de.unibi.techfak.jpredictor.motifs
Class DoubleMotif

java.lang.Object
  de.unibi.techfak.jpredictor.motifs.MotifSearchAdapter
      de.unibi.techfak.jpredictor.motifs.Motif
          de.unibi.techfak.jpredictor.motifs.MultiMotif
              de.unibi.techfak.jpredictor.motifs.DoubleMotif

All Implemented Interfaces:

MotifSearcher, SequenceWindowScorer, Markable, java.lang.Cloneable, java.lang.Comparable

public class DoubleMotif
extends MultiMotif

Class for defining a special MultiMotif - only two motifs are comprised within this motif, furthermore the distances between them and a score.

Nested Class Summary

Nested classes/interfaces inherited from class de.unibi.techfak.jpredictor.motifs.MotifSearchAdapter

MotifSearchAdapter.SearchFields

Field Summary

Fields inherited from class de.unibi.techfak.jpredictor.motifs.MultiMotif

distances, motifs

Fields inherited from class de.unibi.techfak.jpredictor.motifs.Motif

DNA_DEGENERATED_CODE, DNA_DEGENERATED_CODE_JOINING, MARK_USABLE

Fields inherited from class de.unibi.techfak.jpredictor.motifs.MotifSearchAdapter

searchFields

Fields inherited from interface de.unibi.techfak.jpredictor.motifs.MotifSearcher

SEARCH_ALL_ORIENTATIONS, SEARCH_DIRECTION_MAX, SEARCH_DIRECTION_MINUS, SEARCH_DIRECTION_PLUS

Fields inherited from interface de.unibi.techfak.misc.Markable

MARK_BASIC, MARK_DELETED, MARK_EXP, MARK_MOVED, MARK_REPLACED, MARK_SELECTED, MARK_TOBEDELETED, MARK_TOBEMOVED, MARK_TOBEREPLACED

Constructor Summary

DoubleMotif(java.lang.String name, Motif motif1, int minDistance, int maxDistance, Motif motif2, double weight)
Creates a double motif by extending a MultiMotif.

Method Summary

static MotifList	createDoubleMotifs(MotifList motifs, ICommunicator comm, boolean permutations, boolean self) Evaluates the distanceMode got from the ICommunicator-interface and then creates the DoubleMotifs with the distances.
static MotifList	createDoubleMotifs(MotifList motifs, int minDist, int maxDist, boolean permutations, boolean self) Creates a list of DoubleMotifs from the single motifs of the given MotifList.

Methods inherited from class de.unibi.techfak.jpredictor.motifs.MultiMotif

add, add, checkMultiMotif, checkMultiMotifForCycles, clone, compareTo, createReversedComplement, getDistances, getMotif, getMotifs, getRegularExpression, initSearch, length, print, replaceMotif, search, searchAll, searchChoose, testDist, testDistRevComp

Methods inherited from class de.unibi.techfak.jpredictor.motifs.Motif

clearMark, clearMark, equals, getConsensusSequence, getDescription, getMark, getName, getWeight, isMarked, isMarked, print, scoreSequenceWindow, setDescription, setMark, setName, setWeight, toString

Methods inherited from class de.unibi.techfak.jpredictor.motifs.MotifSearchAdapter

getSearchMode, setSearchMode

Methods inherited from class java.lang.Object

finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface de.unibi.techfak.jpredictor.motifs.MotifSearcher

getSearchMode, setSearchMode

Constructor Detail

DoubleMotif

public DoubleMotif(java.lang.String name,
                   Motif motif1,
                   int minDistance,
                   int maxDistance,
                   Motif motif2,
                   double weight)

Creates a double motif by extending a MultiMotif.

Parameters:

name - The name of the double motif.

motif1 - The first motif in the DoubleMotif.

minDistance - The minimal distance between the two motifs.

maxDistance - The maximal distance between the two motifs.

motif2 - The second motif in the DoubleMotif.

weight - The weight of the double motif.

Method Detail

createDoubleMotifs

public static MotifList createDoubleMotifs(MotifList motifs,
                                           ICommunicator comm,
                                           boolean permutations,
                                           boolean self)
                                    throws java.lang.NullPointerException

Evaluates the distanceMode got from the ICommunicator-interface and then creates the DoubleMotifs with the distances.

Parameters:

motifs - A list of single motifs to create DoubleMotifs from.

comm - The ICommunicator.

permutations - Permit or forbid permutations of motif pairs.

self - Permit or forbid self pairing.

Returns:

A MotifList of pairs of single motifs, but null, if no motif is in the given MotifList.

Throws:

java.lang.NullPointerException - If motifs is null.

See Also:

createDoubleMotifs(MotifList,int,int,boolean,boolean)

createDoubleMotifs

public static MotifList createDoubleMotifs(MotifList motifs,
                                           int minDist,
                                           int maxDist,
                                           boolean permutations,
                                           boolean self)
                                    throws java.lang.NullPointerException

Creates a list of DoubleMotifs from the single motifs of the given MotifList. Every motif pair has a distance range from minDist to maxDist.

If parameter permutations is true every possible motif pair is build, e.g. A-B as well as B-A. If it is false motif pair A-B is build but not B-A. If self is true, motifs are paired with itself, e.g. A-A.

The score of every new DoubleMotif is set to Double.NaN. The name is set to "nameA-(minDist,maxDist)-nameB". No description is set.

Parameters:

motifs - A list of single motifs to build pairs from.

minDist - The minimal distance between two single motifs.

maxDist - The maximal distance between two single motifs.

permutations - Permit or forbid permutations of motif pairs.

self - Permit or forbid self pairing.

Returns:

A MotifList of pairs of single motifs, or null, if no motif is in the given MotifList.

Throws:

java.lang.NullPointerException - If motifs is null.