Sequest input file adapter. More...
#include <OpenMS/FORMAT/SequestInfile.h>
Public Member Functions | |
| SequestInfile () | |
| default constructor | |
| SequestInfile (const SequestInfile &sequest_infile) | |
| copy constructor | |
| virtual | ~SequestInfile () |
| destructor | |
| SequestInfile & | operator= (const SequestInfile &sequest_infile) |
| assignment operator | |
| bool | operator== (const SequestInfile &sequest_infile) const |
| equality operator | |
| void | store (const String &filename) |
| const String | getEnzymeInfoAsString () const |
| returns the enzyme list as a string | |
| const String & | getDatabase () const |
| returns the used database | |
| void | setDatabase (const String &database) |
| sets the used database | |
| const String & | getNeutralLossesForIons () const |
| returns whether neutral losses are considered for the a-, b- and y-ions | |
| void | setNeutralLossesForIons (const String &neutral_losses_for_ions) |
| sets whether neutral losses are considered for the a-, b- and y-ions | |
| const String & | getIonSeriesWeights () const |
| returns the weights for the a-, b-, c-, d-, v-, w-, x-, y- and z-ion series | |
| void | setIonSeriesWeights (const String &ion_series_weights) |
| sets the weights for the a-, b-, c-, d-, v-, w-, x-, y- and z-ion series | |
| const String & | getPartialSequence () const |
| returns the partial sequences (space delimited) that have to occur in the theortical spectra | |
| void | setPartialSequence (const String &partial_sequence) |
| sets the partial sequences (space delimited) that have to occur in the theortical spectra | |
| const String & | getSequenceHeaderFilter () const |
| returns the sequences (space delimited) that have to occur, or be absent (preceeded by a tilde) in the header of a protein to be considered | |
| void | setSequenceHeaderFilter (const String &sequence_header_filter) |
| sets the sequences (space delimited) that have to occur, or be absent (preceeded by a tilde) in the header of a protein to be considered | |
| const String & | getProteinMassFilter () const |
| returns the protein mass filter (either min and max mass, or mass and tolerance value in percent) | |
| void | setProteinMassFilter (const String &protein_mass_filter) |
| sets the protein mass filter (either min and max mass, or mass and tolerance value in percent) | |
| Real | getPeakMassTolerance () const |
| returns the peak mass tolerance | |
| void | setPeakMassTolerance (Real peak_mass_tolerance) |
| sets the peak mass tolerance | |
| Real | getPrecursorMassTolerance () const |
| returns the precursor mass tolerance | |
| void | setPrecursorMassTolerance (Real precursor_mass_tolerance) |
| sets the precursor mass tolerance | |
| Real | getMatchPeakTolerance () const |
| returns the match peak tolerance | |
| void | setMatchPeakTolerance (Real match_peak_tolerance) |
| sets the match peak tolerance | |
| Real | getIonCutoffPercentage () const |
| returns the the cutoff of the ratio matching theoretical peaks/theoretical peaks | |
| void | setIonCutoffPercentage (Real ion_cutoff_percentage) |
| sets the ion cutoff of the ratio matching theoretical peaks/theoretical peaks | |
| Size | getPeptideMassUnit () const |
| returns the peptide mass unit | |
| void | setPeptideMassUnit (Size peptide_mass_unit) |
| sets the peptide mass unit | |
| Size | getOutputLines () const |
| return the number of peptides to be displayed | |
| void | setOutputLines (Size output_lines) |
| sets the number of peptides to be displayed | |
| Size | getEnzymeNumber () const |
| returns the enzyme used for cleavage (by means of the number from a list of enzymes) | |
| String | getEnzymeName () const |
| returns the enzyme used for cleavage | |
| Size | setEnzyme (String enzyme_name) |
| sets the enzyme used for cleavage (by means of the number from a list of enzymes) | |
| Size | getMaxAAPerModPerPeptide () const |
| returns the maximum number of amino acids containing the same modification in a peptide | |
| void | setMaxAAPerModPerPeptide (Size max_aa_per_mod_per_peptide) |
| sets the maximum number of amino acids containing the same modification in a peptide | |
| Size | getMaxModsPerPeptide () const |
| returns the maximum number of modifications that are allowed in a peptide | |
| void | setMaxModsPerPeptide (Size max_mods_per_peptide) |
| set the maximum number of modifications that are allowed in a peptide | |
| Size | getNucleotideReadingFrame () const |
| returns the nucleotide reading frame | |
| void | setNucleotideReadingFrame (Size nucleotide_reading_frame) |
| Size | getMaxInternalCleavageSites () const |
| returns the maximum number of internal cleavage sites | |
| void | setMaxInternalCleavageSites (Size max_internal_cleavage_sites) |
| sets the maximum number of internal cleavage sites | |
| Size | getMatchPeakCount () const |
| returns the number of top abundant peaks to match with theoretical ones | |
| void | setMatchPeakCount (Size match_peak_count) |
| sets the number of top abundant peaks to with theoretical ones | |
| Size | getMatchPeakAllowedError () const |
| returns the number of top abundant peaks that are allowed not to match with a theoretical peak | |
| void | setMatchPeakAllowedError (Size match_peak_allowed_error) |
| sets the number of top abundant peaks that are allowed not to match with a theoretical peak | |
| bool | getShowFragmentIons () const |
| returns whether fragment ions shall be displayed | |
| void | setShowFragmentIons (bool show_fragments) |
| sets whether fragment ions shall be displayed | |
| bool | getPrintDuplicateReferences () const |
| returns whether all proteins containing a found peptide should be displayed | |
| void | setPrintDuplicateReferences (bool print_duplicate_references) |
| sets whether all proteins containing a found peptide should be displayed | |
| bool | getRemovePrecursorNearPeaks () const |
| return whether peaks near (15 amu) the precursor peak are removed | |
| void | setRemovePrecursorNearPeaks (bool remove_precursor_near_peaks) |
| sets whether peaks near (15 amu) the precursor peak are removed | |
| bool | getMassTypeParent () const |
| return the mass type of the parent (0 - monoisotopic, 1 - average mass) | |
| void | setMassTypeParent (bool mass_type_parent) |
| sets the mass type of the parent (0 - monoisotopic, 1 - average mass) | |
| bool | getMassTypeFragment () const |
| return the mass type of the fragments (0 - monoisotopic, 1 - average mass) | |
| void | setMassTypeFragment (bool mass_type_fragment) |
| sets the mass type of the fragments (0 - monoisotopic, 1 - average mass) | |
| bool | getNormalizeXcorr () const |
| returns whether normalized xcorr values are displayed | |
| void | setNormalizeXcorr (bool normalize_xcorr) |
| sets whether normalized xcorr values are displayed | |
| bool | getResiduesInUpperCase () const |
| returns whether residues are in upper case | |
| void | setResiduesInUpperCase (bool residues_in_upper_case) |
| sets whether residues are in upper case | |
| void | addEnzymeInfo (std::vector< String > &enzyme_info) |
| const std::map< String, std::vector< String > > & | getModifications () const |
| return the modifications (the modification names map to the affected residues, the mass change and the type) | |
| void | handlePTMs (const String &modification_line, const String &modifications_filename, const bool monoisotopic) |
Protected Member Functions | |
| const std::map< String, std::vector< String > > & | getEnzymeInfo_ () const |
| returns the enzyme list | |
| void | setStandardEnzymeInfo_ () |
| returns some standard enzymes (used to initialize the enzyme list) | |
Protected Attributes | |
| std::map< String, std::vector < String > > | enzyme_info_ |
| an endline-delimited list of enzymes; each with cutting direction 0 (N to C) /1; cuts after (list of aa); doesn't cut before (list of aa); the attributes are tab-delimited | |
| String | database_ |
| database used | |
| String | snd_database_ |
| second database used | |
| String | neutral_losses_for_ions_ |
| whether neutral losses are considered for the a-; b- and y-ions (e.g. 011 for b- and y-ions) | |
| String | ion_series_weights_ |
| weights for the a-; b-; c-; d-; v-; w-; x-; y- and z-ion series; space delimited | |
| String | partial_sequence_ |
| space-delimited list of sequence parts that have to occur in the theortical spectra | |
| String | sequence_header_filter_ |
| space-delimited list of sequences that have to occur or be absend (preceeded by a tilde) in a protein header; to be considered | |
| String | protein_mass_filter_ |
| Real | precursor_mass_tolerance_ |
| tolerance for matching a theoretical to an experimental peptide | |
| Real | peak_mass_tolerance_ |
| tolerance for matching a theoretical to an experimental peak | |
| Real | match_peak_tolerance_ |
| minimum distance between two experimental peaks | |
| Real | ion_cutoff_percentage_ |
| cutoff of the ratio matching theoretical peaks/theoretical peaks | |
| Size | peptide_mass_unit_ |
| peptide mass unit (0 = amu; 1 = mmu; 2 = ppm) | |
| Size | output_lines_ |
| number of peptides to be displayed | |
| Size | enzyme_number_ |
| number of the enzyme used for cleavage | |
| Size | max_AA_per_mod_per_peptide_ |
| maximum number of amino acids containing the same modification in a peptide | |
| Size | max_mods_per_peptide_ |
| maximum number of modifications per peptide | |
| Size | nucleotide_reading_frame_ |
| Size | max_internal_cleavage_sites_ |
| maximum number of internal cleavage sites | |
| Size | match_peak_count_ |
| number of the top abundant peaks to match with theoretical one | |
| Size | match_peak_allowed_error_ |
| number of peaks that may lack this test | |
| bool | show_fragment_ions_ |
| whether to display fragment ions | |
| bool | print_duplicate_references_ |
| whether all proteins containing a found peptide should be displayed | |
| bool | remove_precursor_near_peaks_ |
| whether peaks near (15 amu) the precursor peak are removed | |
| bool | mass_type_parent_ |
| mass type of the parent peak (0 - monoisotopic; 1 - average) | |
| bool | mass_type_fragment_ |
| mass type of fragment peaks (0 - monoisotopic; 1 - average) | |
| bool | normalize_xcorr_ |
| whether to display normalized xcorr values | |
| bool | residues_in_upper_case_ |
| whether residues are in upper case | |
| std::map< String, std::vector < String > > | PTMname_residues_mass_type_ |
| the modification names map to the affected residues, the mass change and the type | |
Sequest input file adapter.
Creates a sequest.params file for Sequest search from a peak list.
| SequestInfile | ( | ) |
default constructor
| SequestInfile | ( | const SequestInfile & | sequest_infile | ) |
copy constructor
| virtual ~SequestInfile | ( | ) | [virtual] |
destructor
| void addEnzymeInfo | ( | std::vector< String > & | enzyme_info | ) |
adds an enzyme to the list and sets is as used the vector constists of four strings: name, cut direction: 0 (N to C) / 1, cuts after (list of aa), doesn't cut before (list of aa)
| const String& getDatabase | ( | ) | const |
returns the used database
returns the enzyme list
| const String getEnzymeInfoAsString | ( | ) | const |
returns the enzyme list as a string
| String getEnzymeName | ( | ) | const |
returns the enzyme used for cleavage
| Size getEnzymeNumber | ( | ) | const |
returns the enzyme used for cleavage (by means of the number from a list of enzymes)
| Real getIonCutoffPercentage | ( | ) | const |
returns the the cutoff of the ratio matching theoretical peaks/theoretical peaks
| const String& getIonSeriesWeights | ( | ) | const |
returns the weights for the a-, b-, c-, d-, v-, w-, x-, y- and z-ion series
| bool getMassTypeFragment | ( | ) | const |
return the mass type of the fragments (0 - monoisotopic, 1 - average mass)
| bool getMassTypeParent | ( | ) | const |
return the mass type of the parent (0 - monoisotopic, 1 - average mass)
| Size getMatchPeakAllowedError | ( | ) | const |
returns the number of top abundant peaks that are allowed not to match with a theoretical peak
| Size getMatchPeakCount | ( | ) | const |
returns the number of top abundant peaks to match with theoretical ones
| Real getMatchPeakTolerance | ( | ) | const |
returns the match peak tolerance
| Size getMaxAAPerModPerPeptide | ( | ) | const |
returns the maximum number of amino acids containing the same modification in a peptide
| Size getMaxInternalCleavageSites | ( | ) | const |
returns the maximum number of internal cleavage sites
| Size getMaxModsPerPeptide | ( | ) | const |
returns the maximum number of modifications that are allowed in a peptide
return the modifications (the modification names map to the affected residues, the mass change and the type)
| const String& getNeutralLossesForIons | ( | ) | const |
returns whether neutral losses are considered for the a-, b- and y-ions
| bool getNormalizeXcorr | ( | ) | const |
returns whether normalized xcorr values are displayed
| Size getNucleotideReadingFrame | ( | ) | const |
returns the nucleotide reading frame
| Size getOutputLines | ( | ) | const |
return the number of peptides to be displayed
| const String& getPartialSequence | ( | ) | const |
returns the partial sequences (space delimited) that have to occur in the theortical spectra
| Real getPeakMassTolerance | ( | ) | const |
returns the peak mass tolerance
| Size getPeptideMassUnit | ( | ) | const |
returns the peptide mass unit
| Real getPrecursorMassTolerance | ( | ) | const |
returns the precursor mass tolerance
| bool getPrintDuplicateReferences | ( | ) | const |
returns whether all proteins containing a found peptide should be displayed
| const String& getProteinMassFilter | ( | ) | const |
returns the protein mass filter (either min and max mass, or mass and tolerance value in percent)
| bool getRemovePrecursorNearPeaks | ( | ) | const |
return whether peaks near (15 amu) the precursor peak are removed
| bool getResiduesInUpperCase | ( | ) | const |
returns whether residues are in upper case
| const String& getSequenceHeaderFilter | ( | ) | const |
returns the sequences (space delimited) that have to occur, or be absent (preceeded by a tilde) in the header of a protein to be considered
| bool getShowFragmentIons | ( | ) | const |
returns whether fragment ions shall be displayed
| void handlePTMs | ( | const String & | modification_line, | |
| const String & | modifications_filename, | |||
| const bool | monoisotopic | |||
| ) |
retrieves the name, mass change, affected residues, type and position for all modifications from a string
| modification_line | ||
| modifications_filename | ||
| monoisotopic |
| Exception::FileNotFound | is thrown if the given file is not found | |
| Exception::FileNotReadable | is thrown if the given file could not be read | |
| Exception::ParseError | is thrown if the given file could not be parsed |
| SequestInfile& operator= | ( | const SequestInfile & | sequest_infile | ) |
assignment operator
| bool operator== | ( | const SequestInfile & | sequest_infile | ) | const |
equality operator
| void setDatabase | ( | const String & | database | ) |
sets the used database
sets the enzyme used for cleavage (by means of the number from a list of enzymes)
| void setIonCutoffPercentage | ( | Real | ion_cutoff_percentage | ) |
sets the ion cutoff of the ratio matching theoretical peaks/theoretical peaks
| void setIonSeriesWeights | ( | const String & | ion_series_weights | ) |
sets the weights for the a-, b-, c-, d-, v-, w-, x-, y- and z-ion series
| void setMassTypeFragment | ( | bool | mass_type_fragment | ) |
sets the mass type of the fragments (0 - monoisotopic, 1 - average mass)
| void setMassTypeParent | ( | bool | mass_type_parent | ) |
sets the mass type of the parent (0 - monoisotopic, 1 - average mass)
| void setMatchPeakAllowedError | ( | Size | match_peak_allowed_error | ) |
sets the number of top abundant peaks that are allowed not to match with a theoretical peak
| void setMatchPeakCount | ( | Size | match_peak_count | ) |
sets the number of top abundant peaks to with theoretical ones
| void setMatchPeakTolerance | ( | Real | match_peak_tolerance | ) |
sets the match peak tolerance
| void setMaxAAPerModPerPeptide | ( | Size | max_aa_per_mod_per_peptide | ) |
sets the maximum number of amino acids containing the same modification in a peptide
| void setMaxInternalCleavageSites | ( | Size | max_internal_cleavage_sites | ) |
sets the maximum number of internal cleavage sites
| void setMaxModsPerPeptide | ( | Size | max_mods_per_peptide | ) |
set the maximum number of modifications that are allowed in a peptide
| void setNeutralLossesForIons | ( | const String & | neutral_losses_for_ions | ) |
sets whether neutral losses are considered for the a-, b- and y-ions
| void setNormalizeXcorr | ( | bool | normalize_xcorr | ) |
sets whether normalized xcorr values are displayed
| void setNucleotideReadingFrame | ( | Size | nucleotide_reading_frame | ) |
sets the nucleotide reading frame: 0 The FASTA file contains amino acid codes. No translation is needed. This is the best and fastest case. 1 The DNA sequence is scanned left to right (forward direction). The amino acid code starts with the first DNA code. 2 The DNA sequence is scanned left to right (forward direction). The amino acid code starts with the second DNA code. 3 The DNA sequence is scanned left to right (forward direction). The amino acid code starts with the third DNA code. 4 The DNA sequence is scanned right to left (backward direction for the complementary strand). The amino acid code starts with the first DNA code. 5 The DNA sequence is scanned right to left (backward direction for the complementary strand). The amino acid code starts with the second DNA code. 6 The DNA sequence is scanned right to left (backward direction for the complementary strand). The amino acid code starts with the third DNA code. 7 Use each of the DNA translations of the codes 1, 2, 3. 8 Use each of the DNA translations of the codes 4, 5, 6. 9 Use each of the DNA translations of the codes 1, 2, 3, 4, 5, 6.
| void setOutputLines | ( | Size | output_lines | ) |
sets the number of peptides to be displayed
| void setPartialSequence | ( | const String & | partial_sequence | ) |
sets the partial sequences (space delimited) that have to occur in the theortical spectra
| void setPeakMassTolerance | ( | Real | peak_mass_tolerance | ) |
sets the peak mass tolerance
| void setPeptideMassUnit | ( | Size | peptide_mass_unit | ) |
sets the peptide mass unit
| void setPrecursorMassTolerance | ( | Real | precursor_mass_tolerance | ) |
sets the precursor mass tolerance
| void setPrintDuplicateReferences | ( | bool | print_duplicate_references | ) |
sets whether all proteins containing a found peptide should be displayed
| void setProteinMassFilter | ( | const String & | protein_mass_filter | ) |
sets the protein mass filter (either min and max mass, or mass and tolerance value in percent)
| void setRemovePrecursorNearPeaks | ( | bool | remove_precursor_near_peaks | ) |
sets whether peaks near (15 amu) the precursor peak are removed
| void setResiduesInUpperCase | ( | bool | residues_in_upper_case | ) |
sets whether residues are in upper case
| void setSequenceHeaderFilter | ( | const String & | sequence_header_filter | ) |
sets the sequences (space delimited) that have to occur, or be absent (preceeded by a tilde) in the header of a protein to be considered
| void setShowFragmentIons | ( | bool | show_fragments | ) |
sets whether fragment ions shall be displayed
| void setStandardEnzymeInfo_ | ( | ) | [protected] |
returns some standard enzymes (used to initialize the enzyme list)
| void store | ( | const String & | filename | ) |
stores the experiment data in a Sequest input file that can be used as input for Sequest shell execution
| filename | the name of the file in which the infile is stored into |
| Exception::UnableToCreateFile | is thrown if the file could not be created |
std::map<String, std::vector<String> > enzyme_info_ [protected] |
an endline-delimited list of enzymes; each with cutting direction 0 (N to C) /1; cuts after (list of aa); doesn't cut before (list of aa); the attributes are tab-delimited
Size enzyme_number_ [protected] |
number of the enzyme used for cleavage
Real ion_cutoff_percentage_ [protected] |
cutoff of the ratio matching theoretical peaks/theoretical peaks
String ion_series_weights_ [protected] |
weights for the a-; b-; c-; d-; v-; w-; x-; y- and z-ion series; space delimited
bool mass_type_fragment_ [protected] |
mass type of fragment peaks (0 - monoisotopic; 1 - average)
bool mass_type_parent_ [protected] |
mass type of the parent peak (0 - monoisotopic; 1 - average)
Size match_peak_allowed_error_ [protected] |
number of peaks that may lack this test
Size match_peak_count_ [protected] |
number of the top abundant peaks to match with theoretical one
Real match_peak_tolerance_ [protected] |
minimum distance between two experimental peaks
Size max_AA_per_mod_per_peptide_ [protected] |
maximum number of amino acids containing the same modification in a peptide
Size max_internal_cleavage_sites_ [protected] |
maximum number of internal cleavage sites
0 The FASTA file contains amino acid codes. No translation is needed. This is the best and fastest case. 1 The DNA sequence is scanned left to right (forward direction). The amino acid code starts with the first DNA code. 2 The DNA sequence is scanned left to right (forward direction). The amino acid code starts with the second DNA code. 3 The DNA sequence is scanned left to right (forward direction). The amino acid code starts with the third DNA code. 4 The DNA sequence is scanned right to left (backward direction for the complementary strand). The amino acid code starts with the first DNA code. 5 The DNA sequence is scanned right to left (backward direction for the complementary strand). The amino acid code starts with the second DNA code. 6 The DNA sequence is scanned right to left (backward direction for the complementary strand). The amino acid code starts with the third DNA code. 7 Use each of the DNA translations of the codes 1; 2; 3. 8 Use each of the DNA translations of the codes 4; 5; 6. 9 Use each of the DNA translations of the codes 1; 2; 3; 4; 5; 6.
Size max_mods_per_peptide_ [protected] |
maximum number of modifications per peptide
String neutral_losses_for_ions_ [protected] |
whether neutral losses are considered for the a-; b- and y-ions (e.g. 011 for b- and y-ions)
bool normalize_xcorr_ [protected] |
whether to display normalized xcorr values
Size nucleotide_reading_frame_ [protected] |
nucleotide reading frame:
Size output_lines_ [protected] |
number of peptides to be displayed
String partial_sequence_ [protected] |
space-delimited list of sequence parts that have to occur in the theortical spectra
Real peak_mass_tolerance_ [protected] |
tolerance for matching a theoretical to an experimental peak
Size peptide_mass_unit_ [protected] |
peptide mass unit (0 = amu; 1 = mmu; 2 = ppm)
Real precursor_mass_tolerance_ [protected] |
tolerance for matching a theoretical to an experimental peptide
bool print_duplicate_references_ [protected] |
whether all proteins containing a found peptide should be displayed
String protein_mass_filter_ [protected] |
std::map<String, std::vector<String> > PTMname_residues_mass_type_ [protected] |
the modification names map to the affected residues, the mass change and the type
bool remove_precursor_near_peaks_ [protected] |
whether peaks near (15 amu) the precursor peak are removed
bool residues_in_upper_case_ [protected] |
whether residues are in upper case
String sequence_header_filter_ [protected] |
space-delimited list of sequences that have to occur or be absend (preceeded by a tilde) in a protein header; to be considered
bool show_fragment_ions_ [protected] |
whether to display fragment ions
String snd_database_ [protected] |
second database used
| OpenMS / TOPP release 1.10.0 | Documentation generated on Thu Mar 7 2013 09:42:54 using doxygen 1.7.1 |