import java.util.Map.Entry;
import java.util.TreeMap;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.FeatureProperties;
int slashPos = line.indexOf('/');
if (slashPos == -1)
{
- Cache.error("Unexpected EMBL line ignored: " + line);
+ Console.error("Unexpected EMBL line ignored: " + line);
line = nextLine();
continue;
}
data.codonStart = Integer.parseInt(featureValue.trim());
} catch (NumberFormatException e)
{
- Cache.error("Invalid codon_start in XML for " + this.accession
+ Console.error("Invalid codon_start in XML for " + this.accession
+ ": " + e.getMessage());
}
}
}
else
{
- Cache.error("Ignoring CDS feature with no protein_id for "
+ Console.error("Ignoring CDS feature with no protein_id for "
+ sourceDb + ":" + accession);
}
{
if (this.accession == null || this.sequenceString == null)
{
- Cache.error("Failed to parse data from EMBL");
+ Console.error("Failed to parse data from EMBL");
return;
}
* workaround until we handle all 'location' formats fully
* e.g. X53828.1:60..1058 or <123..>289
*/
- Cache.error(String.format(
+ Console.error(String.format(
"Implementation Notice: EMBLCDS location '%s'not properly supported yet"
+ " - Making up the CDNA region of (%s:%s)... may be incorrect",
data.cdsLocation, sourceDb, this.accession));
if (peptideLength * 3 == completeCodonsLength)
{
// this might occur for CDS sequences where no features are marked
- Cache.warn("Assuming no stop codon at end of cDNA fragment");
+ Console.warn("Assuming no stop codon at end of cDNA fragment");
mappedDnaEnd = dna.getEnd();
}
else if ((peptideLength + 1) * 3 == completeCodonsLength)
{
- Cache.warn("Assuming stop codon at end of cDNA fragment");
+ Console.warn("Assuming stop codon at end of cDNA fragment");
mappedDnaEnd = dna.getEnd() - 3;
}
return MappingUtils.rangeListToArray(ranges);
} catch (ParseException e)
{
- Cache.warn(
+ Console.warn(
String.format("Not parsing inexact CDS location %s in ENA %s",
location, accession));
return new int[] {};
String[] tokens = line.split(WHITESPACE);
if (tokens.length < 2)
{
- Cache.error("Ignoring bad EMBL line for " + this.accession
+ Console.error("Ignoring bad EMBL line for " + this.accession
+ ": " + line);
break;
}