uk.ac.ebi.intact.business
Interface SearchI

All Known Implementing Classes:

IntactHelper

public interface SearchI

Method Summary

java.util.Collection	paramSearch(java.lang.String objectType, java.lang.String searchParam, java.lang.String searchValue, boolean includeSubClass, boolean matchSubString) This method provides a means of searching intact objects, within the constraints provided by the parameters to the method.
java.util.List	stringSearch(java.lang.String objectType, java.lang.String searchString, boolean includeSubClass, boolean matchSubString) Searches objects by searchString in all "relevant" fields.
Graph	subGraph(Interactor startNode, int graphDepth, java.util.Collection experiments, int complexExpansion, Graph graph) Returns a subgraph centered on startNode.

Method Detail

paramSearch

public java.util.Collection paramSearch(java.lang.String objectType,
                                        java.lang.String searchParam,
                                        java.lang.String searchValue,
                                        boolean includeSubClass,
                                        boolean matchSubString)
                                 throws IntactException

This method provides a means of searching intact objects, within the constraints provided by the parameters to the method.

Parameters:

objectType - - the object type to be searched

searchParam - - the parameter to search on (eg field)

searchValue - - the search value to match with the parameter

includeSubClass - - if true, known subclasses of objectType will be searched, too.

matchSubString - - if true, substring matches of searchValue to object properties will also be hits.

Returns:

Collection - the results of the search (empty Collection if no matches found)

Throws:

IntactException - - thrown if problems are encountered during the search process

stringSearch

public java.util.List stringSearch(java.lang.String objectType,
                                   java.lang.String searchString,
                                   boolean includeSubClass,
                                   boolean matchSubString)
                            throws IntactException

Searches objects by searchString in all "relevant" fields. The definition of "relevant" depends on the class. Resulting objects are ordered on descending relevance.

Parameters:

objectType - - the object type to be searched

searchString - - the String to search for

includeSubClass - - if true, known subclasses of objectType will be searched, too.

matchSubString - - if true, substring matches of searchValue to object properties will also be hits.

Returns:

List - the results of the search (empty List if no matches found)

Throws:

IntactException - - thrown if problems are encountered during the search process

subGraph

public Graph subGraph(Interactor startNode,
                      int graphDepth,
                      java.util.Collection experiments,
                      int complexExpansion,
                      Graph graph)
               throws IntactException

Returns a subgraph centered on startNode. The subgraph will contain all nodes which are up to graphDepth interactions away from startNode. Only Interactions which belong to one of the Experiments in experiments will be taken into account. If experiments is empty, all Interactions are taken into account. Expansion: If an Interaction has more than two interactors, it has to be defined how pairwise interactions are generated from the complex data. The possible values are defined in the beginning of this file.

Parameters:

startNode - - the start node of the subgraph.

graphDepth - - depth of the graph

experiments - - Experiments which should be taken into account

complexExpansion - - Mode of expansion of complexes into pairwise interactions

graph - - the graph we have to fill with interaction data

Returns:

To be further defined, probably a simple GraphII object.

Throws:

IntactException - - thrown if problems are encountered