From: Jim Procter <j.procter@dundee.ac.uk>
Date: Thu, 6 Jan 2022 12:29:01 +0000 (+0000)
Subject: JAL-3806 JAL-3725 propagate relaxed criteria for stop codon truncation from EMBLXmlSo... 
X-Git-Tag: Release_2_11_2_0~13^2~4^2~7
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=07cb43d5a1e477b16582f98519343c162d7428ef;p=jalview.git

JAL-3806 JAL-3725 propagate relaxed criteria for stop codon truncation from EMBLXmlSource to EMBLFlatFile parser
---

diff --git a/src/jalview/io/EMBLLikeFlatFile.java b/src/jalview/io/EMBLLikeFlatFile.java
index 64943b2..100fb8d 100644
--- a/src/jalview/io/EMBLLikeFlatFile.java
+++ b/src/jalview/io/EMBLLikeFlatFile.java
@@ -83,8 +83,7 @@ public abstract class EMBLLikeFlatFile extends AlignFile
 
   /**
    * Truncates (if necessary) the exon intervals to match 3 times the length of
-   * the protein; also accepts 3 bases longer (for stop codon not included in
-   * protein)
+   * the protein(including truncation for stop codon included in exon)
    * 
    * @param proteinLength
    * @param exon
@@ -102,11 +101,9 @@ public abstract class EMBLLikeFlatFile extends AlignFile
     int exonLength = MappingUtils.getLength(Arrays.asList(exon));
 
     /*
-     * if exon length matches protein, or is shorter, or longer by the 
-     * length of a stop codon (3 bases), then leave it unchanged
+     * if exon length matches protein, or is shorter, then leave it unchanged
      */
-    if (expectedCdsLength >= exonLength
-            || expectedCdsLength == exonLength - 3)
+    if (expectedCdsLength >= exonLength)
     {
       return exon;
     }
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);