*/
package jalview.io;
-import jalview.bin.Cache;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.SequenceI;
+import jalview.util.Platform;
+import jalview.bin.Console;
import java.util.List;
}
};
+ private static Regex VALIDATION_REGEX;
+
+ private static Regex getRegex()
+ {
+ return (VALIDATION_REGEX == null
+ ? VALIDATION_REGEX = Platform
+ .newRegex("\\s*((([-0-9]+).?)|FIRST|LAST|@)", null)
+ : VALIDATION_REGEX);
+ }
private resCode validResidueCode(String field)
{
Integer val = null;
- Regex r = new Regex("\\s*((([-0-9]+).?)|FIRST|LAST|@)");
+ Regex r = getRegex();
if (!r.search(field))
{
{
value = r.stringMatched(1);
}
- // Cache.debug("from '" + field + "' matched '" + value +
+ // jalview.bin.Console.debug("from '" + field + "' matched '" + value +
// "'");
try
{
}
else
{
- // Cache.debug(
+ // jalview.bin.Console.debug(
// "Ignoring non-Modeller description: invalid integer-like
// field '" + field + "'");
type = -1; /* invalid field! - throw the FieldSet away */
List<DBRefEntry> dbr = seq.getDatasetSequence().getDBRefs();
for (int i = 0, ni = dbr.size(); i < ni; i++)
{
- DBRefEntry dbri = dbr.get(i);
+ DBRefEntry dbri = dbr.get(i);
if (dbri != null)
{
// JBPNote PDB dbRefEntry needs properties to propagate onto
// ModellerField
// JBPNote Need to get info from the user about whether the sequence
// is the one being modelled, or if it is a template.
- if (dbri.getSource().equals(jalview.datamodel.DBRefSource.PDB))
+ if (dbri.getSource()
+ .equals(jalview.datamodel.DBRefSource.PDB))
{
fields.put(Fields[LOCALID], dbri.getAccessionId());
t = 2;