Uses of Class
com.compomics.util.experiment.biology.AminoAcidPattern

Packages that use AminoAcidPattern
com.compomics.util.experiment.biology This package contains experiement classes related to biological entities. 
com.compomics.util.gui This package contains basic GUI classes. 
 

Uses of AminoAcidPattern in com.compomics.util.experiment.biology
 

Methods in com.compomics.util.experiment.biology that return AminoAcidPattern
 AminoAcidPattern PTM.getPattern()
          Returns the amino acid pattern targeted by this modification.
 AminoAcidPattern Peptide.getSequenceAsPattern()
          Returns the sequence of this peptide as AminoAcidPattern.
static AminoAcidPattern Peptide.getSequenceAsPattern(String sequence)
          Returns the given sequence as AminoAcidPattern.
 AminoAcidPattern AminoAcidPattern.getStandardSearchPattern()
          Computes a pattern which can be searched by standard search engines, i.e., a pattern targeting a single amino-acid and not a complex pattern.
static AminoAcidPattern AminoAcidPattern.getTrypsinExample()
          Returns the trypsin example as amino acid pattern.
static AminoAcidPattern AminoAcidPattern.merge(AminoAcidPattern pattern1, AminoAcidPattern pattern2)
          Convenience method merging two different patterns (see public void merge(AminoAcidPattern otherPattern) for detailed information of the merging procedure).
 

Methods in com.compomics.util.experiment.biology with parameters of type AminoAcidPattern
 boolean AminoAcidPattern.isSameAs(AminoAcidPattern anotherPattern)
          Indicates whether another AminoAcidPattern targets the same pattern.
 void AminoAcidPattern.merge(AminoAcidPattern otherPattern)
          Simple merger for two patterns.
static AminoAcidPattern AminoAcidPattern.merge(AminoAcidPattern pattern1, AminoAcidPattern pattern2)
          Convenience method merging two different patterns (see public void merge(AminoAcidPattern otherPattern) for detailed information of the merging procedure).
 void PTM.setPattern(AminoAcidPattern pattern)
          Sets the amino acid pattern targeted by this modification.
 

Constructors in com.compomics.util.experiment.biology with parameters of type AminoAcidPattern
AminoAcidPattern(AminoAcidPattern aminoAcidPattern)
          Creates a pattern from another pattern.
PTM(int type, String name, double mass, AminoAcidPattern aminoAcidPattern)
          Constructor for a reference modification.
PTM(int type, String name, String shortName, double mass, AminoAcidPattern aminoAcidPattern)
          Constructor for a reference modification.
 

Uses of AminoAcidPattern in com.compomics.util.gui
 

Methods in com.compomics.util.gui that return AminoAcidPattern
 AminoAcidPattern AminoAcidPatternDialog.getPattern()
          Returns the pattern as edited by the user.
 

Constructors in com.compomics.util.gui with parameters of type AminoAcidPattern
AminoAcidPatternDialog(Frame parent, AminoAcidPattern pattern, boolean editable)
          Creates a new AminoAcidPatternDialog.
 



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