From 6c89ed59f96a34f51b1cb06592c75583986295ea Mon Sep 17 00:00:00 2001
From: James Procter <j.procter@dundee.ac.uk>
Date: Wed, 13 Sep 2023 12:47:13 +0100
Subject: [PATCH] JAL-4225 failed attempts to force MFE structure to appear as
 2D RNA helices

---
 src/jalview/datamodel/AlignmentAnnotation.java     |    2 +-
 src/jalview/ws/jws2/RNAalifoldClient.java          |    6 +++-
 .../datamodel/AlignmentAnnotationTests.java        |   34 ++++++++++++++++++++
 3 files changed, 40 insertions(+), 2 deletions(-)

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 7e6b904..81cee32 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -478,7 +478,7 @@ public class AlignmentAnnotation
                 && firstChar != 'R' && firstChar != 'S' && firstChar != 'T'
                 && firstChar != 'U' && firstChar != 'V' && firstChar != 'W'
                 && firstChar != 'X' && firstChar != 'Y' && firstChar != 'Z'
-                && firstChar != '-'
+                && firstChar != '-' && firstChar != '.'
                 && firstChar < jalview.schemes.ResidueProperties.aaIndex.length)
         {
           if (jalview.schemes.ResidueProperties.aaIndex[firstChar] < 23) // TODO:
diff --git a/src/jalview/ws/jws2/RNAalifoldClient.java b/src/jalview/ws/jws2/RNAalifoldClient.java
index f9e597f..3c5e3b8 100644
--- a/src/jalview/ws/jws2/RNAalifoldClient.java
+++ b/src/jalview/ws/jws2/RNAalifoldClient.java
@@ -295,6 +295,10 @@ public class RNAalifoldClient extends JabawsCalcWorker
             break;
           }
         }
+        if (struct.charAt(i+0)=='.')
+        {
+          continue;
+        }
         anns[ri] = new Annotation(struct.substring(i, i + 1), "",
                 isSS(struct.charAt(i)), Float.NaN);
       }
@@ -303,7 +307,7 @@ public class RNAalifoldClient extends JabawsCalcWorker
     }
 
     annotation.annotations = anns;
-
+    annotation.validateRangeAndDisplay(); // fixes up RNA secondary structure
     return annotation;
   }
 
diff --git a/test/jalview/datamodel/AlignmentAnnotationTests.java b/test/jalview/datamodel/AlignmentAnnotationTests.java
index 4615204..19b14ff 100644
--- a/test/jalview/datamodel/AlignmentAnnotationTests.java
+++ b/test/jalview/datamodel/AlignmentAnnotationTests.java
@@ -311,6 +311,40 @@ public class AlignmentAnnotationTests
   }
 
   @Test(groups = { "Functional" })
+  public void testRNAalifoldOutputisRNA()
+  {
+    Annotation[] anns=new Annotation[16];
+    /*
+     * .(.[.{.<.}.>.).].
+     */
+    anns[1] = new Annotation("(", "S", '(', 0f);
+    anns[2] = new Annotation(".", "", '.', 0f);
+    anns[3] = new Annotation("[", "S", '[', 0f);
+    anns[4] = new Annotation(".", "", '.', 0f);
+    anns[5] = new Annotation("{", "S", '{', 0f);
+    anns[6] = new Annotation(".", "", '.', 0f);
+    anns[7] = new Annotation("<", "S", '<', 0f);
+    anns[8] = new Annotation(".", "", '.', 0f);
+    anns[9] = new Annotation("}", "S", '}', 0f);
+    anns[10] = new Annotation(".", "", '.', 0f);
+    anns[11] = new Annotation(">", "S", '>', 0f);
+    anns[12] = new Annotation(".", "", '.', 0f);
+    anns[13] = new Annotation(")", "S", ')', 0f);
+    anns[14] = new Annotation(".", "", '.', 0f);
+    anns[15] = new Annotation("]", "S", ']', 0f);
+
+    AlignmentAnnotation ann = new AlignmentAnnotation("RNASecStru","Struc",anns);
+
+    String expected = "(())]]}}>>>>]]]](";
+    for (int i = 0; i < expected.length(); i++)
+    {
+      assertEquals("column " + i, String.valueOf(expected.charAt(i)),
+              ann.getDefaultRnaHelixSymbol(i));
+    }
+    assertTrue(ann.isRNA());
+    
+  }
+  @Test(groups = { "Functional" })
   public void testIsQuantitative()
   {
     AlignmentAnnotation ann = null;
-- 
1.7.10.2