de.unibi.techfak.jpredictor.motifs
Class SequenceMotif

java.lang.Object
  de.unibi.techfak.jpredictor.motifs.MotifSearchAdapter
      de.unibi.techfak.jpredictor.motifs.Motif
          de.unibi.techfak.jpredictor.motifs.RegularExpressionMotif
              de.unibi.techfak.jpredictor.motifs.SequenceMotif

All Implemented Interfaces:

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

public class SequenceMotif
extends RegularExpressionMotif

Specialization of a RegularExpressionMotif. Contains a single sequence as motif, that is given as a string, e.g. "CCAT". No degenerated code is allowed to be used.

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.RegularExpressionMotif

motif

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

SequenceMotif()
Inits all values and strings with null.

SequenceMotif(java.lang.String name, java.lang.String description, java.lang.String motif, int errorNumberAllowedForMatch)
Sets all the motif's characteristics.

Method Summary

java.lang.Object	clone() Clones the motif by creating the same motif again and copying all importent fields.
Motif	createReversedComplement() Creates the reversed complementary motif.
java.lang.String	getConsensusSequence() Calculates the consensus sequence from the motif, replaces the degenerated letter-representations of DNA with the base letters in the order A,C,G,T.
protected boolean	match(char sequ, char reg) Matches two chars.
void	setMotif(java.lang.String motif) Sets the motif from a given String.

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

compareTo, createConsensusFromMotifBlock, getErrorNumberAllowedForMatch, getRegularExpression, getRegularExpressionChar, length, matchComplement, print, readMotifBlockFromFile, search, setErrorNumberAllowedForMatch

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

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

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

getSearchMode, initSearch, searchAll, 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, initSearch, searchAll, setSearchMode

Constructor Detail

SequenceMotif

public SequenceMotif()

Inits all values and strings with null.

SequenceMotif

public SequenceMotif(java.lang.String name,
                     java.lang.String description,
                     java.lang.String motif,
                     int errorNumberAllowedForMatch)

Sets all the motif's characteristics. The motif is marked not usable (this mark has nothing to do with being incomplete or so but tells the program to not use this motif for operations until otherwise stated).

Parameters:

name - The name of the motif.

description - A short description of the motif.

motif - The motif itself as a short sequence.

errorNumberAllowedForMatch - The number of mismatch errors allowed for a perfect match.

Method Detail

setMotif

public void setMotif(java.lang.String motif)

Sets the motif from a given String. The motif is filtered to represent only valid DNA- or RNA-sequences, respectivly.

Overrides:

setMotif in class RegularExpressionMotif

Parameters:

motif - The motifs representation as RNA,DNA-String.

See Also:

MotifFilter.DNA_RNA_FILTER

getConsensusSequence

public java.lang.String getConsensusSequence()

Description copied from class: RegularExpressionMotif

Calculates the consensus sequence from the motif, replaces the degenerated letter-representations of DNA with the base letters in the order A,C,G,T. So a Y is always replaced with a C, and an N always with an A.

Overrides:

getConsensusSequence in class RegularExpressionMotif

Returns:

the motif as it is.

See Also:

Motif.getConsensusSequence()

match

protected boolean match(char sequ,
                        char reg)

Matches two chars.

Overrides:

match in class RegularExpressionMotif

Parameters:

sequ - The char from the sequence.

reg - The char from the motif.

Returns:

true iff the chars are equal, false otherwise

createReversedComplement

public Motif createReversedComplement()

Description copied from class: Motif

Creates the reversed complementary motif.

Overrides:

createReversedComplement in class RegularExpressionMotif

Returns:

The reversed and complemented motif.

clone

public java.lang.Object clone()

Description copied from class: Motif

Clones the motif by creating the same motif again and copying all importent fields. The result is at least of class Motif. When cloning a MultiMotif the referred single motifs are not cloned.

The fields that are copied are: Name, Description, the Motif itself, errorNumberAllowedForMatch or Threshold, respectively, Weight and searchMode (altogether 6 fields by now). What is not copied are the fields of the MotifSearchAdapter.

Note, that any matrices are not cloned. Thus, if cloning a PSPMotif or a PSSMotif the cloned motif does contain a reference to the matrix of the old motif. This was done to preserve memory.

Overrides:

clone in class RegularExpressionMotif

Returns:

The Motif itself as a doubled copy.

See Also:

Object.clone()