AminoAcidSequence (computational omics utilities 4.5.7 API)

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

All Implemented Interfaces:

TagComponent, Serializable, Cloneable
```
public class AminoAcidSequence
extends ExperimentObject
implements TagComponent
```
This class represents a series of amino acids with associated modifications.

Author:

Marc Vaudel

See Also:

Serialized Form

Constructor Summary

Constructors
Constructor and Description
`AminoAcidSequence()` Creates a blank sequence.
`AminoAcidSequence(AminoAcidSequence sequence)` Creates a sequence from another sequence.
`AminoAcidSequence(String sequence)` Constructor taking a sequence of amino acids as input.
`AminoAcidSequence(String sequence, HashMap<Integer,ArrayList<ModificationMatch>> modifications)` Constructor taking a sequence of amino acids as input.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addModificationMatch(int localization, ModificationMatch modificationMatch)` Adds a modification to one of the amino acid sequence.
`void`	`addModificationMatches(int localization, ArrayList<ModificationMatch> modificationMatches)` Adds a list of modifications to one of the amino acid sequence.
`void`	`appendCTerm(AminoAcidSequence otherSequence)` Appends another sequence at the end of this sequence.
`void`	`appendCTerm(String otherSequence)` Appends a series of unmodified amino acids to the sequence.
`void`	`appendNTerm(AminoAcidSequence otherSequence)` Appends another sequence at the beginning of this sequence keeping the original order.
`void`	`appendNTerm(String otherSequence)` Appends a series of unmodified amino acids to the beginning sequence keeping the original order.
`String`	`asSequence()` Returns the tag component as String like a peptide sequence.
`void`	`changeModificationSite(ModificationMatch modificationMatch, int oldLocalization, int newLocalization)` Changes the localization of a modification match.
`char`	`charAt(int aa)` Returns the amino acid at the given index on the sequence in its single letter code.
`void`	`clearModificationMatches()` Clears the list of imported modification matches.
`void`	`emptyInternalCaches()` the sequence is kept in different formats internally.
`int`	`firstIndex(String aminoAcidSequence, SequenceMatchingPreferences sequenceMatchingPreferences)` Returns the first index where the amino acid sequence is found in the given sequence.
`AminoAcid`	`getAminoAcidAt(int aa)` Returns the amino acid at the given index on the sequence.
`AminoAcidPattern`	`getAsAminoAcidPattern()` Returns this amino acid sequence as amino acid pattern.
`static ArrayList<StringBuilder>`	`getCombinations(String sequence)` Returns a list of all combinations which can be created from a sequence when expanding ambiguous amino acids like Xs.
`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 in a map: aa number > modification matches.
`ArrayList<ModificationMatch>`	`getModificationsAt(int localization)` Returns the modifications found at a given localization.
`String`	`getSequence()` Returns the sequence as String.
`String`	`getTaggedModifiedSequence(PtmSettings 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>.
`static String`	`getTaggedModifiedSequence(PtmSettings modificationProfile, String sequence, HashMap<Integer,ArrayList<String>> confidentModificationSites, HashMap<Integer,ArrayList<String>> representativeAmbiguousModificationSites, HashMap<Integer,ArrayList<String>> secondaryAmbiguousModificationSites, 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>.
`static String`	`getTaggedResidue(char residue, String ptmName, PtmSettings modificationProfile, int localizationConfidenceLevel, boolean useHtmlColorCoding, boolean useShortName)` Returns the single residue as a tagged string (HTML color or PTM tag).
`static boolean`	`hasCombination(String sequence)` Indicates whether the given sequence contains an amino acid which is in fact a combination of amino acids.
`void`	`insert(int offset, AminoAcidSequence otherSequence)` Inserts another sequence in this sequence.
`void`	`insert(int offset, String otherSequence)` Inserts another sequence in this sequence.
`boolean`	`isSameAs(AminoAcidSequence anotherSequence, SequenceMatchingPreferences sequenceMatchingPreferences)` Indicates whether another sequence has a matching sequence.
`boolean`	`isSameAs(TagComponent anotherCompontent, SequenceMatchingPreferences sequenceMatchingPreferences)` Indicates whether another component is the same as the component of interest.
`boolean`	`isSameSequenceAndModificationStatusAs(AminoAcidPattern anotherPattern, SequenceMatchingPreferences sequenceMatchingPreferences)` Indicates whether another AminoAcidPattern targets the same sequence without accounting for PTM localization.
`boolean`	`isSameSequenceAndModificationStatusAs(AminoAcidSequence anotherSequence, SequenceMatchingPreferences sequenceMatchingPreferences)` Indicates whether another sequence targets the same sequence without accounting for PTM localization.
`boolean`	`isSameSequenceAndModificationStatusAs(TagComponent anotherCompontent, SequenceMatchingPreferences sequenceMatchingPreferences)` Indicates whether another component is the same as the component of interest.
`int`	`length()` Returns the length of the sequence in amino acids.
`boolean`	`matches(AminoAcidSequence aminoAcidSequence, SequenceMatchingPreferences sequenceMatchingPreferences)` Indicates whether the sequence matches the given amino acid sequence in size and according to the given matching preferences.
`boolean`	`matches(String aminoAcidSequence, SequenceMatchingPreferences sequenceMatchingPreferences)` Indicates whether the sequence matches the given amino acid sequence in size and according to the given matching preferences.
`boolean`	`matchesIn(AminoAcidSequence aminoAcidSequence, SequenceMatchingPreferences sequenceMatchingPreferences)` Indicates whether the sequence is found in the given amino acid sequence.
`boolean`	`matchesIn(String aminoAcidSequence, SequenceMatchingPreferences sequenceMatchingPreferences)` Indicates whether the sequence is found in the given amino acid sequence.
`int`	`nMutations(String aminoAcidSequence, SequenceMatchingPreferences sequenceMatchingPreferences)` Returns the number of mutations used when matching the given reference sequence.
`void`	`removeModificationMatch(int localisation, ModificationMatch modificationMatch)` Removes a modification match in the given sequence.
`AminoAcidSequence`	`reverse()` Returns an amino acid sequence which is a reversed version of the current pattern.
`void`	`setAaAtIndex(int index, char aa)` replaces the amino acid at the given position by the given amino acid represented by its single letter code.
`void`	`setSequence(String aminoAcidSequence)` Sets the sequence.
`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
  - AminoAcidSequence
```
public AminoAcidSequence()
```
    Creates a blank sequence. All maps are null.
  - AminoAcidSequence
```
public AminoAcidSequence(String sequence)
```
    Constructor taking a sequence of amino acids as input.
    
    Parameters:
    
    sequence - a sequence of amino acids
  - AminoAcidSequence
```
public AminoAcidSequence(String sequence,
                         HashMap<Integer,ArrayList<ModificationMatch>> modifications)
```
    Constructor taking a sequence of amino acids as input.
    
    Parameters:
    
    sequence - a sequence of amino acids
    
    modifications - the modifications of this sequence in a map
  - AminoAcidSequence
```
public AminoAcidSequence(AminoAcidSequence sequence)
```
    Creates a sequence from another sequence.
    
    Parameters:
    
    sequence - the other sequence
- Method Detail
  - getSequence
```
public String getSequence()
```
    Returns the sequence as String.
    
    Returns:
    
    the sequence as String
  - charAt
```
public char charAt(int aa)
```
    Returns the amino acid at the given index on the sequence in its single letter code. 0 is the first amino acid.
    
    Parameters:
    
    aa - the index on the sequence
    
    Returns:
    
    the amino acid at the given index on the sequence in its single letter code
  - getAminoAcidAt
```
public AminoAcid getAminoAcidAt(int aa)
```
    Returns the amino acid at the given index on the sequence. 0 is the first amino acid.
    
    Parameters:
    
    aa - the index on the sequence
    
    Returns:
    
    the amino acid at the given index on the sequence
  - setSequence
```
public void setSequence(String aminoAcidSequence)
```
    Sets the sequence.
    
    Parameters:
    
    aminoAcidSequence - the sequence
  - setAaAtIndex
```
public void setAaAtIndex(int index,
                         char aa)
```
    replaces the amino acid at the given position by the given amino acid represented by its single letter code. 0 is the first amino acid.
    
    Parameters:
    
    index - the index where the amino acid should be set.
    
    aa - the amino acid to be set
  - getAsAminoAcidPattern
```
public AminoAcidPattern getAsAminoAcidPattern()
```
    Returns this amino acid sequence as amino acid pattern.
    
    Returns:
    
    this amino acid sequence as amino acid pattern
  - emptyInternalCaches
```
public void emptyInternalCaches()
```
    the sequence is kept in different formats internally. Calling this method removes them from the cache.
  - matchesIn
```
public boolean matchesIn(String aminoAcidSequence,
                         SequenceMatchingPreferences sequenceMatchingPreferences)
```
    Indicates whether the sequence is found in the given amino acid sequence.
    
    Parameters:
    
    aminoAcidSequence - the amino acid sequence
    
    sequenceMatchingPreferences - the sequence matching preferences
    
    Returns:
    
    a boolean indicating whether the sequence is found in the given amino acid sequence
  - matchesIn
```
public boolean matchesIn(AminoAcidSequence aminoAcidSequence,
                         SequenceMatchingPreferences sequenceMatchingPreferences)
```
    Indicates whether the sequence is found in the given amino acid sequence.
    
    Parameters:
    
    aminoAcidSequence - the amino acid sequence
    
    sequenceMatchingPreferences - the sequence matching preferences
    
    Returns:
    
    a boolean indicating whether the sequence is found in the given amino acid sequence
  - matches
```
public boolean matches(String aminoAcidSequence,
                       SequenceMatchingPreferences sequenceMatchingPreferences)
```
    Indicates whether the sequence matches the given amino acid sequence in size and according to the given matching preferences.
    
    Parameters:
    
    aminoAcidSequence - the amino acid sequence
    
    sequenceMatchingPreferences - the sequence matching preferences
    
    Returns:
    
    a boolean indicating whether the sequence is found in the given amino acid sequence
  - matches
```
public boolean matches(AminoAcidSequence aminoAcidSequence,
                       SequenceMatchingPreferences sequenceMatchingPreferences)
```
    Indicates whether the sequence matches the given amino acid sequence in size and according to the given matching preferences.
    
    Parameters:
    
    aminoAcidSequence - the amino acid sequence
    
    sequenceMatchingPreferences - the sequence matching preferences
    
    Returns:
    
    a boolean indicating whether the sequence is found in the given amino acid sequence
  - nMutations
```
public int nMutations(String aminoAcidSequence,
                      SequenceMatchingPreferences sequenceMatchingPreferences)
```
    Returns the number of mutations used when matching the given reference sequence.
    
    Parameters:
    
    aminoAcidSequence - the sequence to compare to
    
    sequenceMatchingPreferences - the sequence matching preferences
    
    Returns:
    
    the number of mutations used when matching the given reference sequence
  - firstIndex
```
public int firstIndex(String aminoAcidSequence,
                      SequenceMatchingPreferences sequenceMatchingPreferences)
```
    Returns the first index where the amino acid sequence is found in the given sequence. -1 if not found. 0 is the first amino acid.
    
    Parameters:
    
    aminoAcidSequence - the amino acid sequence to look into
    
    sequenceMatchingPreferences - the sequence matching preferences
    
    Returns:
    
    the first index where the amino acid sequence is found
  - isSameSequenceAndModificationStatusAs
```
public boolean isSameSequenceAndModificationStatusAs(AminoAcidPattern anotherPattern,
                                                     SequenceMatchingPreferences sequenceMatchingPreferences)
```
    Indicates whether another AminoAcidPattern targets the same sequence without accounting for PTM localization. Modifications are considered equal when of same mass. Modifications should be loaded in the PTM factory.
    
    Parameters:
    
    anotherPattern - the other AminoAcidPattern
    
    sequenceMatchingPreferences - the sequence matching preferences
    
    Returns:
    
    true if the other AminoAcidPattern targets the same sequence
  - length
```
public int length()
```
    Returns the length of the sequence in amino acids.
    
    Returns:
    
    the length of the sequence in amino acids
  - appendCTerm
```
public void appendCTerm(AminoAcidSequence otherSequence)
```
    Appends another sequence at the end of this sequence.
    
    Parameters:
    
    otherSequence - the other sequence to append.
  - appendCTerm
```
public void appendCTerm(String otherSequence)
```
    Appends a series of unmodified amino acids to the sequence.
    
    Parameters:
    
    otherSequence - a series of unmodified amino acids represented by their single letter code
  - insert
```
public void insert(int offset,
                   AminoAcidSequence otherSequence)
```
    Inserts another sequence in this sequence.
    
    Parameters:
    
    offset - the index where this sequence should be inserted, 0 is the first amino acid.
    
    otherSequence - the other sequence to insert.
  - insert
```
public void insert(int offset,
                   String otherSequence)
```
    Inserts another sequence in this sequence.
    
    Parameters:
    
    offset - the index where this sequence should be inserted, 0 is the first amino acid.
    
    otherSequence - the other sequence to insert.
  - appendNTerm
```
public void appendNTerm(AminoAcidSequence otherSequence)
```
    Appends another sequence at the beginning of this sequence keeping the original order.
    
    Parameters:
    
    otherSequence - the other sequence to append.
  - appendNTerm
```
public void appendNTerm(String otherSequence)
```
    Appends a series of unmodified amino acids to the beginning sequence keeping the original order.
    
    Parameters:
    
    otherSequence - a series of unmodified amino acids represented by their single letter code
  - getModificationMatches
```
public HashMap<Integer,ArrayList<ModificationMatch>> getModificationMatches()
```
    Getter for the modifications carried by this sequence in a map: aa number > modification matches. 1 is the first amino acid.
    
    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 sequence.
    
    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 sequence.
    
    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 sequence.
    
    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(PtmSettings 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(PtmSettings modificationProfile,
                                               String sequence,
                                               HashMap<Integer,ArrayList<String>> confidentModificationSites,
                                               HashMap<Integer,ArrayList<String>> representativeAmbiguousModificationSites,
                                               HashMap<Integer,ArrayList<String>> secondaryAmbiguousModificationSites,
                                               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.
    
    Parameters:
    
    modificationProfile - the modification profile of the search
    
    sequence - the amino acid sequence to annotate
    
    confidentModificationSites - the confidently localized variable modification sites in a map: aa number > list of modifications (1 is the first AA) (can be null)
    
    representativeAmbiguousModificationSites - the representative site of the ambiguously localized variable modifications in a map: aa number > list of modifications (1 is the first AA) (can be null)
    
    secondaryAmbiguousModificationSites - the secondary sites of the ambiguously localized variable modifications 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
  - getTaggedResidue
```
public static String getTaggedResidue(char residue,
                                      String ptmName,
                                      PtmSettings modificationProfile,
                                      int localizationConfidenceLevel,
                                      boolean useHtmlColorCoding,
                                      boolean useShortName)
```
    Returns the single residue as a tagged string (HTML color or PTM tag). Modified sites are color coded according to three levels: 1- black foreground, colored background 2- colored foreground, white background 3- colored foreground
    
    Parameters:
    
    residue - the residue to tag
    
    ptmName - the name of the PTM
    
    modificationProfile - the modification profile
    
    localizationConfidenceLevel - the localization confidence level
    
    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 single residue as a tagged string
  - isSameAs
```
public boolean isSameAs(AminoAcidSequence anotherSequence,
                        SequenceMatchingPreferences sequenceMatchingPreferences)
```
    Indicates whether another sequence has a matching sequence. Modifications are considered equal when of same mass. Modifications should be loaded in the PTM factory.
    
    Parameters:
    
    anotherSequence - the other AminoAcidPattern
    
    sequenceMatchingPreferences - the sequence matching preferences
    
    Returns:
    
    true if the other AminoAcidPattern targets the same sequence
  - isSameSequenceAndModificationStatusAs
```
public boolean isSameSequenceAndModificationStatusAs(AminoAcidSequence anotherSequence,
                                                     SequenceMatchingPreferences sequenceMatchingPreferences)
```
    Indicates whether another sequence targets the same sequence without accounting for PTM localization. Modifications are considered equal when of same mass. Modifications should be loaded in the PTM factory.
    
    Parameters:
    
    anotherSequence - the other sequence
    
    sequenceMatchingPreferences - the sequence matching preferences
    
    Returns:
    
    true if the other AminoAcidPattern targets the same sequence
  - reverse
```
public AminoAcidSequence reverse()
```
    Returns an amino acid sequence which is a reversed version of the current pattern.
    
    Returns:
    
    an amino acid sequence which is a reversed version of the current pattern
  - hasCombination
```
public static boolean hasCombination(String sequence)
```
    Indicates whether the given sequence contains an amino acid which is in fact a combination of amino acids.
    
    Parameters:
    
    sequence - the sequence of interest
    
    Returns:
    
    a boolean indicating whether the given sequence contains an amino acid which is in fact a combination of amino acids
  - getCombinations
```
public static ArrayList<StringBuilder> getCombinations(String sequence)
```
    Returns a list of all combinations which can be created from a sequence when expanding ambiguous amino acids like Xs.
    
    Parameters:
    
    sequence - the sequence of interest
    
    Returns:
    
    a list of all combinations which can be created from a sequence when expanding ambiguous amino acids like Xs
  - 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
  - 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
  - isSameAs
```
public boolean isSameAs(TagComponent anotherCompontent,
                        SequenceMatchingPreferences sequenceMatchingPreferences)
```
    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
    
    sequenceMatchingPreferences - the sequence matching preferences
    
    Returns:
    
    a boolean indicating whether the other component is the same as the one of interest
  - isSameSequenceAndModificationStatusAs
```
public boolean isSameSequenceAndModificationStatusAs(TagComponent anotherCompontent,
                                                     SequenceMatchingPreferences sequenceMatchingPreferences)
```
    Description copied from interface: TagComponent
    
    Indicates whether another component is the same as the component of interest.
    
    Specified by:
    
    isSameSequenceAndModificationStatusAs in interface TagComponent
    
    Parameters:
    
    anotherCompontent - another component
    
    sequenceMatchingPreferences - the sequence matching preferences
    
    Returns:
    
    a boolean indicating whether the other component is the same as the one of interest

Class AminoAcidSequence

Constructor Summary

Method Summary

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

Methods inherited from class java.lang.Object

Constructor Detail

AminoAcidSequence

AminoAcidSequence

AminoAcidSequence

AminoAcidSequence

Method Detail

getSequence

charAt

getAminoAcidAt

setSequence

setAaAtIndex

getAsAminoAcidPattern

emptyInternalCaches

matchesIn

matchesIn

matches

matches

nMutations

firstIndex

isSameSequenceAndModificationStatusAs

length

appendCTerm

appendCTerm

insert

insert

appendNTerm

appendNTerm

getModificationMatches

getModificationIndexes

getModificationsAt

removeModificationMatch

clearModificationMatches

addModificationMatch

addModificationMatches

changeModificationSite

getTaggedModifiedSequence

getTaggedModifiedSequence

getTaggedResidue

isSameAs

isSameSequenceAndModificationStatusAs

reverse

hasCombination

getCombinations

toString

asSequence

getMass

isSameAs

isSameSequenceAndModificationStatusAs