From a30fd1f85809e9865c21870a550a3bd17d527eb2 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Thu, 18 May 2017 14:15:04 +0100 Subject: [PATCH 1/1] JAL-2541 fix to initSeqFrom (and minor code tidy); more tests for deleteChars --- src/jalview/datamodel/Sequence.java | 50 +++++++------ test/jalview/datamodel/SequenceTest.java | 113 ++++++++++++++++++++++++++++++ 2 files changed, 142 insertions(+), 21 deletions(-) diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java index b0faf21..9994675 100755 --- 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 subset = new Vector(); + Enumeration 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 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 --- 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" }) -- 1.7.10.2