com.compomics.util.protein_sequences_manager.gui.sequences_import.taxonomy

Class UniprotTaxonomyProvider

java.lang.Object

com.compomics.util.protein_sequences_manager.gui.sequences_import.taxonomy.UniprotTaxonomyProvider

public class UniprotTaxonomyProvider
extends Object

UniProt taxonomy provider.

Author:

Kenneth Verheggen

Constructor Summary

Constructors

Constructor and Description
UniprotTaxonomyProvider() Normal constructor, GUI-less mode.
UniprotTaxonomyProvider(DefaultTreeModel model) GUI constructor.

Method Summary

Modifier and Type	Method and Description
String	getCachedTaxonomyID(String taxonomyName) Returns the taxonomyID that was encountered for a taxonomyName.
List<String>	getChildTaxonomies(String taxonomyName) Returns the child taxonomies.
Set<String>	getLineagesForTaxonomyID(String taxonomyName) Returns the possible lineages for a given taxonomy.
Set<String>	getLineagesFromFile(File taxonomyFile) Returns the possible lineages for a given taxonomy
DefaultTreeModel	getModelAfterClick(String taxonomyName) Returns a model for a known taxonomy name (for example after node click).
DefaultTreeModel	getModelAfterSearch(String taxonomyName) Returns a model after searching for an unknown taxonomy name (for example after a search).
DefaultTreeModel	getModelFromFile(File taxonomyTabFile) Returns a model after searching for an unknown taxonomy name (for example after a search).
String	queryTaxonomy(String queryTerm, boolean returnID) Returns the query taxonomy.

Methods inherited from class java.lang.Object

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

Constructor Detail

UniprotTaxonomyProvider

public UniprotTaxonomyProvider(DefaultTreeModel model)

GUI constructor.

Parameters:

model - the tree model you want to update

UniprotTaxonomyProvider

public UniprotTaxonomyProvider()

Normal constructor, GUI-less mode.

Method Detail

getChildTaxonomies

public List<String> getChildTaxonomies(String taxonomyName)
                                throws MalformedURLException,
                                       IOException

Returns the child taxonomies.

Parameters:

taxonomyName - the taxonomy name

Returns:

all the children names for a given taxonomy name (or identifier)

Throws:

MalformedURLException - if a MalformedURLException occurs

IOException - if an IOException occurs

getLineagesForTaxonomyID

public Set<String> getLineagesForTaxonomyID(String taxonomyName)
                                     throws MalformedURLException,
                                            IOException,
                                            IllegalArgumentException,
                                            URISyntaxException

Returns the possible lineages for a given taxonomy.

Parameters:

taxonomyName - the taxonomy name

Returns:

the possible lineages for a given taxonomy

Throws:

MalformedURLException - if a MalformedURLException occurs

IOException - if an IOException occurs

URISyntaxException - if a URISyntaxException occurs

IllegalArgumentException

getLineagesFromFile

public Set<String> getLineagesFromFile(File taxonomyFile)
                                throws MalformedURLException,
                                       IOException

Returns the possible lineages for a given taxonomy

Parameters:

taxonomyFile - taxonomy file from the UniProt web page

Returns:

the possible lineages for a given taxonomy

Throws:

MalformedURLException - if a MalformedURLException occurs

IOException - if an IOException occurs

getModelFromFile

public DefaultTreeModel getModelFromFile(File taxonomyTabFile)
                                  throws IOException,
                                         InterruptedException

Returns a model after searching for an unknown taxonomy name (for example after a search).

Parameters:

taxonomyTabFile - taxonomy file from the UniProt web page

Returns:

a model after searching for an unknown taxonomy name (for example after a search)

Throws:

IOException - if an IOException occurs

InterruptedException - if an InterruptedException occurs

getModelAfterSearch

public DefaultTreeModel getModelAfterSearch(String taxonomyName)
                                     throws IllegalArgumentException,
                                            IOException,
                                            MalformedURLException,
                                            URISyntaxException

Returns a model after searching for an unknown taxonomy name (for example after a search).

Parameters:

taxonomyName - the taxonomy name

Returns:

a model after searching for an unknown taxonomy name (for example after a search)

Throws:

MalformedURLException - if a MalformedURLException occurs

IOException - if an IOException occurs

URISyntaxException - if a URISyntaxException occurs

IllegalArgumentException

getModelAfterClick

public DefaultTreeModel getModelAfterClick(String taxonomyName)
                                    throws IOException

Returns a model for a known taxonomy name (for example after node click).

Parameters:

taxonomyName - the taxonomy name

Returns:

a model for a known taxonomy name (for example after node click)

Throws:

IOException - if an IOException occurs

getCachedTaxonomyID

public String getCachedTaxonomyID(String taxonomyName)

Returns the taxonomyID that was encountered for a taxonomyName. This is required to speed up the tree considerably.

Parameters:

taxonomyName - the taxonomy name

Returns:

the taxonomyID

queryTaxonomy

public String queryTaxonomy(String queryTerm,
                            boolean returnID)
                     throws MalformedURLException,
                            IOException

Returns the query taxonomy.

Parameters:

queryTerm - the term you wish to search for (example "human" or 9606)

returnID - boolean indicating whether you want the taxonomyID or the taxonomy name

Returns:

the query taxonomy

Throws:

MalformedURLException - if a MalformedURLException occurs

IOException - if an IOException occurs