Package edu.duke.cs.osprey.coffee.seqdb

Class SeqDB

java.lang.Object

edu.duke.cs.osprey.coffee.seqdb.SeqDB

All Implemented Interfaces:

AutoCloseable

public class SeqDB
extends Object
implements 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

Modifier and Type	Class	Description
static class	SeqDB.Builder

Field Summary

Fields

Modifier and Type	Field	Description
final MultiStateConfSpace	confSpace
final File	file
final MathContext	mathContext
final ClusterMember	member
final int	numBestConfs
static final String	ServiceName

Method Summary

Modifier and Type	Method	Description
Batch	batch()
BigMath	bigMath()
void	close()
String	dump()
StateZ	get(MultiStateConfSpace.State state, Sequence seq)	Returns the current Z bounds and dropped Z for the state and sequence.
SeqInfo	get(Sequence seq)	Returns the current sequenced state Z bounds for the fully-assigned sequence.
List<ConfSearch.EnergiedConf>	getBestConfs(MultiStateConfSpace.State state)
List<ConfSearch.EnergiedConf>	getBestConfs(MultiStateConfSpace.State state, Sequence seq)
Iterable<Map.Entry<Sequence,SeqInfo>>	getSequenced()	returns Z bounds for all sequences returns bounds for both full and partial sequences
SeqInfo	getUnexplored(Sequence seq)	Returns the current state Z bounds for unexplored subtrees of the partially-assigned sequence.
StateZ	getUnsequenced(MultiStateConfSpace.State state)	Returns the current Z bounds and dropped Z for the unsequenced state.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details

ServiceName

public static final String ServiceName

See Also:

• Constant Field Values

confSpace

public final MultiStateConfSpace confSpace

member

public final ClusterMember member

mathContext

public final MathContext mathContext

file

public final File file

numBestConfs

public final int numBestConfs

Method Details

bigMath

public BigMath bigMath()

batch

public Batch batch()

close

public void close()

Specified by:

close in interface AutoCloseable

get

public StateZ get(MultiStateConfSpace.State state,
 Sequence seq)

Returns the current Z bounds and dropped Z for the state and sequence. If the state is unsequenced, the given sequence is ignored.

getUnsequenced

public StateZ getUnsequenced(MultiStateConfSpace.State state)

Returns the current Z bounds and dropped Z for the unsequenced state.

getUnexplored

public SeqInfo getUnexplored(Sequence seq)

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

public SeqInfo get(Sequence seq)

Returns the current sequenced state Z bounds for the fully-assigned sequence.

getSequenced

public Iterable<Map.Entry<Sequence,SeqInfo>> getSequenced()

returns Z bounds for all sequences returns bounds for both full and partial sequences

getBestConfs

public List<ConfSearch.EnergiedConf> getBestConfs(MultiStateConfSpace.State state,
 Sequence seq)

getBestConfs

public List<ConfSearch.EnergiedConf> getBestConfs(MultiStateConfSpace.State state)

dump

public String dump()