AminoAcidPattern (computational omics utilities 3.28.20 API)

java.lang.Object
- com.compomics.util.experiment.personalization.ExperimentObject
- - com.compomics.util.experiment.biology.AminoAcidPattern

All Implemented Interfaces:

TagComponent, Serializable, Cloneable
```
public class AminoAcidPattern
extends ExperimentObject
implements TagComponent
```
An amino acid pattern is a sequence of amino acids. For example for trypsin: Target R or K not followed by P. the Indexing starts with 0.

Author:

Marc Vaudel

See Also:
Serialized Form

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

static class AminoAcidPattern.MatchingType
The different types of amino acid matching.

Nested Classes
Modifier and Type	Class and Description
`static class`	`AminoAcidPattern.MatchingType` The different types of amino acid matching.

Constructor Summary

Constructors
Constructor and Description
`AminoAcidPattern()` Creates a blank pattern.
`AminoAcidPattern(AminoAcidPattern aminoAcidPattern)` Creates a pattern from another pattern.
`AminoAcidPattern(ArrayList<String> targetTesidues)` Convenience constructor giving a list of targeted residues as input.
`AminoAcidPattern(String sequence)` Constructor taking a sequence of targeted amino acids as input.

Method Summary

Methods
Modifier and Type	Method and Description
`void`	`addModificationMatch(int localization, ModificationMatch modificationMatch)` Adds a modification to one of the amino acid pattern.
`void`	`addModificationMatches(int localization, ArrayList<ModificationMatch> modificationMatches)` Adds a list of modifications to one of the amino acid pattern.
`void`	`append(AminoAcidPattern otherPattern)` Appends another pattern at the end of this pattern.
`String`	`asSequence()` Returns the tag component as String like a peptide sequence.
`String`	`asSequence(int index)` Returns the component of the amino acid pattern at the given index.
`void`	`changeModificationSite(ModificationMatch modificationMatch, int oldLocalization, int newLocalization)` Changes the localization of a modification match.
`void`	`clearModificationMatches()` Clears the list of imported modification matches.
`int`	`firstIndex(AminoAcidPattern aminoAcidPattern, AminoAcidPattern.MatchingType matchingType, Double massTolerance)` Returns the first index where the amino acid pattern is found.
`int`	`firstIndex(AminoAcidPattern aminoAcidPattern, AminoAcidPattern.MatchingType matchingType, Double massTolerance, int startIndex)` Returns the first index where the amino acid pattern is found.
`int`	`firstIndex(String aminoAcidSequence, AminoAcidPattern.MatchingType matchingType, Double massTolerance)` Returns the first index where the amino acid pattern is found.
`int`	`firstIndex(String aminoAcidSequence, AminoAcidPattern.MatchingType matchingType, Double massTolerance, int startIndex)` Returns the first index where the amino acid pattern is found.
`HashMap<Integer,ArrayList<AminoAcid>>`	`getAaExcluded()` Returns the map of excluded amino acids.
`HashMap<Integer,ArrayList<AminoAcid>>`	`getAaTargeted()` Returns the map of targeted amino acids.
`ArrayList<String>`	`getAllPossibleSequences()` Returns all possible sequences which can be obtained from the targeted amino acids.
`ArrayList<AminoAcid>`	`getAminoAcidsAtTarget()` Returns the targeted amino acids at position "target".
`Pattern`	`getAsStringPattern()` Returns the amino acid pattern as case insensitive pattern for String matching using default single letter code of amino acids.
`Pattern`	`getAsStringPattern(AminoAcidPattern.MatchingType matchingType, Double massTolerance)` Returns the amino acid pattern as case insensitive pattern for String matching.
`ArrayList<AminoAcid>`	`getExcludedAA(int index)` Returns the excluded amino acids at a given index in the pattern.
`ArrayList<Integer>`	`getIndexes(AminoAcidPattern input)` Returns the indexes where the amino acid pattern was found in the input using default single letter code of amino acids.
`ArrayList<Integer>`	`getIndexes(AminoAcidPattern input, AminoAcidPattern.MatchingType matchingType, Double massTolerance)` Returns the indexes where the amino acid pattern was found in the input.
`ArrayList<Integer>`	`getIndexes(String input)` Returns the indexes where the amino acid pattern was found in the input using default single letter code of amino acids.
`ArrayList<Integer>`	`getIndexes(String input, AminoAcidPattern.MatchingType matchingType, Double massTolerance)` Returns the indexes where the amino acid pattern was found in the input.
`Double`	`getMass()` Returns the mass of the tag component.
`ArrayList<Integer>`	`getModificationIndexes()` Returns a list of the indexes of the amino acids carrying a modification.
`HashMap<Integer,ArrayList<ModificationMatch>>`	`getModificationMatches()` Getter for the modifications carried by this sequence.
`ArrayList<ModificationMatch>`	`getModificationsAt(int localization)` Returns the modifications found at a given localization.
`int`	`getNExcludedAA(int index)` Returns the number of excluded amino acids at the given index.
`int`	`getNTargetedAA(int index)` Returns the number of targeted amino acids at the given index.
`String`	`getPrositeFormat()` Returns the pattern in the prosite format.
`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.
`AminoAcidPattern`	`getSubPattern(int startIndex, boolean updateTarget)` Returns a sub pattern of the pattern.
`AminoAcidPattern`	`getSubPattern(int startIndex, int endIndex, boolean updateTarget)` Returns a sub pattern of the pattern.
`static String`	`getTaggedModifiedSequence(ModificationProfile modificationProfile, AminoAcidPattern aminoAcidPattern, HashMap<Integer,ArrayList<String>> mainModificationSites, HashMap<Integer,ArrayList<String>> secondaryModificationSites, HashMap<Integer,ArrayList<String>> fixedModificationSites, boolean useHtmlColorCoding, boolean useShortName)` Returns the modified sequence as an tagged string with potential modification sites color coded or with PTM tags, e.g, <mox>.
`String`	`getTaggedModifiedSequence(ModificationProfile modificationProfile, boolean useHtmlColorCoding, boolean useShortName, boolean excludeAllFixedPtms)` Returns the modified sequence as an tagged string with potential modification sites color coded or with PTM tags, e.g, <mox>.
`Integer`	`getTarget()` Returns the index of the amino acid of interest in the pattern.
`ArrayList<AminoAcid>`	`getTargetedAA(int index)` Returns the targeted amino acids at a given index in the pattern.
`static AminoAcidPattern`	`getTrypsinExample()` Returns the trypsin example as amino acid pattern.
`boolean`	`isEnding(AminoAcidPattern aminoAcidPattern)` Indicates whether the given amino acid sequence ends with the pattern using default single letter code of amino acids.
`boolean`	`isEnding(AminoAcidPattern aminoAcidPattern, AminoAcidPattern.MatchingType matchingType, Double massTolerance)` Indicates whether the given amino acid sequence ends with the pattern.
`boolean`	`isEnding(String aminoAcidSequence)` Indicates whether the given amino acid sequence ends with the pattern using default single letter code of amino acids.
`boolean`	`isEnding(String aminoAcidSequence, AminoAcidPattern.MatchingType matchingType, Double massTolerance)` Indicates whether the given amino acid sequence ends with the pattern.
`boolean`	`isExcluded(char aa, int index, AminoAcidPattern.MatchingType matchingType, Double massTolerance)` Indicates whether the given amino acid at the given index of the pattern shall be excluded.
`boolean`	`isSameAs(AminoAcidPattern anotherPattern)` Indicates whether another AminoAcidPattern targets the same pattern.
`boolean`	`isSameAs(TagComponent anotherCompontent)` Indicates whether another component is the same as the component of interest
`boolean`	`isStarting(AminoAcidPattern aminoAcidPattern)` Indicates whether the given amino acid sequence starts with the pattern using default single letter code of amino acids.
`boolean`	`isStarting(AminoAcidPattern aminoAcidPattern, AminoAcidPattern.MatchingType matchingType, Double massTolerance)` Indicates whether the given amino acid sequence starts with the pattern.
`boolean`	`isStarting(String aminoAcidSequence)` Indicates whether the given amino acid sequence starts with the pattern using default single letter code of amino acids.
`boolean`	`isStarting(String aminoAcidSequence, AminoAcidPattern.MatchingType matchingType, Double massTolerance)` Indicates whether the given amino acid sequence starts with the pattern.
`boolean`	`isTargeted(char aa, int index, AminoAcidPattern.MatchingType matchingType, Double massTolerance)` Indicates whether the given amino acid at the given index of the pattern is targeted.
`int`	`length()` Returns the length of the pattern in amino acids.
`boolean`	`matches(AminoAcidPattern aminoAcidPattern, AminoAcidPattern.MatchingType matchingType, Double massTolerance)` Indicates whether the pattern is found in the given amino acid sequence.
`boolean`	`matches(String aminoAcidSequence)` Indicates whether the pattern is found in the given amino acid sequence using default single letter code of amino acids.
`boolean`	`matches(String aminoAcidSequence, AminoAcidPattern.MatchingType matchingType, Double massTolerance)` Indicates whether the pattern is found in the given amino acid sequence.
`void`	`merge(AminoAcidPattern otherPattern)` Simple merger for two patterns.
`static 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`	`removeAA(int index)` Removes an amino acid index from the pattern.
`void`	`removeModificationMatch(int localisation, ModificationMatch modificationMatch)` Removes a modification match in the given pattern.
`void`	`setExcluded(int index, ArrayList<AminoAcid> exclusions)` Sets the amino acids excluded at a given index.
`void`	`setTarget(Integer target)` Sets the index of the amino acid of interest in the pattern.
`void`	`setTargeted(int index, ArrayList<AminoAcid> targets)` Sets the amino acids targeted at a given index.
`void`	`swapRows(int fromRow, int toRow)` Swap two rows in the pattern.
`String`	`toString()`

Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject
addUrParam, getParameterKey, getUrParam

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Constructor Detail
  - AminoAcidPattern
```
public AminoAcidPattern()
```
    Creates a blank pattern. All maps are null.
  - AminoAcidPattern
```
public AminoAcidPattern(String sequence)
```
    Constructor taking a sequence of targeted amino acids as input.
    
    Parameters:
    sequence - a sequence of targeted amino acids
  - AminoAcidPattern
```
public AminoAcidPattern(AminoAcidPattern aminoAcidPattern)
```
    Creates a pattern from another pattern.
    
    Parameters:
    aminoAcidPattern - the other pattern
  - AminoAcidPattern
```
public AminoAcidPattern(ArrayList<String> targetTesidues)
                 throws IllegalArgumentException
```
    Convenience constructor giving a list of targeted residues as input. For instance (S, T, Y)
    
    Parameters:
    targetTesidues - a list of targeted residues
    
    Throws:
    
    IllegalArgumentException - exception thrown whenever a letter is not recognized as amino acid
- Method Detail
  - getAaTargeted
```
public HashMap<Integer,ArrayList<AminoAcid>> getAaTargeted()
```
    Returns the map of targeted amino acids. Null if not set.
    
    Returns:
    the map of targeted amino acids
  - getAaExcluded
```
public HashMap<Integer,ArrayList<AminoAcid>> getAaExcluded()
```
    Returns the map of excluded amino acids. Null if not set.
    
    Returns:
    the map of excluded amino acids
  - swapRows
```
public void swapRows(int fromRow,
            int toRow)
              throws IllegalArgumentException
```
    Swap two rows in the pattern. The first amino acid is 0.
    
    Parameters:
    fromRow -
    toRow -
    
    Throws:
    
    IllegalArgumentException
  - getTarget
```
public Integer getTarget()
```
    Returns the index of the amino acid of interest in the pattern. Null if none.
    
    Returns:
    the index of the amino acid of interest in the pattern.
  - setTarget
```
public void setTarget(Integer target)
```
    Sets the index of the amino acid of interest in the pattern.
    
    Parameters:
    target - the index of the amino acid of interest in the pattern.
  - getAminoAcidsAtTarget
```
public ArrayList<AminoAcid> getAminoAcidsAtTarget()
```
    Returns the targeted amino acids at position "target". An empty list if none.
    
    Returns:
    the targeted amino acids at position "target"
  - setTargeted
```
public void setTargeted(int index,
               ArrayList<AminoAcid> targets)
```
    Sets the amino acids targeted at a given index. The first amino acid is 0. Previous value will be silently overwritten.
    
    Parameters:
    index - the index in the pattern
    targets - the amino acids targeted
  - getTargetedAA
```
public ArrayList<AminoAcid> getTargetedAA(int index)
```
    Returns the targeted amino acids at a given index in the pattern. The first amino acid is 0.
    
    Parameters:
    index - the index in the pattern
    
    Returns:
    the targeted amino acids
  - getExcludedAA
```
public ArrayList<AminoAcid> getExcludedAA(int index)
```
    Returns the excluded amino acids at a given index in the pattern. The first amino acid is 0.
    
    Parameters:
    index - the index in the pattern
    
    Returns:
    the excluded amino acids
  - getNTargetedAA
```
public int getNTargetedAA(int index)
```
    Returns the number of targeted amino acids at the given index. The first amino acid is 0.
    
    Parameters:
    index - the index of interest
    
    Returns:
    the number of excluded amino acids
  - getNExcludedAA
```
public int getNExcludedAA(int index)
```
    Returns the number of excluded amino acids at the given index. The first amino acid is 0.
    
    Parameters:
    index - the index of interest
    
    Returns:
    the number of excluded amino acids
  - setExcluded
```
public void setExcluded(int index,
               ArrayList<AminoAcid> exclusions)
```
    Sets the amino acids excluded at a given index. There shall be no excluded amino acid at the targeted index. The first amino acid is 0. Previous value will be silently overwritten.
    
    Parameters:
    index - the index in the pattern
    exclusions - the amino acids excluded
  - removeAA
```
public void removeAA(int index)
```
    Removes an amino acid index from the pattern. The first amino acid is 0.
    
    Parameters:
    index - the index of the amino acid to remove
  - getAsStringPattern
```
public Pattern getAsStringPattern()
```
    Returns the amino acid pattern as case insensitive pattern for String matching using default single letter code of amino acids.
    
    Returns:
    the amino acid pattern as java string pattern
  - getAsStringPattern
```
public Pattern getAsStringPattern(AminoAcidPattern.MatchingType matchingType,
                         Double massTolerance)
```
    Returns the amino acid pattern as case insensitive pattern for String matching.
    
    Parameters:
    matchingType - the type of sequence matching
    massTolerance - the mass tolerance for matching type 'indistiguishibleAminoAcids'. Can be null otherwise
    
    Returns:
    the amino acid pattern as java string pattern
  - getPrositeFormat
```
public String getPrositeFormat()
```
    Returns the pattern in the prosite format.
    
    Returns:
    the pattern in the prosite format
  - getIndexes
```
public ArrayList<Integer> getIndexes(String input)
```
    Returns the indexes where the amino acid pattern was found in the input using default single letter code of amino acids. 1 is the first amino acid.
    
    Parameters:
    input - the amino acid input sequence as string
    
    Returns:
    a list of indexes where the amino acid pattern was found
  - getIndexes
```
public ArrayList<Integer> getIndexes(AminoAcidPattern input)
```
    Returns the indexes where the amino acid pattern was found in the input using default single letter code of amino acids. 1 is the first amino acid.
    
    Parameters:
    input - the amino acid input sequence as AminoAcidPattern
    
    Returns:
    a list of indexes where the amino acid pattern was found
  - getIndexes
```
public ArrayList<Integer> getIndexes(String input,
                            AminoAcidPattern.MatchingType matchingType,
                            Double massTolerance)
```
    Returns the indexes where the amino acid pattern was found in the input. 1 is the first amino acid.
    
    Parameters:
    input - the amino acid input sequence as string
    matchingType - the type of sequence matching
    massTolerance - the mass tolerance for matching type
    
    Returns:
    a list of indexes where the amino acid pattern was found
  - getIndexes
```
public ArrayList<Integer> getIndexes(AminoAcidPattern input,
                            AminoAcidPattern.MatchingType matchingType,
                            Double massTolerance)
```
    Returns the indexes where the amino acid pattern was found in the input. 1 is the first amino acid.
    
    Parameters:
    input - the amino acid input sequence as AminoAcidPattern
    matchingType - the type of sequence matching
    massTolerance - the mass tolerance for matching type
    
    Returns:
    a list of indexes where the amino acid pattern was found
  - matches
```
public boolean matches(String aminoAcidSequence)
```
    Indicates whether the pattern is found in the given amino acid sequence using default single letter code of amino acids.
    
    Parameters:
    aminoAcidSequence - the amino acid sequence
    
    Returns:
    a boolean indicating whether the pattern is found in the given amino acid sequence
  - firstIndex
```
public int firstIndex(String aminoAcidSequence,
             AminoAcidPattern.MatchingType matchingType,
             Double massTolerance)
```
    Returns the first index where the amino acid pattern is found. -1 if not found. 0 is the first amino acid.
    
    Parameters:
    aminoAcidSequence - the amino acid sequence to look into
    matchingType - the type of sequence matching
    massTolerance - the mass tolerance for matching type
    
    Returns:
    the first index where the amino acid pattern is found
  - firstIndex
```
public int firstIndex(AminoAcidPattern aminoAcidPattern,
             AminoAcidPattern.MatchingType matchingType,
             Double massTolerance)
```
    Returns the first index where the amino acid pattern is found. -1 if not found. 0 is the first amino acid.
    
    Parameters:
    aminoAcidPattern - the amino acid sequence to look into
    matchingType - the type of sequence matching
    massTolerance - the mass tolerance for matching type
    
    Returns:
    the first index where the amino acid pattern is found
  - firstIndex
```
public int firstIndex(String aminoAcidSequence,
             AminoAcidPattern.MatchingType matchingType,
             Double massTolerance,
             int startIndex)
```
    Returns the first index where the amino acid pattern is found. -1 if not found. 0 is the first amino acid.
    
    Parameters:
    aminoAcidSequence - the amino acid sequence to look into
    matchingType - the type of sequence matching
    massTolerance - the mass tolerance for matching type
    startIndex - the start index where to start looking for
    
    Returns:
    the first index where the amino acid pattern is found
  - firstIndex
```
public int firstIndex(AminoAcidPattern aminoAcidPattern,
             AminoAcidPattern.MatchingType matchingType,
             Double massTolerance,
             int startIndex)
```
    Returns the first index where the amino acid pattern is found. -1 if not found. 0 is the first amino acid.
    
    Parameters:
    aminoAcidPattern - the amino acid sequence to look into
    matchingType - the type of sequence matching
    massTolerance - the mass tolerance for matching type
    startIndex - the start index where to start looking for
    
    Returns:
    the first index where the amino acid pattern is found
  - isTargeted
```
public boolean isTargeted(char aa,
                 int index,
                 AminoAcidPattern.MatchingType matchingType,
                 Double massTolerance)
```
    Indicates whether the given amino acid at the given index of the pattern is targeted.
    
    Parameters:
    aa - the amino acid as character
    index - the index in the pattern
    matchingType - the type of sequence matching
    massTolerance - the mass tolerance for matching type
    
    Returns:
    true if the given amino acid at the given index of the pattern is targeted
  - isExcluded
```
public boolean isExcluded(char aa,
                 int index,
                 AminoAcidPattern.MatchingType matchingType,
                 Double massTolerance)
```
    Indicates whether the given amino acid at the given index of the pattern shall be excluded.
    
    Parameters:
    aa - the amino acid as character
    index - the index in the pattern
    matchingType - the type of sequence matching
    massTolerance - the mass tolerance for matching type
    
    Returns:
    true if the given amino acid at the given index of the pattern shall be excluded
  - matches
```
public boolean matches(String aminoAcidSequence,
              AminoAcidPattern.MatchingType matchingType,
              Double massTolerance)
```
    Indicates whether the pattern is found in the given amino acid sequence.
    
    Parameters:
    aminoAcidSequence - the amino acid sequence
    matchingType - the type of sequence matching
    massTolerance - the mass tolerance for matching type
    
    Returns:
    a boolean indicating whether the pattern is found in the given amino acid sequence
  - matches
```
public boolean matches(AminoAcidPattern aminoAcidPattern,
              AminoAcidPattern.MatchingType matchingType,
              Double massTolerance)
```
    Indicates whether the pattern is found in the given amino acid sequence.
    
    Parameters:
    aminoAcidPattern - the amino acid sequence
    matchingType - the type of sequence matching
    massTolerance - the mass tolerance for matching type
    
    Returns:
    a boolean indicating whether the pattern is found in the given amino acid sequence
  - isStarting
```
public boolean isStarting(String aminoAcidSequence)
```
    Indicates whether the given amino acid sequence starts with the pattern using default single letter code of amino acids.
    
    Parameters:
    aminoAcidSequence - the amino acid sequence
    
    Returns:
    a boolean indicating whether the given amino acid sequence starts with the pattern
  - isStarting
```
public boolean isStarting(AminoAcidPattern aminoAcidPattern)
```
    Indicates whether the given amino acid sequence starts with the pattern using default single letter code of amino acids.
    
    Parameters:
    aminoAcidPattern - the amino acid sequence
    
    Returns:
    a boolean indicating whether the given amino acid sequence starts with the pattern
  - isStarting
```
public boolean isStarting(String aminoAcidSequence,
                 AminoAcidPattern.MatchingType matchingType,
                 Double massTolerance)
```
    Indicates whether the given amino acid sequence starts with the pattern.
    
    Parameters:
    aminoAcidSequence - the amino acid sequence
    matchingType - the type of sequence matching
    massTolerance - the mass tolerance for matching type
    
    Returns:
    a boolean indicating whether the given amino acid sequence starts with the pattern
  - isStarting
```
public boolean isStarting(AminoAcidPattern aminoAcidPattern,
                 AminoAcidPattern.MatchingType matchingType,
                 Double massTolerance)
```
    Indicates whether the given amino acid sequence starts with the pattern.
    
    Parameters:
    aminoAcidPattern - the amino acid sequence
    matchingType - the type of sequence matching
    massTolerance - the mass tolerance for matching type
    
    Returns:
    a boolean indicating whether the given amino acid sequence starts with the pattern
  - isEnding
```
public boolean isEnding(String aminoAcidSequence)
```
    Indicates whether the given amino acid sequence ends with the pattern using default single letter code of amino acids.
    
    Parameters:
    aminoAcidSequence - the amino acid sequence
    
    Returns:
    a boolean indicating whether the given amino acid sequence ends with the pattern
  - isEnding
```
public boolean isEnding(AminoAcidPattern aminoAcidPattern)
```
    Indicates whether the given amino acid sequence ends with the pattern using default single letter code of amino acids.
    
    Parameters:
    aminoAcidPattern - the amino acid sequence
    
    Returns:
    a boolean indicating whether the given amino acid sequence ends with the pattern
  - isEnding
```
public boolean isEnding(AminoAcidPattern aminoAcidPattern,
               AminoAcidPattern.MatchingType matchingType,
               Double massTolerance)
```
    Indicates whether the given amino acid sequence ends with the pattern.
    
    Parameters:
    aminoAcidPattern - the amino acid sequence
    matchingType - the type of sequence matching
    massTolerance - the mass tolerance for matching type
    
    Returns:
    a boolean indicating whether the given amino acid sequence ends with the pattern
  - isEnding
```
public boolean isEnding(String aminoAcidSequence,
               AminoAcidPattern.MatchingType matchingType,
               Double massTolerance)
```
    Indicates whether the given amino acid sequence ends with the pattern.
    
    Parameters:
    aminoAcidSequence - the amino acid sequence
    matchingType - the type of sequence matching
    massTolerance - the mass tolerance for matching type
    
    Returns:
    a boolean indicating whether the given amino acid sequence ends with the pattern
  - isSameAs
```
public boolean isSameAs(AminoAcidPattern anotherPattern)
```
    Indicates whether another AminoAcidPattern targets the same pattern.
    
    Parameters:
    anotherPattern - the other AminoAcidPattern
    
    Returns:
    true if the other AminoAcidPattern targets the same pattern
  - length
```
public int length()
```
    Returns the length of the pattern in amino acids.
    
    Returns:
    the length of the pattern in amino acids
  - getStandardSearchPattern
```
public 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.
    
    Returns:
    a pattern which can be searched by standard search engines
  - getTrypsinExample
```
public static AminoAcidPattern getTrypsinExample()
```
    Returns the trypsin example as amino acid pattern.
    
    Returns:
    the trypsin example as amino acid pattern
  - merge
```
public void merge(AminoAcidPattern otherPattern)
```
    Simple merger for two patterns. To be used carefully. Example: this: target{0->S} exclusion{} otherPattern: target{0->T} exclusion{} result (this): target{0->S|T} exclusion{} Example of misuse: this: target{0->S} exclusion{0->null, 1>P} otherPattern: target{0->T, 1->P} exclusion{} result (this): target{0->S|T, 1->P} exclusion{0->null, 1>P}
    
    Parameters:
    otherPattern - another pattern to be merged with this
  - append
```
public void append(AminoAcidPattern otherPattern)
```
    Appends another pattern at the end of this pattern.
    
    Parameters:
    otherPattern - the other pattern to append.
  - merge
```
public static 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).
    
    Parameters:
    pattern1 - the first pattern
    pattern2 - the second pattern
    
    Returns:
    a merged version of the two patterns
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class Object
  - asSequence
```
public String asSequence()
```
    Description copied from interface: TagComponent
    
    Returns the tag component as String like a peptide sequence. Note: this does not include modifications.
    
    Specified by:
    
    asSequence in interface TagComponent
    
    Returns:
    the tag component as String like a peptide sequence
  - asSequence
```
public String asSequence(int index)
```
    Returns the component of the amino acid pattern at the given index. 0 is the first amino acid.
    
    Parameters:
    index - the index in the pattern. 0 is the first amino acid
    
    Returns:
    the component of the amino acid pattern at the given index
  - getModificationMatches
```
public HashMap<Integer,ArrayList<ModificationMatch>> getModificationMatches()
```
    Getter for the modifications carried by this sequence.
    
    Returns:
    the modifications matches as found by the search engine
  - getModificationIndexes
```
public ArrayList<Integer> getModificationIndexes()
```
    Returns a list of the indexes of the amino acids carrying a modification. 1 is the first amino acid.
    
    Returns:
    a list of the indexes of the amino acids carrying a modification
  - getModificationsAt
```
public ArrayList<ModificationMatch> getModificationsAt(int localization)
```
    Returns the modifications found at a given localization.
    
    Parameters:
    localization - the localization as amino acid number. 1 is the first amino acid.
    
    Returns:
    the modifications found at a given localization as a list.
  - removeModificationMatch
```
public void removeModificationMatch(int localisation,
                           ModificationMatch modificationMatch)
```
    Removes a modification match in the given pattern.
    
    Parameters:
    localisation - the localization of the modification
    modificationMatch - the modification match to remove
  - clearModificationMatches
```
public void clearModificationMatches()
```
    Clears the list of imported modification matches.
  - addModificationMatch
```
public void addModificationMatch(int localization,
                        ModificationMatch modificationMatch)
```
    Adds a modification to one of the amino acid pattern.
    
    Parameters:
    localization - the index of the amino acid retained as target of the modification. 1 is the first amino acid.
    modificationMatch - the modification match
  - addModificationMatches
```
public void addModificationMatches(int localization,
                          ArrayList<ModificationMatch> modificationMatches)
```
    Adds a list of modifications to one of the amino acid pattern.
    
    Parameters:
    localization - the index of the amino acid retained as target of the modification. 1 is the first amino acid.
    modificationMatches - the modification matches
  - changeModificationSite
```
public void changeModificationSite(ModificationMatch modificationMatch,
                          int oldLocalization,
                          int newLocalization)
```
    Changes the localization of a modification match.
    
    Parameters:
    modificationMatch - the modification match of interest
    oldLocalization - the old localization
    newLocalization - the new localization
  - getTaggedModifiedSequence
```
public String getTaggedModifiedSequence(ModificationProfile modificationProfile,
                               boolean useHtmlColorCoding,
                               boolean useShortName,
                               boolean excludeAllFixedPtms)
```
    Returns the modified sequence as an tagged string with potential modification sites color coded or with PTM tags, e.g, <mox>. /!\ this method will work only if the PTM found in the peptide are in the PTMFactory. /!\ This method uses the modifications as set in the modification matches of this peptide and displays all of them. Note: this does not include html start end tags or terminal annotation.
    
    Parameters:
    modificationProfile - the modification profile of the search
    useHtmlColorCoding - if true, color coded HTML is used, otherwise PTM tags, e.g, <mox>, are used
    useShortName - if true the short names are used in the tags
    excludeAllFixedPtms - if true, all fixed PTMs are excluded
    
    Returns:
    the modified sequence as a tagged string
  - getTaggedModifiedSequence
```
public static String getTaggedModifiedSequence(ModificationProfile modificationProfile,
                               AminoAcidPattern aminoAcidPattern,
                               HashMap<Integer,ArrayList<String>> mainModificationSites,
                               HashMap<Integer,ArrayList<String>> secondaryModificationSites,
                               HashMap<Integer,ArrayList<String>> fixedModificationSites,
                               boolean useHtmlColorCoding,
                               boolean useShortName)
```
    Returns the modified sequence as an tagged string with potential modification sites color coded or with PTM tags, e.g, <mox>. /!\ This method will work only if the PTM found in the peptide are in the PTMFactory. /!\ This method uses the modifications as set in the modification matches of this peptide and displays all of them.
    
    Parameters:
    modificationProfile - the modification profile of the search
    aminoAcidPattern - the amino acid pattern to annotate
    mainModificationSites - the main variable modification sites in a map: aa number -> list of modifications (1 is the first AA) (can be null)
    secondaryModificationSites - the secondary variable modification sites in a map: aa number -> list of modifications (1 is the first AA) (can be null)
    fixedModificationSites - the fixed modification sites in a map: aa number -> list of modifications (1 is the first AA) (can be null)
    useHtmlColorCoding - if true, color coded HTML is used, otherwise PTM tags, e.g, <mox>, are used
    useShortName - if true the short names are used in the tags
    
    Returns:
    the tagged modified sequence as a string
  - getAllPossibleSequences
```
public ArrayList<String> getAllPossibleSequences()
```
    Returns all possible sequences which can be obtained from the targeted amino acids. Missing amino acids will be denoted as 'X'. This does not implement excluded amino acids.
    
    Returns:
    all possible sequences which can be obtained from the targeted amino acids
  - getMass
```
public Double getMass()
```
    Description copied from interface: TagComponent
    
    Returns the mass of the tag component.
    
    Specified by:
    
    getMass in interface TagComponent
    
    Returns:
    the mass of the tag component
  - getSubPattern
```
public AminoAcidPattern getSubPattern(int startIndex,
                             int endIndex,
                             boolean updateTarget)
```
    Returns a sub pattern of the pattern.
    
    Parameters:
    startIndex - the start index, inclusive (0 is the first amino acid)
    endIndex - the end index, inclusive
    updateTarget - boolean indicating whether the target of the pattern shall be updated. If yes it will be shifted by startIndex, simply copied otherwise.
    
    Returns:
    a sub pattern
  - getSubPattern
```
public AminoAcidPattern getSubPattern(int startIndex,
                             boolean updateTarget)
```
    Returns a sub pattern of the pattern.
    
    Parameters:
    startIndex - the start index, inclusive (0 is the first amino acid)
    updateTarget - boolean indicating whether the target of the pattern shall be updated. If yes it will be shifted by startIndex, simply copied otherwise.
    
    Returns:
    a sub pattern
  - isSameAs
```
public boolean isSameAs(TagComponent anotherCompontent)
```
    Description copied from interface: TagComponent
    
    Indicates whether another component is the same as the component of interest
    
    Specified by:
    
    isSameAs in interface TagComponent
    
    Parameters:
    anotherCompontent - another component
    
    Returns:
    a boolean indicating whether the other component is the same as the one of interest

Class AminoAcidPattern

Nested Class Summary

Constructor Summary

Method Summary

Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject

Methods inherited from class java.lang.Object

Constructor Detail

AminoAcidPattern

AminoAcidPattern

AminoAcidPattern

AminoAcidPattern

Method Detail

getAaTargeted

getAaExcluded

swapRows

getTarget

setTarget

getAminoAcidsAtTarget

setTargeted

getTargetedAA

getExcludedAA

getNTargetedAA

getNExcludedAA

setExcluded

removeAA

getAsStringPattern

getAsStringPattern

getPrositeFormat

getIndexes

getIndexes

getIndexes

getIndexes

matches

firstIndex

firstIndex

firstIndex

firstIndex

isTargeted

isExcluded

matches

matches

isStarting

isStarting

isStarting

isStarting

isEnding

isEnding

isEnding

isEnding

isSameAs

length

getStandardSearchPattern

getTrypsinExample

merge

append

merge

toString

asSequence

asSequence

getModificationMatches

getModificationIndexes

getModificationsAt

removeModificationMatch

clearModificationMatches

addModificationMatch

addModificationMatches

changeModificationSite

getTaggedModifiedSequence

getTaggedModifiedSequence

getAllPossibleSequences

getMass

getSubPattern

getSubPattern

isSameAs