JAL-629 Better formatting of Arg.Opt options in usage statement

[jalview.git] / src / jalview / ws / dbsources / EmblXmlSource.java

diff --git a/src/jalview/ws/dbsources/EmblXmlSource.java b/src/jalview/ws/dbsources/EmblXmlSource.java
index c5532f5..034ea4f 100644 (file)
--- a/src/jalview/ws/dbsources/EmblXmlSource.java
+++ b/src/jalview/ws/dbsources/EmblXmlSource.java
@@ -28,6 +28,7 @@ import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Hashtable;
 import java.util.List;
+import java.util.Locale;
 import java.util.Map;
 import java.util.Map.Entry;
 
@@ -42,7 +43,7 @@ import javax.xml.stream.XMLStreamReader;
 import com.stevesoft.pat.Regex;
 
 import jalview.analysis.SequenceIdMatcher;
-import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
@@ -63,13 +64,6 @@ import jalview.xml.binding.embl.EntryType.Feature.Qualifier;
 import jalview.xml.binding.embl.ROOT;
 import jalview.xml.binding.embl.XrefType;
 
-/**
- * Provides XML binding and parsing of EMBL or EMBLCDS records retrieved from
- * (e.g.) {@code https://www.ebi.ac.uk/ena/data/view/x53828&display=xml}.
- * 
- * @deprecated endpoint withdrawn August 2020 (JAL-3692), use EmblFlatfileSource
- */
-
 public abstract class EmblXmlSource extends EbiFileRetrievedProxy
 {
   private static final Regex ACCESSION_REGEX = new Regex("^[A-Z]+[0-9]+");
@@ -103,14 +97,14 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
     try
     {
       reply = dbFetch.fetchDataAsFile(
-              emprefx.toLowerCase() + ":" + query.trim(), "display=xml",
-              "xml");
+              emprefx.toLowerCase(Locale.ROOT) + ":" + query.trim(),
+              "display=xml", "xml");
     } catch (Exception e)
     {
       stopQuery();
       throw new Exception(
               String.format("EBI EMBL XML retrieval failed for %s:%s",
-                      emprefx.toLowerCase(), query.trim()),
+                      emprefx.toLowerCase(Locale.ROOT), query.trim()),
               e);
     }
     return getEmblSequenceRecords(emprefx, query, reply);
@@ -454,8 +448,7 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
         else
         {
           // final product length truncation check
-          int [] exons2 = adjustForProteinLength(translationLength,
-                  exons);
+          int[] exons2 = adjustForProteinLength(translationLength, exons);
           dnaToProteinMapping = new Mapping(product, exons2,
                   new int[]
                   { 1, translationLength }, 3, 1);
@@ -665,7 +658,7 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
       return listToArray(ranges);
     } catch (ParseException e)
     {
-      Cache.log.warn(
+      Console.warn(
               String.format("Not parsing inexact CDS location %s in ENA %s",
                       location, accession));
       return new int[] {};