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Symbol
s for a specific Sequence
type.Metric
that counts the invocations of
Metric.getDistance(IndexObject,IndexObject)
.CountedMetric
with a given base Metric
, setting the
internal counter to zero.
DoubleMatrix2D
of the given size.
Iterator
, iterating on the results set.Symbol
s may map to the same byteValue; this is used
to determine the number of distinct byteValues that an Alphabet has.
DNA
is a compact representation of a DNA sequence.double
and an IndexObject
.String
of doubles.
Metric.getDistance(IndexObject,IndexObject)
for the base
Metric
and increments the internal counter.
Image
s
DoubleVector
s with the same dimension.
TandemSpectra
es.
Fragment
s
ObjectIOManager
for this index.
ObjectIOManager
based on the Mckoi(http://www.mckoi.com/database)
I/O mechanism.Metric
is a distance oracle.Metric
interface.Sequence
can be divided up into.
Peptide
is a compact representation of a AminoAcids sequence(Peptide).String
that contains the number of
dimension and meaning for each dimension
byte range.- SequenceFragmentMetric - Class in mobios.dist
- Computes the distance between two
Fragment
s. - SequenceFragmentMetric(WeightMatrix) -
Constructor for class mobios.dist.SequenceFragmentMetric
- Creates a new SequenceFragmentMetric over the given
WeightMatrix
.
- set(int, int, double) -
Method in class mobios.util.LargeDenseDoubleMatrix2D
-
- setChar(char, byte[], int) -
Static method in class mobios.mckoi.util.ByteArrayUtil
- Sets the short at the given offset of the byte array.
- setChildAddress(int, long) -
Method in class mobios.index.InternalNode
-
- setDouble(double) -
Method in class mobios.type.DoubleIndexObjectPair
-
- setFixedArea(byte[], int, int) -
Method in class mobios.mckoi.store.AbstractStore
-
- setInt(int, byte[], int) -
Static method in class mobios.mckoi.util.ByteArrayUtil
- Sets the int at the given offset of the byte array.
- setLong(long, byte[], int) -
Static method in class mobios.mckoi.util.ByteArrayUtil
- Sets the long at the given offset of the byte array.
- setMaxLeafSize(int) -
Method in interface mobios.index.algorithms.PartitionMethod
-
- setMaxRadius(double) -
Method in interface mobios.index.algorithms.PartitionMethod
-
- setNode(InternalNode) -
Method in class mobios.index.algorithms.PartitionResults
-
- setObject(IndexObject) -
Method in class mobios.type.DoubleIndexObjectPair
-
- setQuick(int, int, double) -
Method in class mobios.util.LargeDenseDoubleMatrix2D
- Sets the matrix cell at coordinate [row,column] to the specified value.
- setRowID(int) -
Method in class mobios.type.IndexObject
-
- setRowIDLength(int) -
Method in class mobios.type.IndexObject
-
- setShort(short, byte[], int) -
Static method in class mobios.mckoi.util.ByteArrayUtil
- Sets the short at the given offset of the byte array.
- SIMPLE_ALPHABET -
Static variable in class mobios.type.DNA
- A simple alphabet of DNASymbols.
- SimpleDNAEditDistanceMatrix -
Static variable in class mobios.type.DNA
- The SimpleDNAEditDistanceMatrix looks like: {0,1,1,1}, {1,0,1,1}, {1,1,0,1}, {1,1,1,0}
- SimpleEditDistanceMatrix -
Static variable in class mobios.type.RNA
- The SimpleEditDistanceMatrix looks like:
{0,1,1,1},
{1,0,1,1},
{1,1,0,1},
{1,1,1,0}
- SimpleWeightedDNAMatrix -
Static variable in class mobios.type.DNA
- A simpleWeightedDNAMatrix.
- size() -
Method in class mobios.index.AbstractIndex
-
- size() -
Method in class mobios.index.algorithms.PartitionResults
-
- size() -
Method in interface mobios.index.Index
-
- size() -
Method in class mobios.type.Alphabet
-
- size() -
Method in class mobios.type.DoubleVector
-
- size() -
Method in class mobios.type.Fragment
-
- size() -
Method in class mobios.type.Image
-
- size() -
Method in class mobios.type.IndexObject
-
- size() -
Method in class mobios.type.Sequence
-
- size() -
Method in class mobios.util.Histogram.BinInfo
-
- size() -
Method in class mobios.util.LargeDenseDoubleMatrix2D
-
- size() -
Method in class mobios.util.MckoiObjectIOManager
-
- size() -
Method in interface mobios.util.ObjectIOManager
-
- sizeChange(long, long) -
Method in interface mobios.mckoi.store.FileBufferAccessor
- Notifies the buffering strategy that the size of the file has changed.
- sizeGate -
Static variable in class mobios.util.LargeDenseDoubleMatrix2D
-
- sortAsc() -
Method in class mobios.type.Spectra
- Sorts the Spectra from smallest to largest values.
- Spectra - Class in mobios.type
- Represents a spectra.
- Spectra() -
Constructor for class mobios.type.Spectra
- Default Constructor.
- Spectra(Table, int, String) -
Constructor for class mobios.type.Spectra
- Constructor.
- Spectra(Table, int, double[]) -
Constructor for class mobios.type.Spectra
-
- statistics -
Static variable in class mobios.util.Debug
- Record statistics.
- statsScan(HashMap) -
Method in class mobios.mckoi.store.AbstractStore
- Performs an extensive lookup on all the tables in this store and sets a
number of properties in the given HashMap
(property name(String) -> property description(Object)).
- Store - Interface in mobios.mckoi.store
- A store is a resource where areas can be allocated and freed to store
objects.
- stringValue() -
Method in enum mobios.type.DNA.DNASymbol
-
- stringValue() -
Method in enum mobios.type.Peptide.AminoAcid
-
- stringValue() -
Method in enum mobios.type.RNA.RNASymbol
-
- stringValue() -
Method in interface mobios.type.Symbol
-
- Symbol - Interface in mobios.type
- Interface
Symbol
is implemented for the characters of a biosequence alphabet. - SymmetricSubstitutionWeightMatrix - Class in mobios.dist
- Implements a
WeightMatrix
by providing a symmetric substitution matrix of double
distances for a given Alphabet
. - SymmetricSubstitutionWeightMatrix(Alphabet, double[][]) -
Constructor for class mobios.dist.SymmetricSubstitutionWeightMatrix
- Constructor.
- synch() -
Method in class mobios.mckoi.store.ScatteringFileStore
-
- synch() -
Method in interface mobios.mckoi.store.Store
- Flushes and synchronizes any changes made to the store with the underlying
persistent device.
Cursor
, for KNN search in vp treeLeafNode
in a VPIndex
.Cursor
, for range search in vp treeWeightMatrix
is the substitution matrix of an Alphabet
of Symbol
objects.Fragment
s with Weighted Hamming Distance.
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Mobios v0.91 | ||||||||
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