com.hfg.bio.seq.pattern

Class ProteinPattern

java.lang.Object

com.hfg.bio.seq.pattern.SeqPattern<Protein,ProteinPatternMatch>

com.hfg.bio.seq.pattern.ProteinPattern

All Implemented Interfaces:

Cloneable

public class ProteinPattern
extends SeqPattern<Protein,ProteinPatternMatch>

Container for a protein pattern (motif).

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 inherited from class com.hfg.bio.seq.pattern.SeqPattern

PROSITE_COUNT_PATTERN

Constructor Summary

Constructors

Constructor and Description
ProteinPattern(String inPrositePattern)

Method Summary

Modifier and Type	Method and Description
protected ProteinPatternMatch	createMatch(String inSeq, SeqLocation inLocation)
BioSequenceType	getBioSequenceType()
ProteinPattern	setIgnoreGaps(boolean inValue)
ProteinPattern	setMaxMismatches(int inValue)

Methods inherited from class com.hfg.bio.seq.pattern.SeqPattern

clone, containsMismatchRestrictions, containsPositionAmbiguity, containsRanges, getIgnoreGaps, getMaxLength, getMaxMismatches, getPrositePattern, getPrositePatternPositions, isCaseSensitive, isLocked, isRestrictedToSeqEnd, isRestrictedToSeqStart, lock, matcher, matcher, name, setIsCaseSensitive, setName, setPrositePattern, toString

Methods inherited from class java.lang.Object

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

Constructor Detail

ProteinPattern

public ProteinPattern(String inPrositePattern)

Method Detail

getBioSequenceType

public BioSequenceType getBioSequenceType()

Specified by:

getBioSequenceType in class SeqPattern<Protein,ProteinPatternMatch>

setIgnoreGaps

public ProteinPattern setIgnoreGaps(boolean inValue)

Overrides:

setIgnoreGaps in class SeqPattern<Protein,ProteinPatternMatch>

setMaxMismatches

public ProteinPattern setMaxMismatches(int inValue)

Overrides:

setMaxMismatches in class SeqPattern<Protein,ProteinPatternMatch>

createMatch

protected ProteinPatternMatch createMatch(String inSeq,
                                          SeqLocation inLocation)

Specified by:

createMatch in class SeqPattern<Protein,ProteinPatternMatch>