{
if (mappings.isEmpty())
{
- System.err.println("reportMapping: No PDB/Sequence mappings.");
+ jalview.bin.Console.errPrintln("reportMapping: No PDB/Sequence mappings.");
}
else
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"reportMapping: There are " + mappings.size() + " mappings.");
int i = 0;
for (StructureMapping sm : mappings)
{
- System.err.println("mapping " + i++ + " : " + sm.pdbfile);
+ jalview.bin.Console.errPrintln("mapping " + i++ + " : " + sm.pdbfile);
}
}
}
* @param IProgressIndicator
* reference to UI component that maintains a progress bar for the
* mapping operation
+ * @param tft - specify how to interpret the temperature factor column in the atom data
+ * @param paeFilename - when not null, specifies a filename containing a matrix formatted in JSON using one of the known PAE formats
+ * @param doXferSettings - when true, transfer annotation to mapped sequences in sequenceArray
* @return null or the structure data parsed as a pdb file
*/
synchronized public StructureFile computeMapping(boolean forStructureView,
chain.transferResidueAnnotation(siftsMapping, null);
} catch (SiftsException e)
{
- System.err.println(e.getMessage());
+ jalview.bin.Console.errPrintln(e.getMessage());
} catch (Exception e)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Unexpected exception during SIFTS mapping - falling back to NW for this sequence/structure pair");
- System.err.println(e.getMessage());
+ jalview.bin.Console.errPrintln(e.getMessage());
}
}
if (!foundSiftsMappings.isEmpty())
*
* if (mappings[j].sequence == seq && mappings[j].getPdbId().equals(pdbid)
* && mappings[j].pdbfile.equals(sl.getPdbFile())) {
- * System.out.println(pdbid+" "+mappings[j].getPdbId() +"
+ * jalview.bin.Console.outPrintln(pdbid+" "+mappings[j].getPdbId() +"
* "+mappings[j].pdbfile);
*
* java.awt.Color col; for(int index=0; index<seq.getLength(); index++) {
boolean removed = seqmappings.remove(acf);
if (removed && seqmappings.isEmpty())
{ // debug
- System.out.println("All mappings removed");
+ jalview.bin.Console.outPrintln("All mappings removed");
}
}
}