import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
- System.err.println("EMBL Record " + accession);
- System.err.println("Resulted in exception: " + e.getMessage());
+ jalview.bin.Console.errPrintln("EMBL Record " + accession);
+ jalview.bin.Console
+ .errPrintln("Resulted in exception: " + e.getMessage());
* workaround until we handle dna location for CDS sequence
* e.g. location="X53828.1:60..1058" correctly
*/
* workaround until we handle dna location for CDS sequence
* e.g. location="X53828.1:60..1058" correctly
*/
"Implementation Notice: EMBLCDS records not properly supported yet - Making up the CDNA region of this sequence... may be incorrect ("
+ sourceDb + ":" + entry.getAccession() + ")");
int dnaLength = dna.getLength();
if (translationLength * 3 == (1 - codonStart + dnaLength))
{
"Implementation Notice: EMBLCDS records not properly supported yet - Making up the CDNA region of this sequence... may be incorrect ("
+ sourceDb + ":" + entry.getAccession() + ")");
int dnaLength = dna.getLength();
if (translationLength * 3 == (1 - codonStart + dnaLength))
{
"Not allowing for additional stop codon at end of cDNA fragment... !");
// this might occur for CDS sequences where no features are marked
exons = new int[] { dna.getStart() + (codonStart - 1),
"Not allowing for additional stop codon at end of cDNA fragment... !");
// this might occur for CDS sequences where no features are marked
exons = new int[] { dna.getStart() + (codonStart - 1),
"Allowing for additional stop codon at end of cDNA fragment... will probably cause an error in VAMSAs!");
exons = new int[] { dna.getStart() + (codonStart - 1),
dna.getEnd() - 3 };
"Allowing for additional stop codon at end of cDNA fragment... will probably cause an error in VAMSAs!");
exons = new int[] { dna.getStart() + (codonStart - 1),
dna.getEnd() - 3 };