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Sequence translation fixes in export alignments pretty (#370)
* Several fixes and tests for translation in exportAlignmentsPretty. * More fixes to translation rules. * repseqio SNAPSHOT upgrade
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Submodule repseqio
updated
from e7a557 to 75890b
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src/test/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsFormatterTest.java
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| /* | ||
| * Copyright (c) 2014-2018, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail | ||
| * (here and after addressed as Inventors) | ||
| * All Rights Reserved | ||
| * | ||
| * Permission to use, copy, modify and distribute any part of this program for | ||
| * educational, research and non-profit purposes, by non-profit institutions | ||
| * only, without fee, and without a written agreement is hereby granted, | ||
| * provided that the above copyright notice, this paragraph and the following | ||
| * three paragraphs appear in all copies. | ||
| * | ||
| * Those desiring to incorporate this work into commercial products or use for | ||
| * commercial purposes should contact the Inventors using one of the following | ||
| * email addresses: chudakovdm@mail.ru, chudakovdm@gmail.com | ||
| * | ||
| * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, | ||
| * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, | ||
| * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN | ||
| * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. | ||
| * | ||
| * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS | ||
| * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR | ||
| * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO | ||
| * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT | ||
| * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A | ||
| * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY | ||
| * PATENT, TRADEMARK OR OTHER RIGHTS. | ||
| */ | ||
| package com.milaboratory.mixcr.basictypes; | ||
|
|
||
| import com.milaboratory.core.Range; | ||
| import com.milaboratory.core.alignment.Alignment; | ||
| import com.milaboratory.core.alignment.MultiAlignmentHelper; | ||
| import com.milaboratory.core.mutations.Mutations; | ||
| import com.milaboratory.core.sequence.NucleotideSequence; | ||
| import io.repseq.core.ExtendedReferencePointsBuilder; | ||
| import io.repseq.core.ReferencePoint; | ||
| import org.junit.Assert; | ||
| import org.junit.Test; | ||
|
|
||
| import static com.milaboratory.core.alignment.MultiAlignmentHelper.DEFAULT_SETTINGS; | ||
|
|
||
| public class VDJCAlignmentsFormatterTest { | ||
| boolean show = true; | ||
|
|
||
| @Test | ||
| public void test0() { | ||
| Assert.assertTrue(testWithoutLeftover("GGTTCGGGGACCAGGTTAACCGTTGTAGGG", | ||
| ReferencePoint.CDR3Begin, ReferencePoint.CDR3End).endsWith(" G ")); | ||
| Assert.assertTrue(testWithoutLeftover("GGTTCGGGGACCAGGTAACCGTTGTAGGG", | ||
| ReferencePoint.CDR3Begin, ReferencePoint.CDR3End).endsWith(" G ")); | ||
| Assert.assertTrue(testWithoutLeftover("GGTTCGGGGACCAGGAACCGTTGTAGGG", | ||
| ReferencePoint.CDR3Begin, ReferencePoint.CDR3End).endsWith(" G ")); | ||
| } | ||
|
|
||
| @Test | ||
| public void test1() { | ||
| Assert.assertTrue(testWithoutLeftover("GGTTCGGGGACCAGGTTAACCGTTGTAGGG", | ||
| ReferencePoint.CDR3Begin, ReferencePoint.VEndTrimmed).endsWith(" G ")); | ||
| Assert.assertTrue(testWithoutLeftover("GGTTCGGGGACCAGGTTAACCGTTGTAGG", | ||
| ReferencePoint.CDR3Begin, ReferencePoint.VEndTrimmed).endsWith("_ ")); | ||
| Assert.assertTrue(testWithoutLeftover("GGTTCGGGGACCAGGTTAACCGTTGTAG", | ||
| ReferencePoint.CDR3Begin, ReferencePoint.VEndTrimmed).endsWith("_")); | ||
| } | ||
|
|
||
| @Test | ||
| public void test2() { | ||
| Assert.assertTrue(testWithoutLeftover("GGTTCGGGGACCAGGTTAACCGTTGTAGGG", | ||
| ReferencePoint.JBeginTrimmed, ReferencePoint.CDR3End).startsWith(" G ")); | ||
| Assert.assertTrue(testWithoutLeftover("GTTCGGGGACCAGGTTAACCGTTGTAGGG", | ||
| ReferencePoint.JBeginTrimmed, ReferencePoint.CDR3End).startsWith("_ ")); | ||
| Assert.assertTrue(testWithoutLeftover("TTCGGGGACCAGGTTAACCGTTGTAGGG", | ||
| ReferencePoint.JBeginTrimmed, ReferencePoint.CDR3End).startsWith("_")); | ||
| } | ||
|
|
||
| @Test | ||
| public void test3() { | ||
| testWithLeftover("GGTTCGGGGACCAGGTTAACCGTTGTAGG", "G", | ||
| ReferencePoint.L1Begin, ReferencePoint.L1End, ReferencePoint.L2Begin, ReferencePoint.L2End); | ||
| // Assert.assertTrue(testWithoutLeftover("GGTTCGGGGACCAGGTTAACCGTTGTAGGG", | ||
| // ReferencePoint.JBeginTrimmed, ReferencePoint.CDR3End).startsWith(" G ")); | ||
| // Assert.assertTrue(testWithoutLeftover("GGTTCGGGGACCAGGTTAACCGTTGTAGGG", | ||
| // ReferencePoint.JBeginTrimmed, ReferencePoint.CDR3End).startsWith(" G ")); | ||
| } | ||
|
|
||
| public String testWithoutLeftover(String seqStr, ReferencePoint rp1, ReferencePoint rp2) { | ||
| NucleotideSequence seq = new NucleotideSequence(seqStr); | ||
| Alignment<NucleotideSequence> al = new Alignment<>(seq, Mutations.EMPTY_NUCLEOTIDE_MUTATIONS, | ||
| new Range(0, seq.size()), new Range(0, seq.size()), 100.0f); | ||
| MultiAlignmentHelper ml = MultiAlignmentHelper.build(DEFAULT_SETTINGS, new Range(0, seq.size()), al); | ||
| ExtendedReferencePointsBuilder b = new ExtendedReferencePointsBuilder(); | ||
| b.setPosition(rp1, 0); | ||
| b.setPosition(rp2, seq.size()); | ||
| VDJCAlignmentsFormatter.drawAASequence(ml, b.build(), seq); | ||
| if (show) | ||
| System.out.println(ml); | ||
| return ml.getAnnotationString(0); | ||
| } | ||
|
|
||
| public String testWithLeftover(String seqStr1, String seqStr2, | ||
| ReferencePoint rp1, ReferencePoint rp2, | ||
| ReferencePoint rp3, ReferencePoint rp4) { | ||
| NucleotideSequence seq = new NucleotideSequence(seqStr1 + "AAAAAAAAAA" + seqStr2); | ||
| Alignment<NucleotideSequence> al = new Alignment<>(seq, Mutations.EMPTY_NUCLEOTIDE_MUTATIONS, | ||
| new Range(0, seq.size()), new Range(0, seq.size()), 100.0f); | ||
| MultiAlignmentHelper ml = MultiAlignmentHelper.build(DEFAULT_SETTINGS, new Range(0, seq.size()), al); | ||
| ExtendedReferencePointsBuilder b = new ExtendedReferencePointsBuilder(); | ||
| b.setPosition(rp1, 0); | ||
| b.setPosition(rp2, seqStr1.length()); | ||
| b.setPosition(rp3, seqStr1.length() + 10); | ||
| b.setPosition(rp4, seqStr1.length() + 10 + seqStr2.length()); | ||
| VDJCAlignmentsFormatter.drawAASequence(ml, b.build(), seq); | ||
| if (show) | ||
| System.out.println(ml); | ||
| return ml.getAnnotationString(0); | ||
| } | ||
| } |