fr.umlv.gramofone.graphs
Class DefinedPatterns

java.lang.Object
  extended by fr.umlv.gramofone.graphs.DefinedPatterns

public class DefinedPatterns
extends java.lang.Object

Class managing all predefined patterns, loaded from text files

Author:
fsikora

Constructor Summary
DefinedPatterns()
          Constructor.
DefinedPatterns(java.lang.String fileName)
          load a specific text file with patterns
 
Method Summary
 MyPattern getPattern(java.lang.String specie, java.lang.String patternName)
          get the list of proteins for this specie and this pattern
 java.util.Collection<MyPattern> getPatterns()
          Return all the patterns for all the species
 java.util.Collection<MyPattern> getPatterns(java.lang.String specie)
          Return the patterns for a given specie
 java.util.LinkedList<java.lang.String> getSpecies()
          return names of files
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

DefinedPatterns

public DefinedPatterns()
Constructor. Load all defined patterns which are in text file in a dedicated directory files are like "pattern name" tabulation "list of proteins" separated by tabulations


DefinedPatterns

public DefinedPatterns(java.lang.String fileName)
load a specific text file with patterns

Parameters:
fileName -
Method Detail

getPatterns

public java.util.Collection<MyPattern> getPatterns(java.lang.String specie)
Return the patterns for a given specie

Parameters:
specie -
Returns:
collection of patterns

getPatterns

public java.util.Collection<MyPattern> getPatterns()
Return all the patterns for all the species

Returns:
set of patterns

getSpecies

public java.util.LinkedList<java.lang.String> getSpecies()
return names of files

Returns:
list of string

getPattern

public MyPattern getPattern(java.lang.String specie,
                            java.lang.String patternName)
get the list of proteins for this specie and this pattern

Parameters:
specie -
patternName -
Returns: