Package edu.duke.cs.osprey.tools

Class MapDBTools.SequenceSerializer

java.lang.Object

org.mapdb.serializer.GroupSerializerObjectArray<T>

edu.duke.cs.osprey.tools.MapDBTools.SimpleSerializer<Sequence>

edu.duke.cs.osprey.tools.MapDBTools.SequenceSerializer

All Implemented Interfaces:

Comparator<Sequence>, org.mapdb.Serializer<Sequence>, org.mapdb.serializer.GroupSerializer<Sequence>

Enclosing class:

MapDBTools

public static class MapDBTools.SequenceSerializer
extends MapDBTools.SimpleSerializer<Sequence>

Field Summary

Fields

Modifier and Type	Field	Description
final SeqSpace	seqSpace

Fields inherited from class edu.duke.cs.osprey.tools.MapDBTools.SimpleSerializer

DynamicSize, fixedSize

Fields inherited from interface org.mapdb.Serializer

BIG_DECIMAL, BIG_INTEGER, BOOLEAN, BYTE, BYTE_ARRAY, BYTE_ARRAY_DELTA, BYTE_ARRAY_DELTA2, BYTE_ARRAY_NOSIZE, CHAR, CHAR_ARRAY, CLASS, DATE, DOUBLE, DOUBLE_ARRAY, ELSA, FLOAT, FLOAT_ARRAY, ILLEGAL_ACCESS, INT_ARRAY, INTEGER, INTEGER_DELTA, INTEGER_PACKED, JAVA, LONG, LONG_ARRAY, LONG_DELTA, LONG_PACKED, RECID, RECID_ARRAY, SHORT, SHORT_ARRAY, STRING, STRING_ASCII, STRING_DELTA, STRING_DELTA2, STRING_INTERN, STRING_NOSIZE, STRING_ORIGHASH, UUID

Constructor Summary

Constructors

Constructor	Description
SequenceSerializer(SeqSpace seqSpace)

Method Summary

Modifier and Type	Method	Description
int	compare(Sequence a, Sequence b)
Sequence	deserialize(org.mapdb.DataInput2 in, int available)
String	getSequenceId(Sequence sequence)
Sequence	makeSequenceFromId(String id)
void	serialize(org.mapdb.DataOutput2 out, Sequence sequence)

Methods inherited from class edu.duke.cs.osprey.tools.MapDBTools.SimpleSerializer

fixedSize, isTrusted

Methods inherited from class org.mapdb.serializer.GroupSerializerObjectArray

valueArrayCopyOfRange, valueArrayDeleteValue, valueArrayDeserialize, valueArrayEmpty, valueArrayFromArray, valueArrayGet, valueArrayPut, valueArraySearch, valueArraySearch, valueArraySerialize, valueArraySize, valueArrayToArray, valueArrayUpdateVal

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.util.Comparator

equals, reversed, thenComparing, thenComparing, thenComparing, thenComparingDouble, thenComparingInt, thenComparingLong

Methods inherited from interface org.mapdb.serializer.GroupSerializer

nextValue, valueArrayBinaryGet, valueArrayBinarySearch

Methods inherited from interface org.mapdb.Serializer

clone, deserializeFromLong, equals, hashCode, needsAvailableSizeHint

Field Details

seqSpace

public final SeqSpace seqSpace

Constructor Details

SequenceSerializer

public SequenceSerializer(SeqSpace seqSpace)

Method Details

serialize

public void serialize(@NotNull
 org.mapdb.DataOutput2 out,
 @NotNull
 Sequence sequence)
               throws IOException

Throws:

IOException

deserialize

public Sequence deserialize(@NotNull
 org.mapdb.DataInput2 in,
 int available)
                     throws IOException

Throws:

IOException

compare

public int compare(Sequence a,
 Sequence b)

getSequenceId

public String getSequenceId(Sequence sequence)

makeSequenceFromId

public Sequence makeSequenceFromId(String id)