JAL-629 Change all stdout and stderr output to use Console.outPrintln and Console...

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

diff --git a/src/jalview/analysis/GeneticCodes.java b/src/jalview/analysis/GeneticCodes.java
index 59b698d..4c826b2 100644 (file)
--- a/src/jalview/analysis/GeneticCodes.java
+++ b/src/jalview/analysis/GeneticCodes.java
@@ -21,9 +21,6 @@
 package jalview.analysis;
 
 import java.util.Locale;
-
-import jalview.bin.Cache;
-
 import java.io.BufferedReader;
 import java.io.IOException;
 import java.io.InputStream;
@@ -33,6 +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
  * 
@@ -141,7 +140,7 @@ public final class GeneticCodes
       InputStream is = getClass().getResourceAsStream(fileName);
       if (is == null)
       {
-        System.err.println("Resource file not found: " + fileName);
+        jalview.bin.Console.errPrintln("Resource file not found: " + fileName);
         return;
       }
       BufferedReader dataIn = new BufferedReader(new InputStreamReader(is));
@@ -162,13 +161,12 @@ public final class GeneticCodes
       }
     } catch (IOException | NullPointerException e)
     {
-      Cache.error(
-              "Error reading genetic codes data file " + fileName + ": "
-              + e.getMessage());
+      Console.error("Error reading genetic codes data file " + fileName
+              + ": " + e.getMessage());
     }
     if (codeTables.isEmpty())
     {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "No genetic code tables loaded, check format of file "
                       + fileName);
     }
@@ -192,7 +190,7 @@ public final class GeneticCodes
       InputStream is = getClass().getResourceAsStream(fileName);
       if (is == null)
       {
-        System.err.println("Resource file not found: " + fileName);
+        jalview.bin.Console.errPrintln("Resource file not found: " + fileName);
         return;
       }
       BufferedReader dataIn = new BufferedReader(new InputStreamReader(is));
@@ -205,21 +203,20 @@ public final class GeneticCodes
           String[] tokens = line.split("\\t");
           if (tokens.length == 2)
           {
-          ambiguityCodes.put(tokens[0].toUpperCase(Locale.ROOT),
-                  tokens[1].toUpperCase(Locale.ROOT));
+            ambiguityCodes.put(tokens[0].toUpperCase(Locale.ROOT),
+                    tokens[1].toUpperCase(Locale.ROOT));
           }
           else
           {
-            System.err.println(
+            jalview.bin.Console.errPrintln(
                     "Unexpected data in " + fileName + ": " + line);
           }
         }
       }
     } catch (IOException e)
     {
-      Cache.error(
-              "Error reading nucleotide ambiguity codes data file: "
-                      + e.getMessage());
+      Console.error("Error reading nucleotide ambiguity codes data file: "
+              + e.getMessage());
     }
   }
 
@@ -294,7 +291,7 @@ public final class GeneticCodes
                 line.lastIndexOf(QUOTE));
         if (aminos.length() != NUCS_COUNT_CUBED) // 4 * 4 * 4 combinations
         {
-          Cache.error("wrong data length in code table: " + line);
+          Console.error("wrong data length in code table: " + line);
         }
         else
         {