com.hfg.bio.seq.pattern

Class SeqPattern<S extends BioSequence,T extends SeqPatternMatch>

java.lang.Object

com.hfg.bio.seq.pattern.SeqPattern<S,T>

All Implemented Interfaces:

Cloneable

Direct Known Subclasses:

NucleotidePattern, ProteinPattern

public abstract class SeqPattern<S extends BioSequence,T extends SeqPatternMatch>
extends Object
implements Cloneable

Abstract container for a sequence pattern (motif).

The pattern syntax is based on PROSITE with one addition - the symbol '!' can be added to end of a position specification to indicate that mismatches are not allowed at that position.

From the PROSITE user manual:

The patterns are described using the following conventions:

• The standard IUPAC one-letter codes for the amino acids are used.
• The symbol 'x' is used for a position where any amino acid is accepted.
• Ambiguities are indicated by listing the acceptable amino acids for a given position, between square parentheses '[ ]'. For example: [ALT] stands for Ala or Leu or Thr.
• Ambiguities are also indicated by listing between a pair of curly brackets '{ }' the amino acids that are not accepted at a given position. For example: {AM} stands for any amino acid except Ala and Met.
• Each element in a pattern is separated from its neighbor by a '-'.
• Repetition of an element of the pattern can be indicated by following that element with a numerical value or a numerical range between parenthesis. Examples: x(3) corresponds to x-x-x, x(2,4) corresponds to x-x or x-x-x or x-x-x-x.
• When a pattern is restricted to either the N- or C-terminal of a sequence, that pattern either starts with a '<' symbol or respectively ends with a '>' symbol. In some rare cases (e.g. PS00267 or PS00539), '>' can also occur inside square brackets for the C-terminal element. 'F-[GSTV]-P-R-L-[G>]' means that either 'F-[GSTV]-P-R-L-G' or 'F-[GSTV]-P-R-L>' are considered.
• A period ends the pattern.

Examples:

    PA   [AC]-x-V-x(4)-{ED}.
   

This pattern is translated as: [Ala or Cys]-any-Val-any-any-any-any-{any but Glu or Asp}

    PA   <A-x-[ST](2)-x(0,1)-V.
   

This pattern, which must be in the N-terminal of the sequence ('<'), is translated as: Ala-any-[Ser or Thr]-[Ser or Thr]-(any or none)-Val

Field Summary

Fields

Modifier and Type	Field and Description
protected static Pattern	PROSITE_COUNT_PATTERN

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	SeqPattern()
	SeqPattern(String inPrositePattern)

Method Summary

Modifier and Type	Method and Description
SeqPattern	clone()
boolean	containsMismatchRestrictions()
boolean	containsPositionAmbiguity()
boolean	containsRanges()
protected abstract T	createMatch(String inSeq, SeqLocation inLocation)
abstract BioSequenceType	getBioSequenceType()
boolean	getIgnoreGaps()
int	getMaxLength()
int	getMaxMismatches()
String	getPrositePattern()
List<PrositePatternPosition>	getPrositePatternPositions()
boolean	isCaseSensitive()
boolean	isLocked()
boolean	isRestrictedToSeqEnd()
boolean	isRestrictedToSeqStart()
SeqPattern	lock()
SeqPatternMatcher<S,T>	matcher(S inTarget)
SeqPatternMatcher<S,T>	matcher(S inTarget, SeqLocation inSeqLocation)
String	name()
SeqPattern	setIgnoreGaps(boolean inValue)
SeqPattern	setIsCaseSensitive(boolean inValue)
SeqPattern	setMaxMismatches(int inValue)
SeqPattern	setName(String inValue)
protected void	setPrositePattern(String inValue)
String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

PROSITE_COUNT_PATTERN

protected static final Pattern PROSITE_COUNT_PATTERN

Constructor Detail

SeqPattern

protected SeqPattern()

SeqPattern

public SeqPattern(String inPrositePattern)

Method Detail

clone

public SeqPattern clone()

Overrides:

clone in class Object

toString

public String toString()

Overrides:

toString in class Object

setName

public SeqPattern setName(String inValue)

name

public String name()

isLocked

public boolean isLocked()

lock

public SeqPattern lock()

getBioSequenceType

public abstract BioSequenceType getBioSequenceType()

setIgnoreGaps

public SeqPattern setIgnoreGaps(boolean inValue)

setIsCaseSensitive

public SeqPattern setIsCaseSensitive(boolean inValue)

isCaseSensitive

public boolean isCaseSensitive()

getIgnoreGaps

public boolean getIgnoreGaps()

setPrositePattern

protected void setPrositePattern(String inValue)

getPrositePattern

public String getPrositePattern()

setMaxMismatches

public SeqPattern setMaxMismatches(int inValue)

getMaxMismatches

public int getMaxMismatches()

containsMismatchRestrictions

public boolean containsMismatchRestrictions()

containsPositionAmbiguity

public boolean containsPositionAmbiguity()

containsRanges

public boolean containsRanges()

isRestrictedToSeqStart

public boolean isRestrictedToSeqStart()

isRestrictedToSeqEnd

public boolean isRestrictedToSeqEnd()

getMaxLength

public int getMaxLength()

getPrositePatternPositions

public List<PrositePatternPosition> getPrositePatternPositions()

matcher

public SeqPatternMatcher<S,T> matcher(S inTarget)

matcher

public SeqPatternMatcher<S,T> matcher(S inTarget,
                                      SeqLocation inSeqLocation)

createMatch

protected abstract T createMatch(String inSeq,
                                 SeqLocation inLocation)