org.biopax.paxtools.pattern

Class Searcher

java.lang.Object

org.biopax.paxtools.pattern.Searcher

public class Searcher
extends Object

Searcher for searching a given pattern in a model.

Author:

Ozgun Babur

Constructor Summary

Constructors

Constructor and Description
Searcher()

Method Summary

Modifier and Type	Method and Description
boolean	hasSolution(Pattern p, BioPAXElement... ele) Checks if there is any match for the given pattern if search starts from the given element.
static List<Match>	search(BioPAXElement ele, Pattern pattern) Searches the pattern starting from the given element.
static Map<BioPAXElement,List<Match>>	search(Collection<? extends BioPAXElement> eles, Pattern pattern) Searches the given pattern starting from the given elements.
static List<Match>	search(Match m, Pattern pattern) Searches the pattern starting from the given match.
static Map<BioPAXElement,List<Match>>	search(Model model, Pattern pattern) Searches the given pattern in the given model.
static Map<BioPAXElement,List<Match>>	search(Model model, Pattern pattern, ProgressWatcher prg) Searches the given pattern in the given model.
static <T extends BioPAXElement> Set<T>	searchAndCollect(BioPAXElement ele, Pattern pattern, int index, Class<T> c) Searches the given pattern starting from the given element, then collects the specified elements of the matches and returns.
static <T extends BioPAXElement> Set<T>	searchAndCollect(Collection<? extends BioPAXElement> eles, Pattern pattern, int index, Class<T> c) Searches the given pattern starting from the given elements, then collects the specified elements of the matches and returns.
static <T extends BioPAXElement> Set<T>	searchAndCollect(Model model, Pattern pattern, int index, Class<T> c) Searches a model for the given pattern, then collects the specified elements of the matches and returns.
static void	searchInFile(Pattern p, String inFile, String outFile) Searches a pattern reading the model from the given file, and creates another model that is excised using the matching patterns.
static void	searchInFile(Pattern p, String inFile, String outFile, int seedLimit, int graphPerSeed) Searches a pattern reading the model from the given file, and creates another model that is excised using the matching patterns.
static List<Match>	searchPlain(Collection<? extends BioPAXElement> eles, Pattern pattern) Searches the pattern starting from given elements, but instead of a match map, returns all matches in a list.
static List<Match>	searchPlain(Model model, Pattern pattern) Searches the pattern in a given model, but instead of a match map, returns all matches in a list.
static List<Match>	searchRecursive(Match match, List<MappedConst> mc, int index) Continues searching with the mapped constraint at the given index.

Methods inherited from class java.lang.Object

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

Constructor Detail

Searcher

public Searcher()

Method Detail

search

public static List<Match> search(Match m,
                                 Pattern pattern)

Searches the pattern starting from the given match. The first element of the match should be assigned. Others are optional.

Parameters:

m - match to start from

pattern - pattern to search

Returns:

result matches

search

public static List<Match> search(BioPAXElement ele,
                                 Pattern pattern)

Searches the pattern starting from the given element.

Parameters:

ele - element to start from

pattern - pattern to search

Returns:

matching results

searchRecursive

public static List<Match> searchRecursive(Match match,
                                          List<MappedConst> mc,
                                          int index)

Continues searching with the mapped constraint at the given index.

Parameters:

match - match to start from

mc - mapped constraints of the pattern

index - index of the current mapped constraint

Returns:

matching results

searchPlain

public static List<Match> searchPlain(Model model,
                                      Pattern pattern)

Searches the pattern in a given model, but instead of a match map, returns all matches in a list.

Parameters:

model - model to search in

pattern - pattern to search for

Returns:

matching results

searchPlain

public static List<Match> searchPlain(Collection<? extends BioPAXElement> eles,
                                      Pattern pattern)

Searches the pattern starting from given elements, but instead of a match map, returns all matches in a list.

Parameters:

eles - elements to start from

pattern - pattern to search for

Returns:

matching results

search

public static Map<BioPAXElement,List<Match>> search(Model model,
                                                    Pattern pattern)

Searches the given pattern in the given model.

Parameters:

model - model to search in

pattern - pattern to search for

Returns:

map from starting elements to the list matching results

search

public static Map<BioPAXElement,List<Match>> search(Model model,
                                                    Pattern pattern,
                                                    ProgressWatcher prg)

Searches the given pattern in the given model.

Parameters:

model - model to search in

pattern - pattern to search for

prg - progress watcher to keep track of the progress

Returns:

map from starting elements to the list matching results

search

public static Map<BioPAXElement,List<Match>> search(Collection<? extends BioPAXElement> eles,
                                                    Pattern pattern)

Searches the given pattern starting from the given elements.

Parameters:

eles - elements to start from

pattern - pattern to search for

Returns:

map from starting element to the matching results

searchAndCollect

public static <T extends BioPAXElement> Set<T> searchAndCollect(Model model,
                                                                Pattern pattern,
                                                                int index,
                                                                Class<T> c)

Searches a model for the given pattern, then collects the specified elements of the matches and returns.

Type Parameters:

T - BioPAX type

Parameters:

model - model to search in

pattern - pattern to search for

index - index of the element in the match to collect

c - type of the element to collect

Returns:

set of the elements at the specified index of the matching results

searchAndCollect

public static <T extends BioPAXElement> Set<T> searchAndCollect(Collection<? extends BioPAXElement> eles,
                                                                Pattern pattern,
                                                                int index,
                                                                Class<T> c)

Searches the given pattern starting from the given elements, then collects the specified elements of the matches and returns.

Type Parameters:

T - BioPAX type

Parameters:

eles - elements to start from

pattern - pattern to search for

index - index of the element in the match to collect

c - type of the element to collect

Returns:

set of the elements at the specified index of the matching results

searchAndCollect

public static <T extends BioPAXElement> Set<T> searchAndCollect(BioPAXElement ele,
                                                                Pattern pattern,
                                                                int index,
                                                                Class<T> c)

Searches the given pattern starting from the given element, then collects the specified elements of the matches and returns.

Type Parameters:

T - BioPAX type

Parameters:

ele - element to start from

pattern - pattern to search for

index - index of the element in the match to collect

c - type of the element to collect

Returns:

set of the elements at the specified index of the matching results

hasSolution

public boolean hasSolution(Pattern p,
                           BioPAXElement... ele)

Checks if there is any match for the given pattern if search starts from the given element.

Parameters:

p - pattern to search for

ele - element to start from

Returns:

true if there is a match

searchInFile

public static void searchInFile(Pattern p,
                                String inFile,
                                String outFile)
                         throws FileNotFoundException

Searches a pattern reading the model from the given file, and creates another model that is excised using the matching patterns.

Parameters:

p - pattern to search for

inFile - filename for the model to search in

outFile - filename for the result model

Throws:

FileNotFoundException - when no file exists

searchInFile

public static void searchInFile(Pattern p,
                                String inFile,
                                String outFile,
                                int seedLimit,
                                int graphPerSeed)
                         throws FileNotFoundException

Searches a pattern reading the model from the given file, and creates another model that is excised using the matching patterns. Users can limit the max number of starting element, and max number of matches for any starting element. These parameters is good for limiting the size of the result graph.

Parameters:

p - pattern to search for

inFile - filename for the model to search in

outFile - filename for the result model

seedLimit - max number of starting elements

graphPerSeed - max number of matches for a starting element

Throws:

FileNotFoundException - when no file exists