X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FEmblFlatFileTest.java;fp=test%2Fjalview%2Fio%2FEmblFlatFileTest.java;h=3e2a88eb079f5c6eaa6215674f8e09a1af3f4965;hb=4d71acba1cc4999e8e4061ec3e9ae55e1b37084e;hp=7775c8f3c10c0da55da7f71f889f719688113ec0;hpb=105b70cd101cddf62d694776852bdbf0eeca3261;p=jalview.git

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