From: James Procter <j.procter@dundee.ac.uk>
Date: Mon, 20 Nov 2023 11:34:03 +0000 (+0000)
Subject: JAL-4343 patch for JAL-4347 uniprot non-pos feature parsing
X-Git-Tag: Release_2_11_4_0~73
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=cdc539ef6f32d74747ab857831268dd5954b28f5;p=jalview.git

JAL-4343 patch for JAL-4347 uniprot non-pos feature parsing
---

diff --git a/help/markdown/releases/release-2_11_3_1.md b/help/markdown/releases/release-2_11_3_1.md
index 23f6abf..dc9cf90 100644
--- a/help/markdown/releases/release-2_11_3_1.md
+++ b/help/markdown/releases/release-2_11_3_1.md
@@ -11,6 +11,7 @@ channel: "release"
 ## Issues Resolved
 
 - <!-- JAL-4340 --> Getdown does not preserve executable permission of jalview.sh file when it gets updated
+- <!-- JAL-4347 --> Single position features from Uniprot are incorrectly parsed as non-positional features
 
 ### New Known Issues
 
diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java
index b125ba5..69ee379 100644
--- a/src/jalview/ws/dbsources/Uniprot.java
+++ b/src/jalview/ws/dbsources/Uniprot.java
@@ -298,7 +298,7 @@ public class Uniprot extends DbSourceProxyImpl
         if (location.getPosition() != null)
         {
           if (location.getPosition().getPosition() == null
-                  || !"unknown".equals(location.getPosition().getStatus()))
+                  || "unknown".equals(location.getPosition().getStatus()))
           {
             Console.warn(
                     "Ignoring single position feature with uncertain location "
diff --git a/test/jalview/ws/dbsources/UniprotTest.java b/test/jalview/ws/dbsources/UniprotTest.java
index f2d3b66..a95d520 100644
--- a/test/jalview/ws/dbsources/UniprotTest.java
+++ b/test/jalview/ws/dbsources/UniprotTest.java
@@ -242,6 +242,13 @@ public class UniprotTest
     // FIXME: Jim needs to specify what (promoted) means !! - or perhaps we just
     // ignore it !
     assertEquals("1 (promoted)", (res.get(0).getVersion()));
+
+    List<SequenceFeature> features = seq.getFeatures().findFeatures(41, 41,
+            "sequence variant");
+    // verify single position features are parsed correctly JAL-4347
+    assertNotNull(features);
+    assertEquals(3, features.size());
+
   }
 
   /**