From: Jim Procter <j.procter@dundee.ac.uk>
Date: Fri, 4 Feb 2022 13:19:48 +0000 (+0000)
Subject: JAL-3806 JAL-3725 update tests since CDS mappings now exclude the stop codon
X-Git-Tag: Release_2_11_2_0~13^2~4^2
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=e5c29155a0ac8f9a03b3a7302576dc4223066a65

JAL-3806 JAL-3725 update tests since CDS mappings now exclude the stop codon
---

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);