JAL-3954 Add query sequence aligned to consensus to search result

[jalview.git] / src / jalview / analysis / GeneticCodes.java

diff --git a/src/jalview/analysis/GeneticCodes.java b/src/jalview/analysis/GeneticCodes.java
index df1dd82..133cb3a 100644 (file)
--- a/src/jalview/analysis/GeneticCodes.java
+++ b/src/jalview/analysis/GeneticCodes.java
@@ -20,8 +20,7 @@
  */
 package jalview.analysis;
 
-import jalview.bin.Cache;
-
+import java.util.Locale;
 import java.io.BufferedReader;
 import java.io.IOException;
 import java.io.InputStream;
@@ -31,6 +30,8 @@ import java.util.LinkedHashMap;
 import java.util.Map;
 import java.util.StringTokenizer;
 
+import jalview.bin.Console;
+
 /**
  * A singleton that provides instances of genetic code translation tables
  * 
@@ -160,9 +161,8 @@ public final class GeneticCodes
       }
     } catch (IOException | NullPointerException e)
     {
-      Cache.log.error(
-              "Error reading genetic codes data file " + fileName + ": "
-              + e.getMessage());
+      Console.error("Error reading genetic codes data file " + fileName
+              + ": " + e.getMessage());
     }
     if (codeTables.isEmpty())
     {
@@ -198,13 +198,13 @@ public final class GeneticCodes
       while (line != null)
       {
         line = readLine(dataIn);
-        if (line != null && !"DNA".equals(line.toUpperCase()))
+        if (line != null && !"DNA".equals(line.toUpperCase(Locale.ROOT)))
         {
           String[] tokens = line.split("\\t");
           if (tokens.length == 2)
           {
-          ambiguityCodes.put(tokens[0].toUpperCase(),
-                  tokens[1].toUpperCase());
+            ambiguityCodes.put(tokens[0].toUpperCase(Locale.ROOT),
+                    tokens[1].toUpperCase(Locale.ROOT));
           }
           else
           {
@@ -215,9 +215,8 @@ public final class GeneticCodes
       }
     } catch (IOException e)
     {
-      Cache.log.error(
-              "Error reading nucleotide ambiguity codes data file: "
-                      + e.getMessage());
+      Console.error("Error reading nucleotide ambiguity codes data file: "
+              + e.getMessage());
     }
   }
 
@@ -292,7 +291,7 @@ public final class GeneticCodes
                 line.lastIndexOf(QUOTE));
         if (aminos.length() != NUCS_COUNT_CUBED) // 4 * 4 * 4 combinations
         {
-          Cache.log.error("wrong data length in code table: " + line);
+          Console.error("wrong data length in code table: " + line);
         }
         else
         {
@@ -341,13 +340,13 @@ public final class GeneticCodes
       @Override
       public String translateCanonical(String codon)
       {
-        return codons.get(codon.toUpperCase());
+        return codons.get(codon.toUpperCase(Locale.ROOT));
       }
 
       @Override
       public String translate(String codon)
       {
-        String upper = codon.toUpperCase();
+        String upper = codon.toUpperCase(Locale.ROOT);
         String peptide = translateCanonical(upper);
 
         /*