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SequestInfile Class Reference

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...
 
SequestInfileoperator= (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 StringgetDatabase () const
 returns the used database More...
 
void setDatabase (const String &database)
 sets the used database More...
 
const StringgetNeutralLossesForIons () 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 StringgetIonSeriesWeights () 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 StringgetPartialSequence () const
 returns the partial sequences (space delimited) that have to occur in the theortical spectra More...
 
void setPartialSequence (const String &partial_sequence)
 sets the partial sequences (space delimited) that have to occur in the theortical spectra More...
 
const StringgetSequenceHeaderFilter () 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 More...
 
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 More...
 
const StringgetProteinMassFilter () 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...
 
Real getPeakMassTolerance () const
 returns the peak mass tolerance More...
 
void setPeakMassTolerance (Real peak_mass_tolerance)
 sets the peak mass tolerance More...
 
Real getPrecursorMassTolerance () const
 returns the precursor mass tolerance More...
 
void setPrecursorMassTolerance (Real precursor_mass_tolerance)
 sets the precursor mass tolerance More...
 
Real getMatchPeakTolerance () const
 returns the match peak tolerance More...
 
void setMatchPeakTolerance (Real match_peak_tolerance)
 sets the match peak tolerance More...
 
Real getIonCutoffPercentage () const
 returns the the cutoff of the ratio matching theoretical peaks/theoretical peaks More...
 
void setIonCutoffPercentage (Real 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 theortical spectra More...
 
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 More...
 
String protein_mass_filter_
 
Real precursor_mass_tolerance_
 tolerance for matching a theoretical to an experimental peptide More...
 
Real peak_mass_tolerance_
 tolerance for matching a theoretical to an experimental peak More...
 
Real match_peak_tolerance_
 minimum distance between two experimental peaks More...
 
Real 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...
 

Detailed Description

Sequest input file adapter.

Creates a sequest.params file for Sequest search from a peak list.

Constructor & Destructor Documentation

default constructor

SequestInfile ( const SequestInfile sequest_infile)

copy constructor

virtual ~SequestInfile ( )
virtual

destructor

Member Function Documentation

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

const std::map<String, std::vector<String> >& getEnzymeInfo_ ( ) const
protected

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

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)

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

Parameters
modification_line
modifications_filename
monoisotopic
Exceptions
Exception::FileNotFoundis thrown if the given file is not found
Exception::FileNotReadableis thrown if the given file could not be read
Exception::ParseErroris 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

Size setEnzyme ( String  enzyme_name)

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

Parameters
filenamethe name of the file in which the infile is stored into
Exceptions
Exception::UnableToCreateFileis thrown if the file could not be created

Member Data Documentation

String database_
protected

database used

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 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:31 using doxygen 1.8.5