Serialized Form

Package mobios.dist

Class mobios.dist.CountedMetric extends Object implements Serializable

serialVersionUID: 5436226220280070858L

Serialized Fields

baseMetric

Metric baseMetric

counter

int counter

Class mobios.dist.ImageMetric extends Object implements Serializable

serialVersionUID: 3442536718895037166L

Serialized Fields

feaNum

int feaNum

Feature number for each image. We have three features for each image: structure, texture, and histogram.

feaLength

int[] feaLength

Number of floats that can represent each feature.

minBool

boolean[] minBool

Distance function selection for each feature.

weights

double[] weights

The weights of each feature in the computation of distance.

maxDist

double[] maxDist

The max distance for each feature.

Class mobios.dist.LMetric extends Object implements Serializable

serialVersionUID: -4658067077491099474L

Serialized Fields

dim

int dim

Dimension of the metric

Class mobios.dist.MSMetric extends Object implements Serializable

serialVersionUID: 179878801379011989L

Serialized Fields

min

int min

Convert information of the instance into a String that contains the number of dimension and meaning for each dimension

max

int max

Convert information of the instance into a String that contains the number of dimension and meaning for each dimension

step

double step

tol

double tol

COS_THRESHOLD

double COS_THRESHOLD

Class mobios.dist.MSMSMetric extends Object implements Serializable

serialVersionUID: 8368326281379099335L

Serialized Fields

min

int min

max

int max

step

double step

mscosdist

double mscosdist

absMassDiff

double absMassDiff

massDiffTerm

double massDiffTerm

tol

double tol

COS_THRESHOLD

double COS_THRESHOLD

Class mobios.dist.SequenceFragmentMetric extends Object implements Serializable

Serialized Fields

weightMatrix

WeightMatrix weightMatrix

the WeightMatrix that this SequenceFragmentMetric is defined over.

Class mobios.dist.SymmetricSubstitutionWeightMatrix extends Object implements Serializable

serialVersionUID: 6295557519158168768L

Serialized Fields

alphabet

Alphabet alphabet

alphabetSize

int alphabetSize

distances

double[][] distances

Class mobios.dist.WHDGlobalSequenceFragmentMetric extends SequenceFragmentMetric implements Serializable

serialVersionUID: 7847936320149830952L

Package mobios.index

Class mobios.index.AbstractIndex extends Object implements Serializable

serialVersionUID: 2659219513493819541L

Serialization Methods

readObject

private void readObject(ObjectInputStream in)
                 throws IOException,
                        ClassNotFoundException

Throws:

IOException

ClassNotFoundException

writeObject

private void writeObject(ObjectOutputStream out)
                  throws IOException

Throws:

IOException

Serialized Fields

fileName

String fileName

metric

Metric metric

total_size

int total_size

root

long root

Class mobios.index.InternalNode extends mobios.index.IndexNode implements Serializable

Serialization Methods

readExternal

public void readExternal(ObjectInput in)
                  throws IOException,
                         ClassNotFoundException

Throws:

IOException

ClassNotFoundException

writeExternal

public void writeExternal(ObjectOutput out)
                   throws IOException

Throws:

IOException

Class mobios.index.VPIndex extends AbstractIndex implements Serializable

serialVersionUID: 6928847050089693231L

Serialized Fields

psm

PivotSelectionMethod psm

numPivot

int numPivot

pm

PartitionMethod pm

singlePivotFanout

int singlePivotFanout

maxLeafSize

int maxLeafSize

maxPathLength

int maxPathLength

Class mobios.index.VPInternalNode extends InternalNode implements Serializable

serialVersionUID: 2951629361525110954L

Serialization Methods

readExternal

public void readExternal(ObjectInput in)
                  throws IOException,
                         ClassNotFoundException

Throws:

IOException

ClassNotFoundException

writeExternal

public void writeExternal(ObjectOutput out)
                   throws IOException

Throws:

IOException

Class mobios.index.VPLeafNode extends mobios.index.LeafNode implements Serializable

serialVersionUID: -2816878994630817839L

Serialization Methods

readExternal

public void readExternal(ObjectInput in)
                  throws IOException,
                         ClassNotFoundException

Throws:

IOException

ClassNotFoundException

writeExternal

public void writeExternal(ObjectOutput out)
                   throws IOException

Throws:

IOException

Package mobios.type

Class mobios.type.Alphabet extends Object implements Serializable

serialVersionUID: -3200343173661145001L

Serialized Fields

alphabet

Symbol[] alphabet

distinctSize

int distinctSize

Class mobios.type.DNA extends Sequence implements Serializable

serialVersionUID: 1351256505737923337L

Class mobios.type.DoubleVector extends IndexObject implements Serializable

serialVersionUID: 1275897899226331100L

Serialization Methods

readExternal

public void readExternal(ObjectInput in)
                  throws IOException,
                         ClassNotFoundException

Throws:

IOException

ClassNotFoundException

writeExternal

public void writeExternal(ObjectOutput out)
                   throws IOException

Throws:

IOException

Class mobios.type.Fragment extends IndexObject implements Serializable

serialVersionUID: -7087849259510041868L

Serialization Methods

readExternal

public void readExternal(ObjectInput in)
                  throws IOException,
                         ClassNotFoundException

Throws:

IOException

ClassNotFoundException

writeExternal

public void writeExternal(ObjectOutput out)
                   throws IOException

Throws:

IOException

Class mobios.type.Image extends IndexObject implements Serializable

serialVersionUID: -6207971406392822640L

Serialization Methods

readExternal

public void readExternal(ObjectInput in)
                  throws IOException,
                         ClassNotFoundException

Throws:

IOException

ClassNotFoundException

writeExternal

public void writeExternal(ObjectOutput out)
                   throws IOException

Throws:

IOException

Class mobios.type.IndexObject extends Object implements Serializable

Serialization Methods

readExternal

public void readExternal(ObjectInput in)
                  throws IOException,
                         ClassNotFoundException

Throws:

IOException

ClassNotFoundException

writeExternal

public void writeExternal(ObjectOutput out)
                   throws IOException

Throws:

IOException

Class mobios.type.Pair extends Object implements Serializable

serialVersionUID: 7226016227786370437L

Serialization Methods

readObject

private void readObject(ObjectInputStream objectStream)
                 throws IOException,
                        ClassNotFoundException

method for making the class Serializable. reads information about the object from the ObjectInputStream

Throws:

IOException - if there is any error in reading

ClassNotFoundException

writeObject

private void writeObject(ObjectOutputStream objectStream)
                  throws IOException

method for making the class Serializable. writes information about the object to the ObjectOutputStream provided in the parameter, so that it can be read from the file and reconstructed later.

Throws:

IOException - if there is any error in writing

Serialized Fields

first

Object first

second

Object second

Class mobios.type.Peptide extends Sequence implements Serializable

serialVersionUID: 8791814013616626066L

Class mobios.type.RNA extends Sequence implements Serializable

serialVersionUID: -3352921445817956726L

Class mobios.type.Sequence extends Object implements Serializable

serialVersionUID: 6518919187067691379L

Serialized Fields

sequenceID

String sequenceID

data

byte[] data

Class mobios.type.Spectra extends DoubleVector implements Serializable

serialVersionUID: -8300375927493085758L

Serialization Methods

readExternal

public void readExternal(ObjectInput in)
                  throws IOException,
                         ClassNotFoundException

Throws:

IOException

ClassNotFoundException

writeExternal

public void writeExternal(ObjectOutput out)
                   throws IOException

Throws:

IOException

Class mobios.type.TandemSpectra extends Spectra implements Serializable

serialVersionUID: 1247643270939539788L

Serialization Methods

readExternal

public void readExternal(ObjectInput in)
                  throws ClassNotFoundException,
                         IOException

Throws:

ClassNotFoundException

IOException

writeExternal

public void writeExternal(ObjectOutput out)
                   throws IOException

Throws:

IOException

Package mobios.util

Class mobios.util.LargeDenseDoubleMatrix2D extends cern.colt.matrix.DoubleMatrix2D implements Serializable

serialVersionUID: 1020177651L

Serialized Fields

elements

double[][] elements

The elements of this matrix.