com.compomics.util.preferences

Class GenePreferences

java.lang.Object

com.compomics.util.preferences.GenePreferences

All Implemented Interfaces:

Serializable

public class GenePreferences
extends Object
implements Serializable

Contains methods for downloading gene and GO mappings.

Author:

Harald Barsnes, Marc Vaudel

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static String	GENE_MAPPING_FILE_SUFFIX Deprecated. use the gene factory.
static String	GO_MAPPING_FILE_SUFFIX Deprecated. use the gene factory.

Constructor Summary

Constructors

Constructor and Description
GenePreferences() Create a new GenePreferences object.
GenePreferences(GenePreferences genePreferences) Creates new gene preferences based on a GenePreferences object.

Method Summary

Modifier and Type	Method and Description
boolean	equals(GenePreferences genePreferences) Compares these preferences to other preferences.
Boolean	getAutoUpdate() Indicates whether the gene mappings should be automatically updated.
Integer	getSelectedBackgroundSpecies() Returns the taxon of the species selected as background species.
String	getShortDescription() Returns a short description of the parameters.
Boolean	getUseGeneMapping() Returns a boolean indicating whether gene mappings should be used.
void	setAutoUpdate(Boolean autoUpdate) Sets whether the gene mappings should be automatically updated.
void	setPreferencesFromSearchParameters(SearchParameters searchParameters) Sets the preferences from the given search parameters.
void	setSelectedBackgroundSpecies(Integer selectedBackgroundSpecies) Sets the taxon of the species selected as background species.
void	setUseGeneMapping(Boolean useGeneMapping) Sets whether gene mappings should be used.

Methods inherited from class java.lang.Object

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

Field Detail

GENE_MAPPING_FILE_SUFFIX

public static final String GENE_MAPPING_FILE_SUFFIX

Deprecated. use the gene factory.

The suffix to use for files containing gene mappings.

See Also:

Constant Field Values

GO_MAPPING_FILE_SUFFIX

public static final String GO_MAPPING_FILE_SUFFIX

Deprecated. use the gene factory.

The suffix to use for files containing GO mappings.

See Also:

Constant Field Values

Constructor Detail

GenePreferences

public GenePreferences()

Create a new GenePreferences object.

GenePreferences

public GenePreferences(GenePreferences genePreferences)

Creates new gene preferences based on a GenePreferences object.

Parameters:

genePreferences - the gene preferences

Method Detail

getUseGeneMapping

public Boolean getUseGeneMapping()

Returns a boolean indicating whether gene mappings should be used.

Returns:

a boolean indicating whether gene mappings should be used

setUseGeneMapping

public void setUseGeneMapping(Boolean useGeneMapping)

Sets whether gene mappings should be used.

Parameters:

useGeneMapping - a boolean indicating whether gene mappings should be used

getAutoUpdate

public Boolean getAutoUpdate()

Indicates whether the gene mappings should be automatically updated.

Returns:

a boolean indicating whether the gene mappings should be automatically updated

setAutoUpdate

public void setAutoUpdate(Boolean autoUpdate)

Sets whether the gene mappings should be automatically updated.

Parameters:

autoUpdate - a boolean indicating whether the gene mappings should be automatically updated

equals

public boolean equals(GenePreferences genePreferences)

Compares these preferences to other preferences.

Parameters:

genePreferences - other preferences to compare to.

Returns:

a boolean indicating whether the other preferences are the same as these ones.

getSelectedBackgroundSpecies

public Integer getSelectedBackgroundSpecies()

Returns the taxon of the species selected as background species.

Returns:

the taxon of the species selected as background species

setSelectedBackgroundSpecies

public void setSelectedBackgroundSpecies(Integer selectedBackgroundSpecies)

Sets the taxon of the species selected as background species.

Parameters:

selectedBackgroundSpecies - the taxon of the species selected as background species

setPreferencesFromSearchParameters

public void setPreferencesFromSearchParameters(SearchParameters searchParameters)

Sets the preferences from the given search parameters.

Parameters:

searchParameters - the search parameters

getShortDescription

public String getShortDescription()

Returns a short description of the parameters.

Returns:

a short description of the parameters