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Symbols 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.Symbols 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.
Images
DoubleVectors with the same dimension.
TandemSpectraes.
Fragments
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
Fragments. - 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 Alphabetof Symbol
objects.Fragments with Weighted Hamming Distance.
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