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AASequence & | operator= (const AASequence &rhs) |
| assignment operator More...
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bool | empty () const |
| check if sequence is empty More...
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| AASequence () |
| default constructor More...
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| AASequence (const AASequence &rhs) |
| copy constructor More...
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| AASequence (const String &rhs) |
| copy constructor from a String More...
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| AASequence (const char *rhs) |
| copy constructor from char* string More...
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virtual | ~AASequence () |
| destructor More...
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String | toString () const |
| returns the peptide as string with modifications embedded in brackets More...
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String | toUnmodifiedString () const |
| returns the peptide as string without any modifications More...
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void | setModification (Size index, const String &modification) |
| set the modification of the residue at position index More...
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void | setNTerminalModification (const String &modification) |
| sets the N-terminal modification More...
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const String & | getNTerminalModification () const |
| returns the Id of the N-term modification; an empty string is returned if none was set More...
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void | setCTerminalModification (const String &modification) |
| sets the C-terminal modification More...
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const String & | getCTerminalModification () const |
| returns the Id of the C-term modification; an empty string is returned if none was set More...
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bool | setStringSequence (const String &sequence) |
| sets the string of the sequence; returns true if the conversion to real AASequence was successful, false otherwise More...
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const Residue & | getResidue (SignedSize index) const |
| returns a pointer to the residue, which is at position index More...
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const Residue & | getResidue (Size index) const |
| returns a pointer to the residue, which is at position index More...
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EmpiricalFormula | getFormula (Residue::ResidueType type=Residue::Full, Int charge=0) const |
| returns the formula of the peptide More...
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DoubleReal | getAverageWeight (Residue::ResidueType type=Residue::Full, Int charge=0) const |
| returns the average weight of the peptide More...
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DoubleReal | getMonoWeight (Residue::ResidueType type=Residue::Full, Int charge=0) const |
| returns the mono isotopic weight of the peptide More...
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const Residue & | operator[] (SignedSize index) const |
| returns a pointer to the residue at given position More...
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const Residue & | operator[] (Size index) const |
| returns a pointer to the residue at given position More...
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AASequence | operator+ (const AASequence &peptide) const |
| adds the residues of the peptide More...
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AASequence | operator+ (const String &peptide) const |
| adds the residues of the peptide, which is given as a string More...
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AASequence | operator+ (const char *rhs) const |
| adds the residue of the peptide, which is given as string literal More...
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AASequence | operator+ (const Residue *residue) const |
| adds the residue to the peptide; the residue must be a valid residue of the ResidueDB More...
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AASequence & | operator+= (const AASequence &) |
| adds the residues of a peptide More...
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AASequence & | operator+= (const String &) |
| adds the residues of a peptide, which is given as a string More...
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AASequence & | operator+= (const char *rhs) |
| adds the residues of a peptide, which is given as string literal More...
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AASequence & | operator+= (const Residue *residue) |
| adds the residue to the peptide; the residue must be a valid residue of the ResidueDB More...
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Size | size () const |
| returns the number of residues More...
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AASequence | getPrefix (Size index) const |
| returns a peptide sequence of the first index residues More...
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AASequence | getSuffix (Size index) const |
| returns a peptide sequence of the last index residues More...
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AASequence | getSubsequence (Size index, UInt number) const |
| returns a peptide sequence of number residues, beginning at position index More...
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Size | getNumberOf (const String &residue) const |
| counts the number of occurrences of residue given by a string More...
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void | getAAFrequencies (Map< String, Size > &frequency_table) const |
| compute frequency table of amino acids More...
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bool | isValid () const |
| return true if the instance is valid More...
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bool | has (const Residue &residue) const |
| returns true if the peptide contains the given residue More...
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bool | has (const String &name) const |
| returns true if the peptide contains the given residue More...
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bool | hasSubsequence (const AASequence &peptide) const |
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bool | hasSubsequence (const String &peptide) const |
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bool | hasPrefix (const AASequence &peptide) const |
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bool | hasPrefix (const String &peptide) const |
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bool | hasSuffix (const AASequence &peptide) const |
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bool | hasSuffix (const String &peptide) const |
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bool | hasNTerminalModification () const |
| predicate which is true if the peptide is N-term modified More...
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bool | hasCTerminalModification () const |
| predicate which is true if the peptide is C-term modified More...
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bool | isModified () const |
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bool | isModified (Size index) const |
| returns true if the residue at the position is modified More...
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bool | operator== (const AASequence &rhs) const |
| equality operator More...
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bool | operator== (const String &rhs) const |
| equality operator given the peptide as a string More...
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bool | operator== (const char *rhs) const |
| equality operator given the peptide as string literal More...
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bool | operator< (const AASequence &rhs) const |
| lesser than operator which compares the C-term mods, sequence and N-term mods; can be used for maps More...
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bool | operator!= (const AASequence &rhs) const |
| inequality operator More...
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bool | operator!= (const String &rhs) const |
| inequality operator given the peptide as a string More...
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bool | operator!= (const char *rhs) const |
| inequality operator given the peptide as string literal More...
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Iterator | begin () |
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ConstIterator | begin () const |
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Iterator | end () |
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ConstIterator | end () const |
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Representation of a peptide/protein sequence.
This class represents amino acid sequences in OpenMS. Basically a AASequence instance consists of a sequence of residues. The residues are represented as instances of Residue. Each amino acid has only one instance which is accessible using the ResidueDB instance (singleton).
A critical property of amino acid sequence is that they can be modified. Which means that one or more amino acids are chemically modified, e.g. oxidized. This is represented via Residue instances which carry a ResidueModification object. This is also handled in the ResidueDB.
If one wants to specify a AASequence the easiest way is simply writing the amino acid sequence. For example AASequence seq("DFPIANGER") is sufficient to create a instance of AASequence with DFPIANGER as peptide.
Modifications are specified using a unique string identifier present in the ModificationsDB in brackets after the modified amino acid. For example AASequence seq("DFPIAM(Oxidation)GER") creates an instance of the peptide DFPIAMGER with an oxidized methionine. N-terminal modifications are specified by writing the modification as prefix to the sequence. C-terminal modifications are specified by writing the modification as suffix. C-terminal modifications are distinguished from modifications of the last amino acid by considering the specificity of the modification as stored in ModificationsDB.
Arbitrary/unknown AA's (usually due to an unknown modification) can be specified using tags: '[weight]'. This indicates a new AA with the specified weight, e.g. R[148.5]T. Note that this tag does not alter the AA's to the left or right. It represents an AA on its own. Be careful when converting AASequence to an EmpiricalFormula using .getFormula(), as tags will not be considered in this case. However, they have an influence on .getMonoWeight() and .getAverageWeight()!
If a string cannot be converted into a valid instance of AASequence, the valid flag is false. The flag can be read using the isValid() predicate. However, instances of AASequence which are not valid report wrong weights, because the weight cannot be calculated then. Also other operations might fail.