JAL-3949 - refactor logging from jalview.bin.Cache to jalview.bin.Console

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

diff --git a/src/jalview/ws/dbsources/EmblFlatfileSource.java b/src/jalview/ws/dbsources/EmblFlatfileSource.java
index 2353f22..7cb8f09 100644 (file)
--- a/src/jalview/ws/dbsources/EmblFlatfileSource.java
+++ b/src/jalview/ws/dbsources/EmblFlatfileSource.java
@@ -1,11 +1,13 @@
 package jalview.ws.dbsources;
 
+import java.util.Locale;
+
 import java.io.File;
 import java.io.IOException;
 
 import com.stevesoft.pat.Regex;
 
-import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
@@ -73,13 +75,13 @@ public abstract class EmblFlatfileSource extends EbiFileRetrievedProxy
     try
     {
       reply = dbFetch.fetchDataAsFile(
-              dbName.toLowerCase() + ":" + query.trim(), null, "txt");
+              dbName.toLowerCase(Locale.ROOT) + ":" + query.trim(), null, "gz");
     } catch (Exception e)
     {
       stopQuery();
       throw new Exception(
-              String.format("EBI EMBL XML retrieval failed for %s:%s",
-                      dbName.toLowerCase(), query.trim()),
+              String.format("EBI EMBL retrieval failed for %s:%s",
+                      dbName.toLowerCase(Locale.ROOT), query.trim()),
               e);
     }
     return getEmblSequenceRecords(dbName, query, reply);
@@ -95,7 +97,6 @@ public abstract class EmblFlatfileSource extends EbiFileRetrievedProxy
       file = reply.getAbsolutePath();
       FileParse fp = new FileParse(file, DataSourceType.FILE);
       EmblFlatFile emblParser = new EmblFlatFile(fp, getDbSource());
-      emblParser.parse();
       SequenceI[] seqs = emblParser.getSeqsAsArray();
       if (seqs.length > 0)
       {
@@ -104,7 +105,7 @@ public abstract class EmblFlatfileSource extends EbiFileRetrievedProxy
 
       if (al == null)
       {
-        Cache.log.error(
+        Console.error(
                 "No record found for '" + dbName + ":" + query + "'");
       }
     }
@@ -112,4 +113,10 @@ public abstract class EmblFlatfileSource extends EbiFileRetrievedProxy
     stopQuery();
     return al;
   }
+
+  @Override
+  public boolean isDnaCoding()
+  {
+    return true;
+  }
 }