slib.tools.smltoolkit.sm.cli.core.utils

Class XMLConfUtils

java.lang.Object

slib.tools.smltoolkit.sm.cli.core.utils.XMLConfUtils

public class XMLConfUtils
extends Object

Author:

Sébastien Harispe

Constructor Summary

Constructors

Constructor and Description
XMLConfUtils()

Method Summary

Methods

Modifier and Type	Method and Description
static String	buildSML_FilterGAF2_XML_block(String filterConfAsString) this parameter can be used to filter the GO terms associated to a gene product when the provided annotation file is in GAF2 format.
static String	buildSML_SM_module_XML_block_GO_PROFILE(SML_SM_module_XML_block_conf c) Build a String representation of the Semantic Measures XML tag considering the given configuration.
static String	buildSML_SM_module_XML_block_MESH_PROFILE(SML_SM_module_XML_block_conf c)

Methods inherited from class java.lang.Object

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

Constructor Detail

XMLConfUtils

public XMLConfUtils()

Method Detail

buildSML_FilterGAF2_XML_block

public static String buildSML_FilterGAF2_XML_block(String filterConfAsString)
                                            throws SLIB_Ex_Critic

this parameter can be used to filter the GO terms associated to a gene product when the provided annotation file is in GAF2 format. - EC= evidence_codes evidence codes separated by commas e.g. EC=IEA only IEA annotations will be considered - Taxon=taxon_ids taxon ids separated by commas e.g. Taxon=9696 to only consider annotations associated to Taxon 9696 Example of value -filter EC=IEA,XXX:Taxon=9696

Parameters:

filterConfAsString -

Returns:

a string corresponding to the filter configuration.

Throws:

SLIB_Ex_Critic

buildSML_SM_module_XML_block_GO_PROFILE

public static String buildSML_SM_module_XML_block_GO_PROFILE(SML_SM_module_XML_block_conf c)
                                                      throws SLIB_Ex_Critic

Build a String representation of the Semantic Measures XML tag considering the given configuration.

Parameters:

c - the configuration used to build the XML tag

Returns:

a String representation of the Semantic Measures XML tag corresponding to the given configuration

Throws:

SLIB_Ex_Critic

buildSML_SM_module_XML_block_MESH_PROFILE

public static String buildSML_SM_module_XML_block_MESH_PROFILE(SML_SM_module_XML_block_conf c)
                                                        throws SLIB_Ex_Critic

Throws:

SLIB_Ex_Critic