From b04bbad58a8dd34fe773dfeb758e71e64606ed9e Mon Sep 17 00:00:00 2001 From: gmungoc Date: Wed, 11 Mar 2015 11:20:57 +0000 Subject: [PATCH] JAL-1685 further tests --- test/jalview/schemes/ResiduePropertiesTest.java | 25 ++++++++++++++++++++--- 1 file changed, 22 insertions(+), 3 deletions(-) diff --git a/test/jalview/schemes/ResiduePropertiesTest.java b/test/jalview/schemes/ResiduePropertiesTest.java index d72d1e1..fc85b02 100644 --- a/test/jalview/schemes/ResiduePropertiesTest.java +++ b/test/jalview/schemes/ResiduePropertiesTest.java @@ -90,6 +90,7 @@ public class ResiduePropertiesTest { // Y is C or T assertEquals("C", ResidueProperties.codonTranslate("TGY")); + // Phenylalanine first base variation assertEquals("L", ResidueProperties.codonTranslate("YTA")); // W is A or T @@ -101,11 +102,14 @@ public class ResiduePropertiesTest assertNull(ResidueProperties.codonTranslate("ATS")); // K is T or G - assertEquals("S", ResidueProperties.codonTranslate("TCS")); + assertEquals("S", ResidueProperties.codonTranslate("TCK")); assertNull(ResidueProperties.codonTranslate("ATK")); // M is C or A assertEquals("T", ResidueProperties.codonTranslate("ACM")); + // Arginine first base variation + assertEquals("R", ResidueProperties.codonTranslate("MGA")); + assertEquals("R", ResidueProperties.codonTranslate("MGG")); assertNull(ResidueProperties.codonTranslate("TAM")); // D is A, G or T @@ -126,10 +130,25 @@ public class ResiduePropertiesTest assertNull(ResidueProperties.codonTranslate("TAB")); // R is A or G + assertEquals("L", ResidueProperties.codonTranslate("CTR")); + assertEquals("V", ResidueProperties.codonTranslate("GTR")); + assertEquals("S", ResidueProperties.codonTranslate("TCR")); + assertEquals("P", ResidueProperties.codonTranslate("CCR")); + assertEquals("T", ResidueProperties.codonTranslate("ACR")); + assertEquals("A", ResidueProperties.codonTranslate("GCR")); + assertEquals("R", ResidueProperties.codonTranslate("CGR")); + assertEquals("G", ResidueProperties.codonTranslate("GGR")); + assertNull(ResidueProperties.codonTranslate("ATR")); + + // the following fail JAL-1685 assertEquals("R", ResidueProperties.codonTranslate("AGR")); + assertEquals("E", ResidueProperties.codonTranslate("GAR")); + assertEquals("K", ResidueProperties.codonTranslate("AAR")); + assertEquals("L", ResidueProperties.codonTranslate("TTR")); + assertEquals("Q", ResidueProperties.codonTranslate("CAR")); assertEquals("STOP", ResidueProperties.codonTranslate("TAR")); assertEquals("STOP", ResidueProperties.codonTranslate("TRA")); - assertNull(ResidueProperties.codonTranslate("ATR")); - + // Arginine first and third base ambiguity + assertEquals("R", ResidueProperties.codonTranslate("MGR")); } } -- 1.7.10.2