Package edu.duke.cs.osprey.coffee.seqdb
Class SeqDB
java.lang.Object
edu.duke.cs.osprey.coffee.seqdb.SeqDB
- All Implemented Interfaces:
AutoCloseable
A database of information about sequences.
SeqDB is **NOT** thread-safe!
Callers must explicitly synchronize SeqDB if using from multiple threads.
-
Nested Class Summary
Nested Classes -
Field Summary
FieldsModifier and TypeFieldDescriptionfinal MultiStateConfSpacefinal Filefinal MathContextfinal ClusterMemberfinal intstatic final String -
Method Summary
Modifier and TypeMethodDescriptionbatch()bigMath()voidclose()dump()get(MultiStateConfSpace.State state, Sequence seq) Returns the current Z bounds and dropped Z for the state and sequence.Returns the current sequenced state Z bounds for the fully-assigned sequence.getBestConfs(MultiStateConfSpace.State state, Sequence seq) returns Z bounds for all sequences returns bounds for both full and partial sequencesgetUnexplored(Sequence seq) Returns the current state Z bounds for unexplored subtrees of the partially-assigned sequence.Returns the current Z bounds and dropped Z for the unsequenced state.
-
Field Details
-
ServiceName
- See Also:
-
confSpace
-
member
-
mathContext
-
file
-
numBestConfs
public final int numBestConfs
-
-
Method Details
-
bigMath
-
batch
-
close
public void close()- Specified by:
closein interfaceAutoCloseable
-
get
Returns the current Z bounds and dropped Z for the state and sequence. If the state is unsequenced, the given sequence is ignored. -
getUnsequenced
Returns the current Z bounds and dropped Z for the unsequenced state. -
getUnexplored
Returns the current state Z bounds for unexplored subtrees of the partially-assigned sequence. As more subtrees get explored, those Z values will be transfered to more fully-assigned sequences. Bounds for fully-explored partial sequences will be zero. -
get
Returns the current sequenced state Z bounds for the fully-assigned sequence. -
getSequenced
returns Z bounds for all sequences returns bounds for both full and partial sequences -
getBestConfs
-
getBestConfs
-
dump
-