*/
package jalview.io.vamsas;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.io.VamsasAppDatastore;
DataSetAnnotations dsa = (DataSetAnnotations) vobj;
if (dsa.getSeqRefCount() != 1)
{
- Cache.log.warn("Not binding " + dsa.getVorbaId()
+ Console.warn("Not binding " + dsa.getVorbaId()
+ " to Sequence Feature - has multiple dataset sequence references.");
return;
}
if (dsa.getSeqRefCount() != 1)
{
replaceJvObjMapping(feature, null);
- Cache.log.warn(
+ Console.warn(
"Binding of annotation to jalview feature has changed. Removing binding and recreating.");
doSync(); // re-verify bindings.
}
getDSAnnotationFromJalview(dsa, feature);
if (oldref != dsa.hashCode())
{
- Cache.log
- .debug("Updated dataset sequence annotation from feature.");
+ Console.debug("Updated dataset sequence annotation from feature.");
addProvenance(dsa.getProvenance(), "modified");
}
}
{
// conflicting update from document - we cannot map this feature anymore.
replaceJvObjMapping(feature, null);
- Cache.log.warn("annotation (" + dsa.getVorbaId()
+ Console.warn("annotation (" + dsa.getVorbaId()
+ " bound to jalview feature cannot be mapped. Removing binding, deleting feature, and deleting feature.");
// - consider deleting the feature ?
dsSeq.deleteFeature(feature);
vSeg.setInclusive(true);
if (dsa.getSegCount() > 1)
{
- Cache.log.debug(
+ Console.debug(
"About to destroy complex annotation in vamsas document mapped to sequence feature ("
+ dsa.getVorbaId() + ")");
}