From 551b3a8e53ff6b43f9d0bce08759e46f49373bed Mon Sep 17 00:00:00 2001
From: Ben Soares <b.soares@dundee.ac.uk>
Date: Thu, 16 Sep 2021 10:17:51 +0100
Subject: [PATCH] JAL-3761 listToArray became rangeListToArray

---
 src/jalview/io/EmblFlatFile.java |   32 ++++++++++++++++++--------------
 1 file changed, 18 insertions(+), 14 deletions(-)

diff --git a/src/jalview/io/EmblFlatFile.java b/src/jalview/io/EmblFlatFile.java
index ff18a34..92af0df 100644
--- a/src/jalview/io/EmblFlatFile.java
+++ b/src/jalview/io/EmblFlatFile.java
@@ -50,10 +50,11 @@ public class EmblFlatFile extends AlignFile // FileParse
   private static final String DOUBLED_QUOTE = QUOTE + QUOTE;
 
   /**
-   * when true, interpret the mol_type 'source' feature attribute
-   * and generate an RNA sequence from the DNA record
+   * when true, interpret the mol_type 'source' feature attribute and generate
+   * an RNA sequence from the DNA record
    */
-  private boolean produceRna=true;
+  private boolean produceRna = true;
+
   /**
    * A data bean class to hold values parsed from one CDS Feature (FT)
    */
@@ -91,7 +92,8 @@ public class EmblFlatFile extends AlignFile // FileParse
 
   private List<DBRefEntry> dbrefs; // from DR
 
-  private boolean sequenceStringIsRNA=false;
+  private boolean sequenceStringIsRNA = false;
+
   private String sequenceString; // from SQ lines
 
   /*
@@ -323,11 +325,12 @@ public class EmblFlatFile extends AlignFile // FileParse
   String parseFT(String line) throws IOException
   {
     String[] tokens = line.split(WHITESPACE);
-    if (tokens.length < 3 || (!"CDS".equals(tokens[1]) && !"source".equals(tokens[1])))
+    if (tokens.length < 3
+            || (!"CDS".equals(tokens[1]) && !"source".equals(tokens[1])))
     {
       return nextLine();
     }
-    
+
     if (tokens[1].equals("source"))
     {
       return parseSourceQualifiers(tokens);
@@ -432,8 +435,9 @@ public class EmblFlatFile extends AlignFile // FileParse
   }
 
   /**
-   * process attributes for 'source' until the next FT feature entry
-   * only interested in 'mol_type'
+   * process attributes for 'source' until the next FT feature entry only
+   * interested in 'mol_type'
+   * 
    * @param tokens
    * @return
    * @throws IOException
@@ -461,7 +465,7 @@ public class EmblFlatFile extends AlignFile // FileParse
       int p = line.indexOf("\\mol_type");
       int qs = line.indexOf("\"", p);
       int qe = line.indexOf("\"", qs + 1);
-      String qualifier=line.substring(qs,qe).toLowerCase();
+      String qualifier = line.substring(qs, qe).toLowerCase();
       if (qualifier.indexOf("rna") > -1)
       {
         sequenceStringIsRNA = true;
@@ -470,7 +474,7 @@ public class EmblFlatFile extends AlignFile // FileParse
       {
         sequenceStringIsRNA = false;
       }
-      line=parseFeatureQualifier(sb, "source");
+      line = parseFeatureQualifier(sb, "source");
     }
     return line;
   }
@@ -485,7 +489,7 @@ public class EmblFlatFile extends AlignFile // FileParse
    */
   static String removeQuotes(String value)
   {
-    if (value == null) 
+    if (value == null)
     {
       return null;
     }
@@ -582,12 +586,12 @@ public class EmblFlatFile extends AlignFile // FileParse
     {
       name = this.sourceDb + "|" + name;
     }
-    
+
     if (produceRna && sequenceStringIsRNA)
     {
       sequenceString = sequenceString.replace('T', 'U').replace('t', 'u');
     }
-    
+
     SequenceI seq = new Sequence(name, this.sequenceString);
     seq.setDescription(this.description);
 
@@ -861,7 +865,7 @@ public class EmblFlatFile extends AlignFile // FileParse
     try
     {
       List<int[]> ranges = DnaUtils.parseLocation(location);
-      return MappingUtils.listToArray(ranges);
+      return MappingUtils.rangeListToArray(ranges);
     } catch (ParseException e)
     {
       Cache.log.warn(
-- 
1.7.10.2