JAL-3806 JAL-3725 propagate relaxed criteria for stop codon truncation from EMBLXmlSo...

[jalview.git] / test / jalview / io / EmblFlatFileTest.java

diff --git a/test/jalview/io/EmblFlatFileTest.java b/test/jalview/io/EmblFlatFileTest.java
index 7775c8f..4b5afa7 100644 (file)
--- a/test/jalview/io/EmblFlatFileTest.java
+++ b/test/jalview/io/EmblFlatFileTest.java
@@ -329,21 +329,23 @@ public class EmblFlatFileTest
     // 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));
-
+    // patch from JAL-3725 in EmblXmlSource propagated to Flatfile
+    // match if we assume exons include stop codon not in protein: 
+    int[] truncated = EmblFlatFile.adjustForProteinLength(5, exons);
+    assertEquals(Arrays.toString(truncated), "[11, 15, 21, 25, 31, 35]");
+    
     // truncate last exon by 6bp
-    int[] truncated = EmblFlatFile.adjustForProteinLength(4, exons);
-    assertEquals("[11, 15, 21, 25, 31, 32]", Arrays.toString(truncated));
+    truncated = EmblFlatFile.adjustForProteinLength(4, exons);
+    assertEquals(Arrays.toString(truncated),"[11, 15, 21, 25, 31, 32]");
 
     // remove last exon and truncate preceding by 1bp (so 3bp in total)
     truncated = EmblFlatFile.adjustForProteinLength(3, exons);
-    assertEquals("[11, 15, 21, 24]", Arrays.toString(truncated));
+    assertEquals(Arrays.toString(truncated),"[11, 15, 21, 24]");
 
     // exact removal of exon case:
     exons = new int[] { 11, 15, 21, 27, 33, 38 }; // 18 bp
     truncated = EmblFlatFile.adjustForProteinLength(4, exons);
-    assertEquals("[11, 15, 21, 27]", Arrays.toString(truncated));
+    assertEquals(Arrays.toString(truncated), "[11, 15, 21, 27]");
 
     // what if exons are too short for protein?
     truncated = EmblFlatFile.adjustForProteinLength(7, exons);