X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=test%2Fjalview%2Fio%2FEmblFlatFileTest.java;h=4b5afa7c42bea360a02b1fe13816f678528cda54;hp=7775c8f3c10c0da55da7f71f889f719688113ec0;hb=07cb43d5a1e477b16582f98519343c162d7428ef;hpb=08c7bee16c16563cc7cec7ea4d336b3e0c4c937a

diff --git a/test/jalview/io/EmblFlatFileTest.java b/test/jalview/io/EmblFlatFileTest.java
index 7775c8f..4b5afa7 100644
--- 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);