X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FEmblXmlSource.java;fp=src%2Fjalview%2Fws%2Fdbsources%2FEmblXmlSource.java;h=034ea4f02275b58cedf56a439d6fdb1e987cb9d7;hb=afbff636fa2dfa01daa1f4ec4e8a936e61e3cf16;hp=c2d661baa77e06c6110c523f5b65dd7a79e44548;hpb=c6df3928336440918d23b4e7cb579f134e2f48dd;p=jalview.git

diff --git a/src/jalview/ws/dbsources/EmblXmlSource.java b/src/jalview/ws/dbsources/EmblXmlSource.java
index c2d661b..034ea4f 100644
--- a/src/jalview/ws/dbsources/EmblXmlSource.java
+++ b/src/jalview/ws/dbsources/EmblXmlSource.java
@@ -20,8 +20,6 @@
  */
 package jalview.ws.dbsources;
 
-import java.util.Locale;
-
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.InputStream;
@@ -30,6 +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;
 
@@ -44,7 +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;
@@ -65,12 +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- * @deprecated endpoint withdrawn August 2020 (JAL-3692), use EmblFlatfileSource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]+");
@@ -104,8 +97,8 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
     try
     {
       reply = dbFetch.fetchDataAsFile(
-              emprefx.toLowerCase(Locale.ROOT) + ":" + query.trim(), "display=xml",
-              "xml");
+              emprefx.toLowerCase(Locale.ROOT) + ":" + query.trim(),
+              "display=xml", "xml");
     } catch (Exception e)
     {
       stopQuery();
@@ -455,9 +448,8 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
         else
         {
           // final product length truncation check
-          int[] cdsRanges = adjustForProteinLength(translationLength,
-                  exons);
-          dnaToProteinMapping = new Mapping(product, cdsRanges,
+          int[] exons2 = adjustForProteinLength(translationLength, exons);
+          dnaToProteinMapping = new Mapping(product, exons2,
                   new int[]
                   { 1, translationLength }, 3, 1);
           if (product != null)
@@ -666,7 +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[] {};
@@ -759,8 +751,7 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
 
   /**
    * 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
@@ -777,11 +768,9 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
     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;
     }