be.ac.ulb.mlg.utils.renormalizer

Class TaxonRenormalizer

java.lang.Object

be.ac.ulb.mlg.utils.DefaultRenormalizer

be.ac.ulb.mlg.utils.renormalizer.TaxonRenormalizer

All Implemented Interfaces:

Renormalizer<double[][]>

public class TaxonRenormalizer
extends DefaultRenormalizer

This class represents a normalization with taxa. Each main taxon must be defined by calling addTaxa() method in order to normalize them and assemble them to their own root. Thus, if it exists a main root, you need to pre-remove it before to add taxons otherwise all data will be reduced to one row containing only an array of 1.0. For each row of the next input matrix, the lowest taxa level must be specified with the setTaxa() method after the definition of taxons. To design this class, some hypothesis are assumed: - Taxon are fully specified - Taxon doesn't contain overlaps (can be represented with a Tree: parents to children) => For each taxa, only one highest level All taxa/taxon is not case sensitive (according to the String case specification).

Version:

1.2, 18/08/2015

Author:

Jean-Sébastien Lerat

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	DEFAULT_SEPARATOR Default Taxa separator

Fields inherited from class be.ac.ulb.mlg.utils.DefaultRenormalizer

SUM_NORMILIZER

Constructor Summary

Constructors

Constructor and Description
TaxonRenormalizer() Construct a new TaxonRenormalizer without predefined values Default applied renormalization is the default renormalization of the DefaultRenormalizer

Method Summary

Modifier and Type	Method and Description
void	addTaxa(java.lang.String taxa) Add a taxa defintion of the main taxon according to the string format with the DEFAULT_SEPARATOR
void	addTaxa(java.lang.String lineage, java.lang.String separator) Add a taxa defintion of the main taxon according to the string format
int[]	getGroupResult() Get the mapping from (index) to (groups index identifier) for the new input matrix
int	getTaxaIdentifier(java.lang.String taxa)
boolean	hasNativeImplementation() Know if the current renormalizer owns a native implementation
boolean	isHighestLevel(int taxa)
boolean	isHighestLevel(java.lang.String taxa)
boolean	isHighLevel(int taxa)
boolean	isHighLevel(java.lang.String taxa)
boolean	isLowLevel(int taxa)
boolean	isLowLevel(java.lang.String taxa)
double[][]	normalizeInput(double[][] input) Apply the normalization process on the given vector of data vectors
boolean	processInput() Know if the renormalizer can handle input (call normalizeInput has effect)
boolean	processOutput() Know if the renormalizer can handle output (call normalizeOutput has effect)
void	reset() Reset only (no call to inherited reset methods) all data relative to taxa/taxon and mappings of last results
void	setTaxa(int position, java.lang.String taxa) Set the taxa for a row (null or out of taxon results in considering the row as a feature)
void	setTaxa(int position, java.lang.String taxa, java.lang.String separator) Set the taxa for a row (null or out of taxon results in considering the row as a feature)
void	setTaxa(java.lang.String[] taxas) Set the taxa for all row (null or out of taxon results in considering the row as a feature) This method (instead of addTaxa, addTaxa) is able to handle duplicated values
void	setTaxa(java.lang.String[] taxas, java.lang.String separator) Set the taxa for all row (null or out of taxon results in considering the row as a feature) This method (instead of addTaxa, addTaxa) is able to handle duplicated values
void	updateRenormalization(double[][] sum, double[] vect, int row, boolean ignore) Method called when pairwise renormalization is used in order to ignore or not a row from the original input matrix

Methods inherited from class be.ac.ulb.mlg.utils.DefaultRenormalizer

addFeature, cloneState, countFeatures, countGroups, groupOf, isUsingCustomNormalizer, isUsingFeatures, isUsingGroups, mergeRenormalizer, noFeatures, noGroups, normalizeOutput, prepareRenormalization, resetNormalizer, setGroup, setGroup, setGroups, setGroupsNames, setNormalizer, setNormalizer, setNormalizer, shufflePair, simulateRenormalization, usePairShuffle

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_SEPARATOR

public static final java.lang.String DEFAULT_SEPARATOR

Default Taxa separator

See Also:

Constant Field Values

Constructor Detail

TaxonRenormalizer

public TaxonRenormalizer()

Construct a new TaxonRenormalizer without predefined values Default applied renormalization is the default renormalization of the DefaultRenormalizer

Method Detail

reset

public void reset()

Reset only (no call to inherited reset methods) all data relative to taxa/taxon and mappings of last results

getTaxaIdentifier

public int getTaxaIdentifier(java.lang.String taxa)

Parameters:

taxa - The name of a defined taxa level

Returns:

The corresponding numeric taxa's identifier

isLowLevel

public boolean isLowLevel(java.lang.String taxa)

Parameters:

taxa - The name of a defined taxa level

Returns:

true iff the taxa is one of the lowest levels, false otherwise

isHighLevel

public boolean isHighLevel(java.lang.String taxa)

Parameters:

taxa - The name of a defined taxa level

Returns:

true iff the taxa is one of the higher levels, false if it is a lowest level

isHighestLevel

public boolean isHighestLevel(java.lang.String taxa)

Parameters:

taxa - The index (according to the ordre of definition, see getTaxaIdentifier() method) of a definedtaxa level

Returns:

true iff the taxa is one of the highest levels, false otherwise

isLowLevel

public boolean isLowLevel(int taxa)

Parameters:

taxa - The index (according to the ordre of definition, see getTaxaIdentifier() method) of a defined taxa level

Returns:

true iff the taxa is one of the lowest levels, false otherwise

isHighLevel

public boolean isHighLevel(int taxa)

Parameters:

taxa - The index (according to the ordre of definition, see getTaxaIdentifier() method) of a defined taxa level

Returns:

true iff the taxa is one of the higher levels, false if it is a lowest level

isHighestLevel

public boolean isHighestLevel(int taxa)

Parameters:

taxa - The name of a defined taxa level

Returns:

true iff the taxa is one of the highest levels, false otherwise

setTaxa

public void setTaxa(java.lang.String[] taxas)

Set the taxa for all row (null or out of taxon results in considering the row as a feature) This method (instead of addTaxa, addTaxa) is able to handle duplicated values

Parameters:

taxas - Taxa names of all row with full level mapping for each row of the next input matrix

setTaxa

public void setTaxa(java.lang.String[] taxas,
                    java.lang.String separator)

Set the taxa for all row (null or out of taxon results in considering the row as a feature) This method (instead of addTaxa, addTaxa) is able to handle duplicated values

Parameters:

separator - Specify the used separator (literal string)

taxas - Taxa names of all row with full level mapping for each row of the next input matrix

setTaxa

public void setTaxa(int position,
                    java.lang.String taxa,
                    java.lang.String separator)

Set the taxa for a row (null or out of taxon results in considering the row as a feature)

Parameters:

position - The index of the concerned data row

separator - Specify the used separator (literal string)

taxas - Taxa names of all row, one lowest level mapping for each row of the next input matrix

setTaxa

public void setTaxa(int position,
                    java.lang.String taxa)

Set the taxa for a row (null or out of taxon results in considering the row as a feature)

Parameters:

separator - Specify the used separator (literal string)

taxas - Taxa names of all row, one lowest level mapping for each row of the next input matrix

addTaxa

public void addTaxa(java.lang.String taxa)

Add a taxa defintion of the main taxon according to the string format with the DEFAULT_SEPARATOR

Parameters:

taxa - The taxa definition from the highest level to the lowest level

addTaxa

public void addTaxa(java.lang.String lineage,
                    java.lang.String separator)

Add a taxa defintion of the main taxon according to the string format

Parameters:

lineage - The taxa definition from the highest level to the lowest level (cannot contains spaces see \s in RegularExpression)

separator - Specify the used separator (literal string)

normalizeInput

public double[][] normalizeInput(double[][] input)

Description copied from interface: Renormalizer

Apply the normalization process on the given vector of data vectors

Specified by:

normalizeInput in interface Renormalizer<double[][]>

Overrides:

normalizeInput in class DefaultRenormalizer

Parameters:

input - The given vector of data vectors

Returns:

the input array

updateRenormalization

public void updateRenormalization(double[][] sum,
                                  double[] vect,
                                  int row,
                                  boolean ignore)

Description copied from interface: Renormalizer

Method called when pairwise renormalization is used in order to ignore or not a row from the original input matrix

Specified by:

updateRenormalization in interface Renormalizer<double[][]>

Overrides:

updateRenormalization in class DefaultRenormalizer

Parameters:

sum - The state on which modifications will be applied

vect - A vector which is considerate as a row from the original input matrix corresponding to the row at the given index

row - The index of the vector to map it into the original matrix at this index

ignore - A boolean to tell if the values of the vector must be ignored (typically remove these values from the normalization process as if it was the row "index" from the original input matrix) with the true value (typically false to add it into renormalization)

getGroupResult

public int[] getGroupResult()

Get the mapping from (index) to (groups index identifier) for the new input matrix

Returns:

The mapping row index to the group's index of the resulting new input matrix

hasNativeImplementation

public boolean hasNativeImplementation()

Description copied from interface: Renormalizer

Know if the current renormalizer owns a native implementation

Specified by:

hasNativeImplementation in interface Renormalizer<double[][]>

Overrides:

hasNativeImplementation in class DefaultRenormalizer

Returns:

true if the native implementation exists

processInput

public boolean processInput()

Description copied from interface: Renormalizer

Know if the renormalizer can handle input (call normalizeInput has effect)

Specified by:

processInput in interface Renormalizer<double[][]>

Overrides:

processInput in class DefaultRenormalizer

Returns:

true if it can handle

processOutput

public boolean processOutput()

Description copied from interface: Renormalizer

Know if the renormalizer can handle output (call normalizeOutput has effect)

Specified by:

processOutput in interface Renormalizer<double[][]>

Overrides:

processOutput in class DefaultRenormalizer

Returns:

true if it can handle