*/
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()
- + " to Sequence Feature - has multiple dataset sequence references.");
+ Console.warn("Not binding " + dsa.getVorbaId()
+ + " to Sequence Feature - has multiple dataset sequence references.");
return;
}
jalview.datamodel.SequenceFeature sf = (jalview.datamodel.SequenceFeature) jvobj;
if (dsa.getSeqRefCount() != 1)
{
replaceJvObjMapping(feature, null);
- Cache.log
- .warn("Binding of annotation to jalview feature has changed. Removing binding and recreating.");
+ Console.warn(
+ "Binding of annotation to jalview feature has changed. Removing binding and recreating.");
doSync(); // re-verify bindings.
}
else
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()
- + " bound to jalview feature cannot be mapped. Removing binding, deleting feature, and deleting feature.");
+ 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);
// doSync();
vSeg.setInclusive(true);
if (dsa.getSegCount() > 1)
{
- Cache.log
- .debug("About to destroy complex annotation in vamsas document mapped to sequence feature ("
+ Console.debug(
+ "About to destroy complex annotation in vamsas document mapped to sequence feature ("
+ dsa.getVorbaId() + ")");
}
dsa.setSeg(new Seg[] { vSeg });
else if (vlu instanceof Integer)
{
valid = true;
- nprop.setType(uk.ac.vamsas.objects.utils.Properties.INTEGERTYPE);
+ nprop.setType(
+ uk.ac.vamsas.objects.utils.Properties.INTEGERTYPE);
}
else if (vlu instanceof Float)
{
{
try
{
- val = new Boolean(p.getContent());
+ val = Boolean.valueOf(p.getContent());
} catch (Exception e)
{
}
{
try
{
- val = new Float(p.getContent());
+ val = Float.valueOf(p.getContent());
} catch (Exception e)
{
{
try
{
- val = new Integer(p.getContent());
+ val = Integer.valueOf(p.getContent());
} catch (Exception e)
{
}