*/
package jalview.io.vamsas;
+import jalview.bin.Cache;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
}
if (from != null && sequenceMapping.getLoc() != from)
{
- jalview.bin.Cache.log.warn("Probable IMPLEMENTATION ERROR: " + from
+ Cache.warn("Probable IMPLEMENTATION ERROR: " + from
+ " doesn't match the local mapping sequence.");
}
if (ds != null && sequenceMapping.is__stored_in_document()
&& sequenceMapping.getV_parent() != ds)
{
- jalview.bin.Cache.log.warn("Probable IMPLEMENTATION ERROR: " + ds
+ Cache.warn("Probable IMPLEMENTATION ERROR: " + ds
+ " doesn't match the parent of the bound sequence mapping object.");
}
}
SequenceType to = (SequenceType) getjv2vObj(jvto);
if (to == null)
{
- jalview.bin.Cache.log.warn(
+ Cache.warn(
"FIXME NONFATAL - do a second update: Ignoring Forward Reference to seuqence not yet bound to vamsas seuqence object");
return;
}
if (!dnaToProt)
{
- jalview.bin.Cache.log.warn(
+ Cache.warn(
"Ignoring Mapping - don't support protein to protein mapping in vamsas document yet.");
return;
}
// mapping
bindjvvobj(mjvmapping.getMap(), sequenceMapping);
- jalview.bin.Cache.log.debug(
+ Cache.debug(
"Successfully created mapping " + sequenceMapping.getVorbaId());
}
// private void update(jalview.util.MapList mjvmapping,
// SequenceMapping sequenceMapping)
{
- jalview.bin.Cache.log
- .error("Not implemented: Jalview Update Alcodon Mapping:TODO!");
+ Cache.error("Not implemented: Jalview Update Alcodon Mapping:TODO!");
}
private void update(SequenceMapping sequenceMapping,
jalview.datamodel.Mapping mjvmapping)
{
- jalview.bin.Cache.log
- .error("Not implemented: Update DBRef Mapping from Jalview");
+ Cache.error("Not implemented: Update DBRef Mapping from Jalview");
}
private void update(jalview.datamodel.Mapping mjvmapping,
SequenceMapping sequenceMapping)
{
- jalview.bin.Cache.log.error(
+ Cache.error(
"Not implemented: Jalview Update Sequence DBRef Mapping");
}
}
if (sdloc == null || sdmap == null)
{
- jalview.bin.Cache.log.info("Ignoring non sequence-sequence mapping");
+ Cache.info("Ignoring non sequence-sequence mapping");
return;
}
mobj = this.getvObj2jv(sdloc);
if (from == null || to == null)
{
- jalview.bin.Cache.log.error(
+ Cache.error(
"Probable Vamsas implementation error : unbound dataset sequences involved in a mapping are being parsed!");
return;
}
{
if (from.getDBRefs() == null && to.getDBRefs() == null)
{
- if (jalview.bin.Cache.log.isDebugEnabled())
+ if (Cache.isDebugEnabled())
{
- jalview.bin.Cache.log.debug("Not matching conjugate refs for "
+ Cache.debug("Not matching conjugate refs for "
+ from.getName() + " and " + to.getName());
}
return;
}
- if (jalview.bin.Cache.log.isDebugEnabled())
+ if (Cache.isDebugEnabled())
{
- jalview.bin.Cache.log.debug("Matching conjugate refs for "
+ Cache.debug("Matching conjugate refs for "
+ from.getName() + " and " + to.getName());
}
List<DBRefEntry> fdb = from.getDBRefs();
boolean fmpnnl = (fmp != null);
// if (fmpnnl && fmp.getTo()!=null)
// {
- // jalview.bin.Cache.log.debug("Not overwriting existing To reference in
+ // Cache.debug("Not overwriting existing To reference in
// "+fe);
// continue;
// }