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Merge branch 'update/JAL-3949_jalview_bin_Console_to_cure_sanity_even_more' of https...
[jalview.git]
/
src
/
jalview
/
analysis
/
GeneticCodes.java
diff --git
a/src/jalview/analysis/GeneticCodes.java
b/src/jalview/analysis/GeneticCodes.java
index
59b698d
..
a2ecdca
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;
package jalview.analysis;
import java.util.Locale;
-
-import jalview.bin.Cache;
-
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
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 java.util.Map;
import java.util.StringTokenizer;
+import jalview.bin.Console;
+
/**
* A singleton that provides instances of genetic code translation tables
*
/**
* A singleton that provides instances of genetic code translation tables
*
@@
-162,7
+161,7
@@
public final class GeneticCodes
}
} catch (IOException | NullPointerException e)
{
}
} catch (IOException | NullPointerException e)
{
- Cache.error(
+ Console.error(
"Error reading genetic codes data file " + fileName + ": "
+ e.getMessage());
}
"Error reading genetic codes data file " + fileName + ": "
+ e.getMessage());
}
@@
-217,7
+216,7
@@
public final class GeneticCodes
}
} catch (IOException e)
{
}
} catch (IOException e)
{
- Cache.error(
+ Console.error(
"Error reading nucleotide ambiguity codes data file: "
+ e.getMessage());
}
"Error reading nucleotide ambiguity codes data file: "
+ e.getMessage());
}
@@
-294,7
+293,7
@@
public final class GeneticCodes
line.lastIndexOf(QUOTE));
if (aminos.length() != NUCS_COUNT_CUBED) // 4 * 4 * 4 combinations
{
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
{
}
else
{