From e5c29155a0ac8f9a03b3a7302576dc4223066a65 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Fri, 4 Feb 2022 13:19:48 +0000 Subject: [PATCH] JAL-3806 JAL-3725 update tests since CDS mappings now exclude the stop codon --- test/jalview/io/EmblFlatFileTest.java | 10 +++++----- test/jalview/io/GenBankFileTest.java | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/test/jalview/io/EmblFlatFileTest.java b/test/jalview/io/EmblFlatFileTest.java index 4b5afa7..3e2a88e 100644 --- a/test/jalview/io/EmblFlatFileTest.java +++ b/test/jalview/io/EmblFlatFileTest.java @@ -172,7 +172,7 @@ public class EmblFlatFileTest { assertEquals((ranges = map.getFromRanges()).size(), 1); assertEquals(ranges.get(0)[0], 1579); - assertEquals(ranges.get(0)[1], 2934); + assertEquals(ranges.get(0)[1], 2931); // excludes stop 2934 assertEquals((ranges = map.getToRanges()).size(), 1); assertEquals(ranges.get(0)[0], 1); assertEquals(ranges.get(0)[1], 451); @@ -184,7 +184,7 @@ public class EmblFlatFileTest { assertEquals((ranges = map.getFromRanges()).size(), 1); assertEquals(ranges.get(0)[0], 2928); - assertEquals(ranges.get(0)[1], 3992); + assertEquals(ranges.get(0)[1], 3989); // excludes stop 3992 assertEquals((ranges = map.getToRanges()).size(), 1); assertEquals(ranges.get(0)[0], 1); assertEquals(ranges.get(0)[1], 354); @@ -193,7 +193,7 @@ public class EmblFlatFileTest { assertEquals((ranges = map.getFromRanges()).size(), 1); assertEquals(ranges.get(0)[0], 4054); - assertEquals(ranges.get(0)[1], 4848); + assertEquals(ranges.get(0)[1], 4845); // excludes stop 4848 assertEquals((ranges = map.getToRanges()).size(), 1); assertEquals(ranges.get(0)[0], 1); assertEquals(ranges.get(0)[1], 264); @@ -205,7 +205,7 @@ public class EmblFlatFileTest assertEquals(ranges.get(0)[0], 7022); assertEquals(ranges.get(0)[1], 7502); assertEquals(ranges.get(1)[0], 1); - assertEquals(ranges.get(1)[1], 437); + assertEquals(ranges.get(1)[1], 434); // excludes stop at 437 assertEquals((ranges = map.getToRanges()).size(), 1); assertEquals(ranges.get(0)[0], 1); assertEquals(ranges.get(0)[1], 305); @@ -215,7 +215,7 @@ public class EmblFlatFileTest // complement(488..1480) assertEquals((ranges = map.getFromRanges()).size(), 1); assertEquals(ranges.get(0)[0], 1480); - assertEquals(ranges.get(0)[1], 488); + assertEquals(ranges.get(0)[1], 491); // // excludes stop at 488 assertEquals((ranges = map.getToRanges()).size(), 1); assertEquals(ranges.get(0)[0], 1); assertEquals(ranges.get(0)[1], 330); diff --git a/test/jalview/io/GenBankFileTest.java b/test/jalview/io/GenBankFileTest.java index 97e4754..20d458f 100644 --- a/test/jalview/io/GenBankFileTest.java +++ b/test/jalview/io/GenBankFileTest.java @@ -193,7 +193,7 @@ public class GenBankFileTest assertTrue(seqString.endsWith("FKQKS")); map = mapping.getMap(); assertEquals(map.getFromLowest(), 6045); - assertEquals(map.getFromHighest(), 6788); + assertEquals(map.getFromHighest(), 6785); // excludes stop at 6788 assertEquals(map.getToLowest(), 1); assertEquals(map.getToHighest(), 247); assertEquals(map.getFromRatio(), 3); -- 1.7.10.2