OpenMS
2.5.0
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Sequest input file adapter. More...
#include <OpenMS/FORMAT/SequestInfile.h>
Public Member Functions | |
SequestInfile () | |
default constructor More... | |
SequestInfile (const SequestInfile &sequest_infile) | |
copy constructor More... | |
virtual | ~SequestInfile () |
destructor More... | |
SequestInfile & | operator= (const SequestInfile &sequest_infile) |
assignment operator More... | |
bool | operator== (const SequestInfile &sequest_infile) const |
equality operator More... | |
void | store (const String &filename) |
const String | getEnzymeInfoAsString () const |
returns the enzyme list as a string More... | |
const String & | getDatabase () const |
returns the used database More... | |
void | setDatabase (const String &database) |
sets the used database More... | |
const String & | getNeutralLossesForIons () const |
returns whether neutral losses are considered for the a-, b- and y-ions More... | |
void | setNeutralLossesForIons (const String &neutral_losses_for_ions) |
sets whether neutral losses are considered for the a-, b- and y-ions More... | |
const String & | getIonSeriesWeights () const |
returns the weights for the a-, b-, c-, d-, v-, w-, x-, y- and z-ion series More... | |
void | setIonSeriesWeights (const String &ion_series_weights) |
sets the weights for the a-, b-, c-, d-, v-, w-, x-, y- and z-ion series More... | |
const String & | getPartialSequence () const |
returns the partial sequences (space delimited) that have to occur in the theoretical spectra More... | |
void | setPartialSequence (const String &partial_sequence) |
sets the partial sequences (space delimited) that have to occur in the theoretical spectra More... | |
const String & | getSequenceHeaderFilter () const |
returns the sequences (space delimited) that have to occur, or be absent (preceded by a tilde) in the header of a protein to be considered More... | |
void | setSequenceHeaderFilter (const String &sequence_header_filter) |
sets the sequences (space delimited) that have to occur, or be absent (preceded by a tilde) in the header of a protein to be considered More... | |
const String & | getProteinMassFilter () const |
returns the protein mass filter (either min and max mass, or mass and tolerance value in percent) More... | |
void | setProteinMassFilter (const String &protein_mass_filter) |
sets the protein mass filter (either min and max mass, or mass and tolerance value in percent) More... | |
float | getPeakMassTolerance () const |
returns the peak mass tolerance More... | |
void | setPeakMassTolerance (float peak_mass_tolerance) |
sets the peak mass tolerance More... | |
float | getPrecursorMassTolerance () const |
returns the precursor mass tolerance More... | |
void | setPrecursorMassTolerance (float precursor_mass_tolerance) |
sets the precursor mass tolerance More... | |
float | getMatchPeakTolerance () const |
returns the match peak tolerance More... | |
void | setMatchPeakTolerance (float match_peak_tolerance) |
sets the match peak tolerance More... | |
float | getIonCutoffPercentage () const |
returns the the cutoff of the ratio matching theoretical peaks/theoretical peaks More... | |
void | setIonCutoffPercentage (float ion_cutoff_percentage) |
sets the ion cutoff of the ratio matching theoretical peaks/theoretical peaks More... | |
Size | getPeptideMassUnit () const |
returns the peptide mass unit More... | |
void | setPeptideMassUnit (Size peptide_mass_unit) |
sets the peptide mass unit More... | |
Size | getOutputLines () const |
return the number of peptides to be displayed More... | |
void | setOutputLines (Size output_lines) |
sets the number of peptides to be displayed More... | |
Size | getEnzymeNumber () const |
returns the enzyme used for cleavage (by means of the number from a list of enzymes) More... | |
String | getEnzymeName () const |
returns the enzyme used for cleavage More... | |
Size | setEnzyme (String enzyme_name) |
sets the enzyme used for cleavage (by means of the number from a list of enzymes) More... | |
Size | getMaxAAPerModPerPeptide () const |
returns the maximum number of amino acids containing the same modification in a peptide More... | |
void | setMaxAAPerModPerPeptide (Size max_aa_per_mod_per_peptide) |
sets the maximum number of amino acids containing the same modification in a peptide More... | |
Size | getMaxModsPerPeptide () const |
returns the maximum number of modifications that are allowed in a peptide More... | |
void | setMaxModsPerPeptide (Size max_mods_per_peptide) |
set the maximum number of modifications that are allowed in a peptide More... | |
Size | getNucleotideReadingFrame () const |
returns the nucleotide reading frame More... | |
void | setNucleotideReadingFrame (Size nucleotide_reading_frame) |
Size | getMaxInternalCleavageSites () const |
returns the maximum number of internal cleavage sites More... | |
void | setMaxInternalCleavageSites (Size max_internal_cleavage_sites) |
sets the maximum number of internal cleavage sites More... | |
Size | getMatchPeakCount () const |
returns the number of top abundant peaks to match with theoretical ones More... | |
void | setMatchPeakCount (Size match_peak_count) |
sets the number of top abundant peaks to with theoretical ones More... | |
Size | getMatchPeakAllowedError () const |
returns the number of top abundant peaks that are allowed not to match with a theoretical peak More... | |
void | setMatchPeakAllowedError (Size match_peak_allowed_error) |
sets the number of top abundant peaks that are allowed not to match with a theoretical peak More... | |
bool | getShowFragmentIons () const |
returns whether fragment ions shall be displayed More... | |
void | setShowFragmentIons (bool show_fragments) |
sets whether fragment ions shall be displayed More... | |
bool | getPrintDuplicateReferences () const |
returns whether all proteins containing a found peptide should be displayed More... | |
void | setPrintDuplicateReferences (bool print_duplicate_references) |
sets whether all proteins containing a found peptide should be displayed More... | |
bool | getRemovePrecursorNearPeaks () const |
return whether peaks near (15 amu) the precursor peak are removed More... | |
void | setRemovePrecursorNearPeaks (bool remove_precursor_near_peaks) |
sets whether peaks near (15 amu) the precursor peak are removed More... | |
bool | getMassTypeParent () const |
return the mass type of the parent (0 - monoisotopic, 1 - average mass) More... | |
void | setMassTypeParent (bool mass_type_parent) |
sets the mass type of the parent (0 - monoisotopic, 1 - average mass) More... | |
bool | getMassTypeFragment () const |
return the mass type of the fragments (0 - monoisotopic, 1 - average mass) More... | |
void | setMassTypeFragment (bool mass_type_fragment) |
sets the mass type of the fragments (0 - monoisotopic, 1 - average mass) More... | |
bool | getNormalizeXcorr () const |
returns whether normalized xcorr values are displayed More... | |
void | setNormalizeXcorr (bool normalize_xcorr) |
sets whether normalized xcorr values are displayed More... | |
bool | getResiduesInUpperCase () const |
returns whether residues are in upper case More... | |
void | setResiduesInUpperCase (bool residues_in_upper_case) |
sets whether residues are in upper case More... | |
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) More... | |
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 More... | |
void | setStandardEnzymeInfo_ () |
returns some standard enzymes (used to initialize the enzyme list) More... | |
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 More... | |
String | database_ |
database used More... | |
String | snd_database_ |
second database used More... | |
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) More... | |
String | ion_series_weights_ |
weights for the a-; b-; c-; d-; v-; w-; x-; y- and z-ion series; space delimited More... | |
String | partial_sequence_ |
space-delimited list of sequence parts that have to occur in the theoretical spectra More... | |
String | sequence_header_filter_ |
space-delimited list of sequences that have to occur or be absent (preceded by a tilde) in a protein header; to be considered More... | |
String | protein_mass_filter_ |
float | precursor_mass_tolerance_ |
tolerance for matching a theoretical to an experimental peptide More... | |
float | peak_mass_tolerance_ |
tolerance for matching a theoretical to an experimental peak More... | |
float | match_peak_tolerance_ |
minimum distance between two experimental peaks More... | |
float | ion_cutoff_percentage_ |
cutoff of the ratio matching theoretical peaks/theoretical peaks More... | |
Size | peptide_mass_unit_ |
peptide mass unit (0 = amu; 1 = mmu; 2 = ppm) More... | |
Size | output_lines_ |
number of peptides to be displayed More... | |
Size | enzyme_number_ |
number of the enzyme used for cleavage More... | |
Size | max_AA_per_mod_per_peptide_ |
maximum number of amino acids containing the same modification in a peptide More... | |
Size | max_mods_per_peptide_ |
maximum number of modifications per peptide More... | |
Size | nucleotide_reading_frame_ |
Size | max_internal_cleavage_sites_ |
maximum number of internal cleavage sites More... | |
Size | match_peak_count_ |
number of the top abundant peaks to match with theoretical one More... | |
Size | match_peak_allowed_error_ |
number of peaks that may lack this test More... | |
bool | show_fragment_ions_ |
whether to display fragment ions More... | |
bool | print_duplicate_references_ |
whether all proteins containing a found peptide should be displayed More... | |
bool | remove_precursor_near_peaks_ |
whether peaks near (15 amu) the precursor peak are removed More... | |
bool | mass_type_parent_ |
mass type of the parent peak (0 - monoisotopic; 1 - average) More... | |
bool | mass_type_fragment_ |
mass type of fragment peaks (0 - monoisotopic; 1 - average) More... | |
bool | normalize_xcorr_ |
whether to display normalized xcorr values More... | |
bool | residues_in_upper_case_ |
whether residues are in upper case More... | |
std::map< String, std::vector< String > > | PTMname_residues_mass_type_ |
the modification names map to the affected residues, the mass change and the type More... | |
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
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virtual |
destructor
void addEnzymeInfo | ( | std::vector< String > & | enzyme_info | ) |
adds an enzyme to the list and sets is as used the vector consists 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)
float 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
float 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 theoretical spectra
float getPeakMassTolerance | ( | ) | const |
returns the peak mass tolerance
Size getPeptideMassUnit | ( | ) | const |
returns the peptide mass unit
float 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 (preceded 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 | ( | float | 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 | ( | float | 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 theoretical spectra
void setPeakMassTolerance | ( | float | peak_mass_tolerance | ) |
sets the peak mass tolerance
void setPeptideMassUnit | ( | Size | peptide_mass_unit | ) |
sets the peptide mass unit
void setPrecursorMassTolerance | ( | float | 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 (preceded by a tilde) in the header of a protein to be considered
void setShowFragmentIons | ( | bool | show_fragments | ) |
sets whether fragment ions shall be displayed
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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 |
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protected |
database used
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
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protected |
number of the enzyme used for cleavage
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protected |
cutoff of the ratio matching theoretical peaks/theoretical peaks
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protected |
weights for the a-; b-; c-; d-; v-; w-; x-; y- and z-ion series; space delimited
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protected |
mass type of fragment peaks (0 - monoisotopic; 1 - average)
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protected |
mass type of the parent peak (0 - monoisotopic; 1 - average)
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protected |
number of peaks that may lack this test
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protected |
number of the top abundant peaks to match with theoretical one
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protected |
minimum distance between two experimental peaks
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protected |
maximum number of amino acids containing the same modification in a peptide
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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.
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maximum number of modifications per peptide
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protected |
whether neutral losses are considered for the a-; b- and y-ions (e.g. 011 for b- and y-ions)
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protected |
whether to display normalized xcorr values
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protected |
nucleotide reading frame:
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protected |
number of peptides to be displayed
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protected |
space-delimited list of sequence parts that have to occur in the theoretical spectra
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protected |
tolerance for matching a theoretical to an experimental peak
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protected |
peptide mass unit (0 = amu; 1 = mmu; 2 = ppm)
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protected |
tolerance for matching a theoretical to an experimental peptide
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protected |
whether all proteins containing a found peptide should be displayed
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protected |
the modification names map to the affected residues, the mass change and the type
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protected |
whether peaks near (15 amu) the precursor peak are removed
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protected |
whether residues are in upper case
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protected |
space-delimited list of sequences that have to occur or be absent (preceded by a tilde) in a protein header; to be considered
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protected |
whether to display fragment ions
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protected |
second database used