter.hasNext());
+ // expect reference to sequence 1 in the alignment
+ assertTrue(sqfound == iter.next().sequenceRef);
+ assertFalse(iter.hasNext());
+
+ // null on all parameters == find all annotations
+ anns = al.findAnnotations(null, null, null);
+ iter = anns.iterator();
+ int n = al.getAlignmentAnnotation().length;
+ while (iter.hasNext())
+ {
+ n--;
+ iter.next();
+ }
+ assertTrue("Found " + n + " fewer annotations from search.", n == 0);
}
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testDeleteAllAnnotations_includingAutocalculated()
{
AlignmentAnnotation aa = new AlignmentAnnotation("Consensus",
assertEquals("Not all deleted", 0, al.getAlignmentAnnotation().length);
}
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testDeleteAllAnnotations_excludingAutocalculated()
{
AlignmentAnnotation aa = new AlignmentAnnotation("Consensus",
*
* @throws IOException
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testAlignAs_dnaAsDna() throws IOException
{
// aligned cDNA:
- AlignmentI al1 = loadAlignment(CDNA_SEQS_1, "FASTA");
+ AlignmentI al1 = loadAlignment(CDNA_SEQS_1, FileFormat.Fasta);
// unaligned cDNA:
- AlignmentI al2 = loadAlignment(CDNA_SEQS_2, "FASTA");
+ AlignmentI al2 = loadAlignment(CDNA_SEQS_2, FileFormat.Fasta);
/*
* Make mappings between sequences. The 'aligned cDNA' is playing the role
* of what would normally be protein here.
*/
- AlignedCodonFrame acf = new AlignedCodonFrame();
- MapList ml = new MapList(new int[]
- { 1, 12 }, new int[]
- { 1, 12 }, 1, 1);
- acf.addMap(al2.getSequenceAt(0), al1.getSequenceAt(0), ml);
- acf.addMap(al2.getSequenceAt(1), al1.getSequenceAt(1), ml);
- al1.addCodonFrame(acf);
+ makeMappings(al1, al2);
((Alignment) al2).alignAs(al1, false, true);
- assertEquals("GC-TC--GUC-GTA-CT", al2.getSequenceAt(0)
- .getSequenceAsString());
- assertEquals("-GG-GTC--AGG---CAGT", al2.getSequenceAt(1)
- .getSequenceAsString());
+ assertEquals("GC-TC--GUC-GTACT",
+ al2.getSequenceAt(0).getSequenceAsString());
+ assertEquals("-GG-GTC--AGG--CAGT",
+ al2.getSequenceAt(1).getSequenceAsString());
}
/**
*
* @throws IOException
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testAlignAs_proteinAsCdna() throws IOException
{
// see also AlignmentUtilsTests
- AlignmentI al1 = loadAlignment(CDNA_SEQS_1, "FASTA");
- AlignmentI al2 = loadAlignment(AA_SEQS_1, "FASTA");
- AlignedCodonFrame acf = new AlignedCodonFrame();
- MapList ml = new MapList(new int[]
- { 1, 12 }, new int[]
- { 1, 4 }, 3, 1);
- acf.addMap(al1.getSequenceAt(0), al2.getSequenceAt(0), ml);
- acf.addMap(al1.getSequenceAt(1), al2.getSequenceAt(1), ml);
- al2.addCodonFrame(acf);
+ AlignmentI al1 = loadAlignment(CDNA_SEQS_1, FileFormat.Fasta);
+ AlignmentI al2 = loadAlignment(AA_SEQS_1, FileFormat.Fasta);
+ makeMappings(al1, al2);
+
+ // Fudge - alignProteinAsCdna expects mappings to be on protein
+ al2.getCodonFrames().addAll(al1.getCodonFrames());
((Alignment) al2).alignAs(al1, false, true);
assertEquals("K-Q-Y-L-", al2.getSequenceAt(0).getSequenceAsString());
*
* @throws IOException
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" }, enabled = true)
+ // TODO review / update this test after redesign of alignAs method
public void testAlignAs_cdnaAsProtein() throws IOException
{
/*
* Load alignments and add mappings for cDNA to protein
*/
- AlignmentI al1 = loadAlignment(CDNA_SEQS_1, "FASTA");
- AlignmentI al2 = loadAlignment(AA_SEQS_1, "FASTA");
- AlignedCodonFrame acf = new AlignedCodonFrame();
- MapList ml = new MapList(new int[]
- { 1, 12 }, new int[]
- { 1, 4 }, 3, 1);
- acf.addMap(al1.getSequenceAt(0), al2.getSequenceAt(0), ml);
- acf.addMap(al1.getSequenceAt(1), al2.getSequenceAt(1), ml);
- al2.addCodonFrame(acf);
+ AlignmentI al1 = loadAlignment(CDNA_SEQS_1, FileFormat.Fasta);
+ AlignmentI al2 = loadAlignment(AA_SEQS_1, FileFormat.Fasta);
+ makeMappings(al1, al2);
/*
* Realign DNA; currently keeping existing gaps in introns only
*/
((Alignment) al1).alignAs(al2, false, true);
- assertEquals("ACG---GCUCCA------ACT", al1.getSequenceAt(0)
- .getSequenceAsString());
- assertEquals("---CGT---TAACGA---AGT", al1.getSequenceAt(1)
- .getSequenceAsString());
+ assertEquals("ACG---GCUCCA------ACT---",
+ al1.getSequenceAt(0).getSequenceAsString());
+ assertEquals("---CGT---TAACGA---AGT---",
+ al1.getSequenceAt(1).getSequenceAsString());
+ }
+
+ /**
+ * Test aligning cdna as per protein - single sequences
+ *
+ * @throws IOException
+ */
+ @Test(groups = { "Functional" }, enabled = true)
+ // TODO review / update this test after redesign of alignAs method
+ public void testAlignAs_cdnaAsProtein_singleSequence() throws IOException
+ {
+ /*
+ * simple case insert one gap
+ */
+ verifyAlignAs(">dna\nCAAaaa\n", ">protein\nQ-K\n", "CAA---aaa");
+
+ /*
+ * simple case but with sequence offsets
+ */
+ verifyAlignAs(">dna/5-10\nCAAaaa\n", ">protein/20-21\nQ-K\n",
+ "CAA---aaa");
+
+ /*
+ * insert gaps as per protein, drop gaps within codons
+ */
+ verifyAlignAs(">dna/10-18\nCA-Aa-aa--AGA\n", ">aa/6-8\n-Q-K--R\n",
+ "---CAA---aaa------AGA");
+ }
+
+ /**
+ * Helper method that makes mappings and then aligns the first alignment as
+ * the second
+ *
+ * @param fromSeqs
+ * @param toSeqs
+ * @param expected
+ * @throws IOException
+ */
+ public void verifyAlignAs(String fromSeqs, String toSeqs, String expected)
+ throws IOException
+ {
+ /*
+ * Load alignments and add mappings from nucleotide to protein (or from
+ * first to second if both the same type)
+ */
+ AlignmentI al1 = loadAlignment(fromSeqs, FileFormat.Fasta);
+ AlignmentI al2 = loadAlignment(toSeqs, FileFormat.Fasta);
+ makeMappings(al1, al2);
+
+ /*
+ * Realign DNA; currently keeping existing gaps in introns only
+ */
+ ((Alignment) al1).alignAs(al2, false, true);
+ assertEquals(expected, al1.getSequenceAt(0).getSequenceAsString());
+ }
+
+ /**
+ * Helper method to make mappings between sequences, and add the mappings to
+ * the 'mapped from' alignment
+ *
+ * @param alFrom
+ * @param alTo
+ */
+ public void makeMappings(AlignmentI alFrom, AlignmentI alTo)
+ {
+ int ratio = (alFrom.isNucleotide() == alTo.isNucleotide() ? 1 : 3);
+
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+
+ for (int i = 0; i < alFrom.getHeight(); i++)
+ {
+ SequenceI seqFrom = alFrom.getSequenceAt(i);
+ SequenceI seqTo = alTo.getSequenceAt(i);
+ MapList ml = new MapList(
+ new int[]
+ { seqFrom.getStart(), seqFrom.getEnd() },
+ new int[]
+ { seqTo.getStart(), seqTo.getEnd() }, ratio, 1);
+ 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);
}
/**
*
* @throws IOException
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" }, enabled = false)
+ // TODO review / update this test after redesign of alignAs method
public void testAlignAs_dnaAsProtein_withIntrons() throws IOException
{
/*
*/
String dna1 = "A-Aa-gG-GCC-cT-TT";
String dna2 = "c--CCGgg-TT--T-AA-A";
- AlignmentI al1 = loadAlignment(">Seq1\n" + dna1 + "\n>Seq2\n" + dna2
- + "\n", "FASTA");
- AlignmentI al2 = loadAlignment(">Seq1\n-P--YK\n>Seq2\nG-T--F\n",
- "FASTA");
+ AlignmentI al1 = loadAlignment(
+ ">Dna1/6-17\n" + dna1 + "\n>Dna2/20-31\n" + dna2 + "\n",
+ FileFormat.Fasta);
+ AlignmentI al2 = loadAlignment(
+ ">Pep1/7-9\n-P--YK\n>Pep2/11-13\nG-T--F\n", FileFormat.Fasta);
AlignedCodonFrame acf = new AlignedCodonFrame();
// Seq1 has intron at dna positions 3,4,9 so splice is AAG GCC TTT
// Seq2 has intron at dna positions 1,5,6 so splice is CCG TTT AAA
- MapList ml1 = new MapList(new int[]
- { 1, 2, 5, 8, 10, 12 }, new int[]
- { 1, 3 }, 3, 1);
+ MapList ml1 = new MapList(new int[] { 6, 7, 10, 13, 15, 17 },
+ new int[]
+ { 7, 9 }, 3, 1);
acf.addMap(al1.getSequenceAt(0), al2.getSequenceAt(0), ml1);
- MapList ml2 = new MapList(new int[]
- { 2, 4, 7, 12 }, new int[]
- { 1, 3 }, 3, 1);
+ MapList ml2 = new MapList(new int[] { 21, 23, 26, 31 },
+ new int[]
+ { 11, 13 }, 3, 1);
acf.addMap(al1.getSequenceAt(1), al2.getSequenceAt(1), ml2);
al2.addCodonFrame(acf);
* Align ignoring gaps in dna introns and exons
*/
((Alignment) al1).alignAs(al2, false, false);
- assertEquals("---AAagG------GCCcTTT", al1.getSequenceAt(0)
- .getSequenceAsString());
+ assertEquals("---AAagG------GCCcTTT",
+ al1.getSequenceAt(0).getSequenceAsString());
// note 1 gap in protein corresponds to 'gg-' in DNA (3 positions)
- assertEquals("cCCGgg-TTT------AAA", al1.getSequenceAt(1)
- .getSequenceAsString());
+ assertEquals("cCCGgg-TTT------AAA",
+ al1.getSequenceAt(1).getSequenceAsString());
/*
* Reset and realign, preserving gaps in dna introns and exons
// String dna1 = "A-Aa-gG-GCC-cT-TT";
// String dna2 = "c--CCGgg-TT--T-AA-A";
// assumption: we include 'the greater of' protein/dna gap lengths, not both
- assertEquals("---A-Aa-gG------GCC-cT-TT", al1.getSequenceAt(0)
- .getSequenceAsString());
- assertEquals("c--CCGgg-TT--T------AA-A", al1.getSequenceAt(1)
- .getSequenceAsString());
+ assertEquals("---A-Aa-gG------GCC-cT-TT",
+ al1.getSequenceAt(0).getSequenceAsString());
+ assertEquals("c--CCGgg-TT--T------AA-A",
+ al1.getSequenceAt(1).getSequenceAsString());
+ }
+
+ @Test(groups = "Functional")
+ public void testCopyConstructor() throws IOException
+ {
+ AlignmentI protein = loadAlignment(AA_SEQS_1, FileFormat.Fasta);
+ // create sequence and alignment datasets
+ protein.setDataset(null);
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+ List<AlignedCodonFrame> acfList = Arrays
+ .asList(new AlignedCodonFrame[]
+ { acf });
+ protein.getDataset().setCodonFrames(acfList);
+ AlignmentI copy = new Alignment(protein);
+
+ /*
+ * copy has different aligned sequences but the same dataset sequences
+ */
+ assertFalse(copy.getSequenceAt(0) == protein.getSequenceAt(0));
+ assertFalse(copy.getSequenceAt(1) == protein.getSequenceAt(1));
+ assertSame(copy.getSequenceAt(0).getDatasetSequence(),
+ protein.getSequenceAt(0).getDatasetSequence());
+ assertSame(copy.getSequenceAt(1).getDatasetSequence(),
+ protein.getSequenceAt(1).getDatasetSequence());
+
+ // 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());
+ }
+
+ /**
+ * Test behaviour of createDataset
+ *
+ * @throws IOException
+ */
+ @Test(groups = "Functional")
+ public void testCreateDatasetAlignment() throws IOException
+ {
+ AlignmentI protein = new FormatAdapter().readFile(AA_SEQS_1,
+ DataSourceType.PASTE, FileFormat.Fasta);
+ /*
+ * create a dataset sequence on first sequence
+ * leave the second without one
+ */
+ protein.getSequenceAt(0).createDatasetSequence();
+ assertNotNull(protein.getSequenceAt(0).getDatasetSequence());
+ assertNull(protein.getSequenceAt(1).getDatasetSequence());
+
+ /*
+ * add a mapping to the alignment
+ */
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+ protein.addCodonFrame(acf);
+ assertNull(protein.getDataset());
+ assertTrue(protein.getCodonFrames().contains(acf));
+
+ /*
+ * 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();
+
+ // side-effect: dataset created on second sequence
+ assertNotNull(protein.getSequenceAt(1).getDatasetSequence());
+ // dataset alignment has references to dataset sequences
+ assertEquals(ds.getSequenceAt(0),
+ protein.getSequenceAt(0).getDatasetSequence());
+ assertEquals(ds.getSequenceAt(1),
+ protein.getSequenceAt(1).getDatasetSequence());
+
+ // codon frames should have been moved to the dataset
+ // getCodonFrames() should delegate to the dataset:
+ assertTrue(protein.getCodonFrames().contains(acf));
+ // prove the codon frames are indeed on the dataset:
+ 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()
+ {
+ AlignmentI align = new Alignment(new SequenceI[] {});
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+ align.addCodonFrame(acf);
+ assertEquals(1, align.getCodonFrames().size());
+ assertTrue(align.getCodonFrames().contains(acf));
+ // can't add the same object twice:
+ align.addCodonFrame(acf);
+ assertEquals(1, align.getCodonFrames().size());
+
+ // create dataset alignment - mappings move to dataset
+ ((Alignment) align).createDatasetAlignment();
+ assertSame(align.getCodonFrames(), align.getDataset().getCodonFrames());
+ assertEquals(1, align.getCodonFrames().size());
+
+ AlignedCodonFrame acf2 = new AlignedCodonFrame();
+ align.addCodonFrame(acf2);
+ assertTrue(align.getDataset().getCodonFrames().contains(acf));
+ }
+
+ @Test(groups = "Functional")
+ public void testAddSequencePreserveDatasetIntegrity()
+ {
+ Sequence seq = new Sequence("testSeq", "ABCDEFGHIJKLMNOPQRSTUVWXYZ");
+ Alignment align = new Alignment(new SequenceI[] { seq });
+ align.createDatasetAlignment();
+ AlignmentI ds = align.getDataset();
+ SequenceI copy = new Sequence(seq);
+ copy.insertCharAt(3, 5, '-');
+ align.addSequence(copy);
+ Assert.assertEquals(align.getDataset().getHeight(), 1,
+ "Dataset shouldn't have more than one sequence.");
+
+ Sequence seq2 = new Sequence("newtestSeq",
+ "ABCDEFGHIJKLMNOPQRSTUVWXYZ");
+ align.addSequence(seq2);
+ Assert.assertEquals(align.getDataset().getHeight(), 2,
+ "Dataset should now have two sequences.");
+
+ assertAlignmentDatasetRefs(align,
+ "addSequence broke dataset reference integrity");
+ }
+
+ /**
+ * Tests that dbrefs with mappings to sequence get updated if the sequence
+ * acquires a dataset sequence
+ */
+ @Test(groups = "Functional")
+ public void testCreateDataset_updateDbrefMappings()
+ {
+ SequenceI pep = new Sequence("pep", "ASD");
+ SequenceI dna = new Sequence("dna", "aaaGCCTCGGATggg");
+ SequenceI cds = new Sequence("cds", "GCCTCGGAT");
+
+ // add dbref from dna to peptide
+ DBRefEntry dbr = new DBRefEntry("UNIPROT", "", "pep");
+ dbr.setMap(
+ new Mapping(pep, new MapList(new int[]
+ { 4, 15 }, new int[] { 1, 4 }, 3, 1)));
+ dna.addDBRef(dbr);
+
+ // add dbref from dna to peptide
+ DBRefEntry dbr2 = new DBRefEntry("UNIPROT", "", "pep");
+ dbr2.setMap(
+ new Mapping(pep, new MapList(new int[]
+ { 1, 12 }, new int[] { 1, 4 }, 3, 1)));
+ cds.addDBRef(dbr2);
+
+ // add dbref from peptide to dna
+ DBRefEntry dbr3 = new DBRefEntry("EMBL", "", "dna");
+ dbr3.setMap(
+ new Mapping(dna, new MapList(new int[]
+ { 1, 4 }, new int[] { 4, 15 }, 1, 3)));
+ pep.addDBRef(dbr3);
+
+ // add dbref from peptide to cds
+ DBRefEntry dbr4 = new DBRefEntry("EMBLCDS", "", "cds");
+ dbr4.setMap(
+ new Mapping(cds, new MapList(new int[]
+ { 1, 4 }, new int[] { 1, 12 }, 1, 3)));
+ pep.addDBRef(dbr4);
+
+ AlignmentI protein = new Alignment(new SequenceI[] { pep });
+
+ /*
+ * create the alignment dataset
+ */
+ ((Alignment) protein).createDatasetAlignment();
+
+ AlignmentI ds = protein.getDataset();
+
+ // should be 3 sequences in dataset
+ assertEquals(3, ds.getHeight());
+ assertTrue(ds.getSequences().contains(pep.getDatasetSequence()));
+ assertTrue(ds.getSequences().contains(dna));
+ assertTrue(ds.getSequences().contains(cds));
+
+ /*
+ * verify peptide.cdsdbref.peptidedbref is now mapped to peptide dataset
+ */
+ List<DBRefEntry> dbRefs = pep.getDBRefs();
+ assertEquals(2, dbRefs.size());
+ assertSame(dna, dbRefs.get(0).map.to);
+ assertSame(cds, dbRefs.get(1).map.to);
+ assertEquals(1, dna.getDBRefs().size());
+ assertSame(pep.getDatasetSequence(), dna.getDBRefs().get(0).map.to);
+ assertEquals(1, cds.getDBRefs().size());
+ assertSame(pep.getDatasetSequence(), cds.getDBRefs().get(0).map.to);
+ }
+
+ @Test(groups = { "Functional" })
+ public void testFindGroup()
+ {
+ SequenceI seq1 = new Sequence("seq1", "ABCDEF---GHI");
+ SequenceI seq2 = new Sequence("seq2", "---JKLMNO---");
+ AlignmentI a = new Alignment(new SequenceI[] { seq1, seq2 });
+
+ assertNull(a.findGroup(null, 0));
+ assertNull(a.findGroup(seq1, 1));
+ assertNull(a.findGroup(seq1, -1));
+
+ /*
+ * add a group consisting of just "DEF"
+ */
+ SequenceGroup sg1 = new SequenceGroup();
+ sg1.addSequence(seq1, false);
+ sg1.setStartRes(3);
+ sg1.setEndRes(5);
+ a.addGroup(sg1);
+
+ assertNull(a.findGroup(seq1, 2)); // position not in group
+ assertNull(a.findGroup(seq1, 6)); // position not in group
+ assertNull(a.findGroup(seq2, 5)); // sequence not in group
+ assertSame(a.findGroup(seq1, 3), sg1); // yes
+ assertSame(a.findGroup(seq1, 4), sg1);
+ assertSame(a.findGroup(seq1, 5), sg1);
+
+ /*
+ * add a group consisting of
+ * EF--
+ * KLMN
+ */
+ SequenceGroup sg2 = new SequenceGroup();
+ sg2.addSequence(seq1, false);
+ sg2.addSequence(seq2, false);
+ sg2.setStartRes(4);
+ sg2.setEndRes(7);
+ a.addGroup(sg2);
+
+ assertNull(a.findGroup(seq1, 2)); // unchanged
+ assertSame(a.findGroup(seq1, 3), sg1); // unchanged
+ /*
+ * if a residue is in more than one group, method returns
+ * the first found (in order groups were added)
+ */
+ assertSame(a.findGroup(seq1, 4), sg1);
+ assertSame(a.findGroup(seq1, 5), sg1);
+
+ /*
+ * seq2 only belongs to the second group
+ */
+ assertSame(a.findGroup(seq2, 4), sg2);
+ assertSame(a.findGroup(seq2, 5), sg2);
+ assertSame(a.findGroup(seq2, 6), sg2);
+ assertSame(a.findGroup(seq2, 7), sg2);
+ assertNull(a.findGroup(seq2, 3));
+ assertNull(a.findGroup(seq2, 8));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testDeleteSequenceByIndex()
+ {
+ // create random alignment
+ AlignmentGenerator gen = new AlignmentGenerator(false);
+ AlignmentI a = gen.generate(20, 15, 123, 5, 5);
+
+ // delete sequence 10, alignment reduced by 1
+ int height = a.getAbsoluteHeight();
+ a.deleteSequence(10);
+ assertEquals(a.getAbsoluteHeight(), height - 1);
+
+ // try to delete -ve index, nothing happens
+ a.deleteSequence(-1);
+ assertEquals(a.getAbsoluteHeight(), height - 1);
+
+ // try to delete beyond end of alignment, nothing happens
+ a.deleteSequence(14);
+ assertEquals(a.getAbsoluteHeight(), height - 1);
+ }
+
+ @Test(groups = { "Functional" })
+ public void testDeleteSequenceBySeq()
+ {
+ // create random alignment
+ AlignmentGenerator gen = new AlignmentGenerator(false);
+ AlignmentI a = gen.generate(20, 15, 123, 5, 5);
+
+ // delete sequence 10, alignment reduced by 1
+ int height = a.getAbsoluteHeight();
+ SequenceI seq = a.getSequenceAt(10);
+ a.deleteSequence(seq);
+ assertEquals(a.getAbsoluteHeight(), height - 1);
+
+ // try to delete non-existent sequence, nothing happens
+ seq = new Sequence("cds", "GCCTCGGAT");
+ assertEquals(a.getAbsoluteHeight(), height - 1);
+ }
+
+ @Test(groups = { "Functional" })
+ public void testDeleteHiddenSequence()
+ {
+ // create random alignment
+ AlignmentGenerator gen = new AlignmentGenerator(false);
+ AlignmentI a = gen.generate(20, 15, 123, 5, 5);
+
+ // delete a sequence which is hidden, check it is NOT removed from hidden
+ // sequences
+ int height = a.getAbsoluteHeight();
+ SequenceI seq = a.getSequenceAt(2);
+ a.getHiddenSequences().hideSequence(seq);
+ assertEquals(a.getHiddenSequences().getSize(), 1);
+ a.deleteSequence(2);
+ assertEquals(a.getAbsoluteHeight(), height - 1);
+ assertEquals(a.getHiddenSequences().getSize(), 1);
+
+ // delete a sequence which is not hidden, check hiddenSequences are not
+ // affected
+ a.deleteSequence(10);
+ assertEquals(a.getAbsoluteHeight(), height - 2);
+ assertEquals(a.getHiddenSequences().getSize(), 1);
+ }
+
+ @Test(
+ groups = "Functional",
+ expectedExceptions =
+ { IllegalArgumentException.class })
+ public void testSetDataset_selfReference()
+ {
+ SequenceI seq = new Sequence("a", "a");
+ AlignmentI alignment = new Alignment(new SequenceI[] { seq });
+ alignment.setDataset(alignment);
+ }
+
+ @Test(groups = "Functional")
+ public void testAppend()
+ {
+ SequenceI seq = new Sequence("seq1", "FRMLPSRT-A--L-");
+ AlignmentI alignment = new Alignment(new SequenceI[] { seq });
+ alignment.setGapCharacter('-');
+ SequenceI seq2 = new Sequence("seq1", "KP..L.FQII.");
+ AlignmentI alignment2 = new Alignment(new SequenceI[] { seq2 });
+ alignment2.setGapCharacter('.');
+
+ alignment.append(alignment2);
+
+ assertEquals('-', alignment.getGapCharacter());
+ assertSame(seq, alignment.getSequenceAt(0));
+ assertEquals("KP--L-FQII-",
+ alignment.getSequenceAt(1).getSequenceAsString());
+
+ // todo test coverage for annotations, mappings, groups,
+ // hidden sequences, properties
+ }
+
+ /**
+ * test that calcId == null on findOrCreate doesn't raise an NPE, and yields
+ * an annotation with a null calcId
+ *
+ */
+ @Test(groups = "Functional")
+ public void testFindOrCreateForNullCalcId()
+ {
+ SequenceI seq = new Sequence("seq1", "FRMLPSRT-A--L-");
+ AlignmentI alignment = new Alignment(new SequenceI[] { seq });
+
+ AlignmentAnnotation ala = alignment.findOrCreateAnnotation(
+ "Temperature Factor", null, false, seq, null);
+ assertNotNull(ala);
+ assertEquals(seq, ala.sequenceRef);
+ assertEquals("", ala.calcId);
+ }
+
+ @Test(groups = "Functional")
+ public void testPropagateInsertions()
+ {
+ // create an alignment with no gaps - this will be the profile seq and other
+ // JPRED seqs
+ AlignmentGenerator gen = new AlignmentGenerator(false);
+ AlignmentI al = gen.generate(25, 10, 1234, 0, 0);
+
+ // get the profileseq
+ SequenceI profileseq = al.getSequenceAt(0);
+ SequenceI gappedseq = new Sequence(profileseq);
+ gappedseq.insertCharAt(5, al.getGapCharacter());
+ gappedseq.insertCharAt(6, al.getGapCharacter());
+ gappedseq.insertCharAt(7, al.getGapCharacter());
+ gappedseq.insertCharAt(8, al.getGapCharacter());
+
+ // force different kinds of padding
+ al.getSequenceAt(3).deleteChars(2, 23);
+ al.getSequenceAt(4).deleteChars(2, 27);
+ al.getSequenceAt(5).deleteChars(10, 27);
+
+ // create an alignment view with the gapped sequence
+ SequenceI[] seqs = new SequenceI[1];
+ seqs[0] = gappedseq;
+ AlignmentI newal = new Alignment(seqs);
+ HiddenColumns hidden = new HiddenColumns();
+ hidden.hideColumns(15, 17);
+
+ AlignmentView view = new AlignmentView(newal, hidden, null, true, false,
+ false);
+
+ // confirm that original contigs are as expected
+ Iterator<int[]> visible = hidden.getVisContigsIterator(0, 25, false);
+ int[] region = visible.next();
+ assertEquals("[0, 14]", Arrays.toString(region));
+ region = visible.next();
+ assertEquals("[18, 24]", Arrays.toString(region));
+
+ // propagate insertions
+ HiddenColumns result = al.propagateInsertions(profileseq, view);
+
+ // confirm that the contigs have changed to account for the gaps
+ visible = result.getVisContigsIterator(0, 25, false);
+ region = visible.next();
+ assertEquals("[0, 10]", Arrays.toString(region));
+ region = visible.next();
+ assertEquals("[14, 24]", Arrays.toString(region));
+
+ // confirm the alignment has been changed so that the other sequences have
+ // gaps inserted where the columns are hidden
+ assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[10]));
+ assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[11]));
+ assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[12]));
+ assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[13]));
+ assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[14]));
+
+ }
+
+ @Test(groups = "Functional")
+ public void testPropagateInsertionsOverlap()
+ {
+ // test propagateInsertions where gaps and hiddenColumns overlap
+
+ // create an alignment with no gaps - this will be the profile seq and other
+ // JPRED seqs
+ AlignmentGenerator gen = new AlignmentGenerator(false);
+ AlignmentI al = gen.generate(20, 10, 1234, 0, 0);
+
+ // get the profileseq
+ SequenceI profileseq = al.getSequenceAt(0);
+ SequenceI gappedseq = new Sequence(profileseq);
+ gappedseq.insertCharAt(5, al.getGapCharacter());
+ gappedseq.insertCharAt(6, al.getGapCharacter());
+ gappedseq.insertCharAt(7, al.getGapCharacter());
+ gappedseq.insertCharAt(8, al.getGapCharacter());
+
+ // create an alignment view with the gapped sequence
+ SequenceI[] seqs = new SequenceI[1];
+ seqs[0] = gappedseq;
+ AlignmentI newal = new Alignment(seqs);
+
+ // hide columns so that some overlap with the gaps
+ HiddenColumns hidden = new HiddenColumns();
+ hidden.hideColumns(7, 10);
+
+ AlignmentView view = new AlignmentView(newal, hidden, null, true, false,
+ false);
+
+ // confirm that original contigs are as expected
+ Iterator<int[]> visible = hidden.getVisContigsIterator(0, 20, false);
+ int[] region = visible.next();
+ assertEquals("[0, 6]", Arrays.toString(region));
+ region = visible.next();
+ assertEquals("[11, 19]", Arrays.toString(region));
+ assertFalse(visible.hasNext());
+
+ // propagate insertions
+ HiddenColumns result = al.propagateInsertions(profileseq, view);
+
+ // confirm that the contigs have changed to account for the gaps
+ visible = result.getVisContigsIterator(0, 20, false);
+ region = visible.next();
+ assertEquals("[0, 4]", Arrays.toString(region));
+ region = visible.next();
+ assertEquals("[7, 19]", Arrays.toString(region));
+ assertFalse(visible.hasNext());
+
+ // confirm the alignment has been changed so that the other sequences have
+ // gaps inserted where the columns are hidden
+ assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[4]));
+ assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[5]));
+ assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[6]));
+ assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[7]));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testPadGaps()
+ {
+ SequenceI seq1 = new Sequence("seq1", "ABCDEF--");
+ SequenceI seq2 = new Sequence("seq2", "-JKLMNO--");
+ SequenceI seq3 = new Sequence("seq2", "-PQR");
+ AlignmentI a = new Alignment(new SequenceI[] { seq1, seq2, seq3 });
+ a.setGapCharacter('.'); // this replaces existing gaps
+ assertEquals("ABCDEF..", seq1.getSequenceAsString());
+ a.padGaps();
+ // trailing gaps are pruned, short sequences padded with gap character
+ assertEquals("ABCDEF.", seq1.getSequenceAsString());
+ assertEquals(".JKLMNO", seq2.getSequenceAsString());
+ assertEquals(".PQR...", seq3.getSequenceAsString());
+ }
+
+ /**
+ * Test for setHiddenColumns, to check it returns true if the hidden columns
+ * have changed, else false
+ */
+ @Test(groups = { "Functional" })
+ public void testSetHiddenColumns()
+ {
+ AlignmentI al = new Alignment(new SequenceI[] {});
+ assertFalse(al.getHiddenColumns().hasHiddenColumns());
+
+ HiddenColumns hc = new HiddenColumns();
+ assertFalse(al.setHiddenColumns(hc)); // no change
+ assertSame(hc, al.getHiddenColumns());
+
+ hc.hideColumns(2, 4);
+ assertTrue(al.getHiddenColumns().hasHiddenColumns());
+
+ /*
+ * set a different object but with the same columns hidden
+ */
+ HiddenColumns hc2 = new HiddenColumns();
+ hc2.hideColumns(2, 4);
+ assertFalse(al.setHiddenColumns(hc2)); // no change
+ assertSame(hc2, al.getHiddenColumns());
+
+ assertTrue(al.setHiddenColumns(null));
+ assertNull(al.getHiddenColumns());
+ assertTrue(al.setHiddenColumns(hc));
+ assertSame(hc, al.getHiddenColumns());
+
+ al.getHiddenColumns().hideColumns(10, 12);
+ hc2.hideColumns(10, 12);
+ assertFalse(al.setHiddenColumns(hc2)); // no change
+
+ /*
+ * hide columns 15-16 then 17-18 in hc
+ * hide columns 15-18 in hc2
+ * these are not now 'equal' objects even though they
+ * represent the same set of columns
+ */
+ assertSame(hc2, al.getHiddenColumns());
+ hc.hideColumns(15, 16);
+ hc.hideColumns(17, 18);
+ hc2.hideColumns(15, 18);
+ assertFalse(hc.equals(hc2));
+ assertTrue(al.setHiddenColumns(hc)); // 'changed'
+ }
+
+ @Test(groups = { "Functional" })
+ public void testGetWidth()
+ {
+ SequenceI seq1 = new Sequence("seq1", "ABCDEF--");
+ SequenceI seq2 = new Sequence("seq2", "-JKLMNO--");
+ SequenceI seq3 = new Sequence("seq2", "-PQR");
+ AlignmentI a = new Alignment(new SequenceI[] { seq1, seq2, seq3 });
+
+ assertEquals(9, a.getWidth());
+
+ // width includes hidden columns
+ a.getHiddenColumns().hideColumns(2, 5);
+ assertEquals(9, a.getWidth());
+ }
+
+ @Test(groups = { "Functional" })
+ public void testGetVisibleWidth()
+ {
+ SequenceI seq1 = new Sequence("seq1", "ABCDEF--");
+ SequenceI seq2 = new Sequence("seq2", "-JKLMNO--");
+ SequenceI seq3 = new Sequence("seq2", "-PQR");
+ AlignmentI a = new Alignment(new SequenceI[] { seq1, seq2, seq3 });
+
+ assertEquals(9, a.getVisibleWidth());
+
+ // width excludes hidden columns
+ a.getHiddenColumns().hideColumns(2, 5);
+ assertEquals(5, a.getVisibleWidth());
+ }
+
+ @Test(groups = { "Functional" })
+ public void testGetContactMap()
+ {
+ // TODO
+ // 1. test adding/removing/manipulating contact maps with/without associated
+ // sequence(s) or groups
+ // 2. For sequence associated - ensure that inserting a gap in sequence
+ // results in the contact map being relocated accordingly
+ // 3. RENDERER QUESTION - should contact maps reflect gaps in the alignment
+ // ?
+
}
}
git://source.jalview.org / jalview.git / blobdiff