From d45ee9ced486ee32f3d15346a616d597d37e74ae Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Mon, 5 Feb 2018 16:34:28 +0000 Subject: [PATCH 1/1] JAL-2780 JAL-2781 - patch and first test for AlignmentI.findOrCreateAnnotation --- src/jalview/datamodel/Alignment.java | 5 ++++- test/jalview/datamodel/AlignmentTest.java | 18 ++++++++++++++++++ 2 files changed, 22 insertions(+), 1 deletion(-) diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java index f268d37..97947b6 100755 --- a/src/jalview/datamodel/Alignment.java +++ b/src/jalview/datamodel/Alignment.java @@ -1603,7 +1603,10 @@ public class Alignment implements AlignmentI AlignmentAnnotation annot = new AlignmentAnnotation(name, name, new Annotation[1], 0f, 0f, AlignmentAnnotation.BAR_GRAPH); annot.hasText = false; - annot.setCalcId(new String(calcId)); + if (calcId != null) + { + annot.setCalcId(new String(calcId)); + } annot.autoCalculated = autoCalc; if (seqRef != null) { diff --git a/test/jalview/datamodel/AlignmentTest.java b/test/jalview/datamodel/AlignmentTest.java index 4b5d096..4d86bc7 100644 --- a/test/jalview/datamodel/AlignmentTest.java +++ b/test/jalview/datamodel/AlignmentTest.java @@ -1321,4 +1321,22 @@ public class AlignmentTest // 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); + } } -- 1.7.10.2