JAL-3725 fix tests for EMBLFlatFile parser when mapping doesn’t include stop codon

diff --git a/test/jalview/io/EmblFlatFileTest.java b/test/jalview/io/EmblFlatFileTest.java
index 5d8ef21..2465f27 100644 (file)
--- a/test/jalview/io/EmblFlatFileTest.java
+++ b/test/jalview/io/EmblFlatFileTest.java
@@ -173,7 +173,7 @@ 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);
           assertEquals((ranges = map.getToRanges()).size(), 1);
           assertEquals(ranges.get(0)[0], 1);
           assertEquals(ranges.get(0)[1], 451);
@@ -185,7 +185,7 @@ 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);
           assertEquals((ranges = map.getToRanges()).size(), 1);
           assertEquals(ranges.get(0)[0], 1);
           assertEquals(ranges.get(0)[1], 354);
@@ -194,7 +194,7 @@ 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);
           assertEquals((ranges = map.getToRanges()).size(), 1);
           assertEquals(ranges.get(0)[0], 1);
           assertEquals(ranges.get(0)[1], 264);
@@ -206,7 +206,7 @@ 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);
           assertEquals((ranges = map.getToRanges()).size(), 1);
           assertEquals(ranges.get(0)[0], 1);
           assertEquals(ranges.get(0)[1], 305);
@@ -216,7 +216,7 @@ 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);
           assertEquals((ranges = map.getToRanges()).size(), 1);
           assertEquals(ranges.get(0)[0], 1);
           assertEquals(ranges.get(0)[1], 330);
@@ -312,11 +312,12 @@ public class EmblFlatFileTest
   {
     int[] exons = new int[] { 11, 15, 21, 25, 31, 38 }; // 18 bp
 
+    int[] exons_nostop = new int[] { 11, 15, 21, 25, 31, 35 }; // 15 bp
     // exact length match:
     assertSame(exons, EmblFlatFile.adjustForProteinLength(6, exons));
 
-    // match if we assume exons include stop codon not in protein:
-    assertSame(exons, EmblFlatFile.adjustForProteinLength(5, exons));
+    // trimmed if we assume exons include stop codon not in protein:
+    assertEquals(Arrays.toString(exons_nostop), Arrays.toString(EmblFlatFile.adjustForProteinLength(5, exons)));
 
     // truncate last exon by 6bp
     int[] truncated = EmblFlatFile.adjustForProteinLength(4, exons);