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JAL-4290 new CommandsTest.headlessOrGuiImageOutputTest - uses CommandLineOperations...
[jalview.git]
/
src
/
jalview
/
analysis
/
GeneticCodes.java
diff --git
a/src/jalview/analysis/GeneticCodes.java
b/src/jalview/analysis/GeneticCodes.java
index
df1dd82
..
c91cfa2
100644
(file)
--- a/
src/jalview/analysis/GeneticCodes.java
+++ b/
src/jalview/analysis/GeneticCodes.java
@@
-20,8
+20,7
@@
*/
package jalview.analysis;
*/
package jalview.analysis;
-import jalview.bin.Cache;
-
+import java.util.Locale;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
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 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
*
@@
-139,7
+140,8
@@
public final class GeneticCodes
InputStream is = getClass().getResourceAsStream(fileName);
if (is == null)
{
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));
return;
}
BufferedReader dataIn = new BufferedReader(new InputStreamReader(is));
@@
-160,13
+162,12
@@
public final class GeneticCodes
}
} catch (IOException | NullPointerException e)
{
}
} 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())
{
}
if (codeTables.isEmpty())
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"No genetic code tables loaded, check format of file "
+ fileName);
}
"No genetic code tables loaded, check format of file "
+ fileName);
}
@@
-190,7
+191,8
@@
public final class GeneticCodes
InputStream is = getClass().getResourceAsStream(fileName);
if (is == null)
{
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));
return;
}
BufferedReader dataIn = new BufferedReader(new InputStreamReader(is));
@@
-198,26
+200,25
@@
public final class GeneticCodes
while (line != null)
{
line = readLine(dataIn);
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)
{
{
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
{
}
else
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Unexpected data in " + fileName + ": " + line);
}
}
}
} catch (IOException e)
{
"Unexpected data in " + fileName + ": " + line);
}
}
}
} 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
+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.log.error("wrong data length in code table: " + line);
+ Console.error("wrong data length in code table: " + line);
}
else
{
}
else
{
@@
-341,13
+342,13
@@
public final class GeneticCodes
@Override
public String translateCanonical(String codon)
{
@Override
public String translateCanonical(String codon)
{
- return codons.get(codon.toUpperCase());
+ return codons.get(codon.toUpperCase(Locale.ROOT));
}
@Override
public String translate(String codon)
{
}
@Override
public String translate(String codon)
{
- String upper = codon.toUpperCase();
+ String upper = codon.toUpperCase(Locale.ROOT);
String peptide = translateCanonical(upper);
/*
String peptide = translateCanonical(upper);
/*