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SequestInfile Class Reference
[File IO]

#include <OpenMS/FORMAT/SequestInfile.h>

List of all members.


Detailed Description

Sequest input file adapter.

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

Public Member Functions

 SequestInfile ()
 default constructor
 SequestInfile (const SequestInfile &sequest_infile)
 copy constructor
virtual ~SequestInfile ()
 destructor
SequestInfileoperator= (const SequestInfile &sequest_infile)
 assignment operator
bool operator== (const SequestInfile &sequest_infile) const
 equality operator
void store (const String &filename) throw (Exception::UnableToCreateFile)
 stores the experiment data in a Sequest input file that can be used as input for Sequest shell execution
const String getEnzymeInfoAsString () const
 returns the enzyme list as a string
const StringgetDatabase () const
 returns the used database
void setDatabase (const String &database)
 sets the used database
const StringgetNeutralLossesForIons () 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 StringgetIonSeriesWeights () 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 StringgetPartialSequence () 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 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
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 StringgetProteinMassFilter () 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
UInt getPeptideMassUnit () const
 returns the peptide mass unit
void setPeptideMassUnit (UInt peptide_mass_unit)
 sets the peptide mass unit
UInt getOutputLines () const
 return the number of peptides to be displayed
void setOutputLines (UInt output_lines)
 sets the number of peptides to be displayed
UInt 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
UInt setEnzyme (String enzyme_name)
 sets the enzyme used for cleavage (by means of the number from a list of enzymes)
UInt getMaxAAPerModPerPeptide () const
 returns the maximum number of amino acids containing the same modification in a peptide
void setMaxAAPerModPerPeptide (UInt max_aa_per_mod_per_peptide)
 sets the maximum number of amino acids containing the same modification in a peptide
UInt getMaxModsPerPeptide () const
 returns the maximum number of modifications that are allowed in a peptide
void setMaxModsPerPeptide (UInt max_mods_per_peptide)
 set the maximum number of modifications that are allowed in a peptide
UInt getNucleotideReadingFrame () const
 returns the nucleotide reading frame
void setNucleotideReadingFrame (UInt nucleotide_reading_frame)
UInt getMaxInternalCleavageSites () const
 returns the maximum number of internal cleavage sites
void setMaxInternalCleavageSites (UInt max_internal_cleavage_sites)
 sets the maximum number of internal cleavage sites
UInt getMatchPeakCount () const
 returns the number of top abundant peaks to match with theoretical ones
void setMatchPeakCount (UInt match_peak_count)
 sets the number of top abundant peaks to with theoretical ones
UInt getMatchPeakAllowedError () const
 returns the number of top abundant peaks that are allowed not to match with a theoretical peak
void setMatchPeakAllowedError (UInt 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) throw (Exception::FileNotReadable, Exception::FileNotFound, Exception::ParseError)
 retrieves the name, mass change, affected residues, type and position for all modifications from a string

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
UInt peptide_mass_unit_
 peptide mass unit (0 = amu; 1 = mmu; 2 = ppm)
UInt output_lines_
 number of peptides to be displayed
UInt enzyme_number_
 number of the enzyme used for cleavage
UInt max_AA_per_mod_per_peptide_
 maximum number of amino acids containing the same modification in a peptide
UInt max_mods_per_peptide_
 maximum number of modifications per peptide
UInt nucleotide_reading_frame_
UInt max_internal_cleavage_sites_
 maximum number of internal cleavage sites
UInt match_peak_count_
 number of the top abundant peaks to match with theoretical one
UInt match_peak_allowed_error_
 number of peaks that may lack this test
bool show_fragment_ions_
 wether 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

Static Protected Attributes

static const String aas_single_letter_
 the amino acids in one-letter-code


Constructor & Destructor Documentation

SequestInfile (  ) 

default constructor

SequestInfile ( const SequestInfile sequest_infile  ) 

copy constructor

virtual ~SequestInfile (  )  [virtual]

destructor


Member Function Documentation

SequestInfile& operator= ( const SequestInfile sequest_infile  ) 

assignment operator

bool operator== ( const SequestInfile sequest_infile  )  const

equality operator

void store ( const String filename  )  throw (Exception::UnableToCreateFile)

stores the experiment data in a Sequest input file that can be used as input for Sequest shell execution

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

UInt getPeptideMassUnit (  )  const

returns the peptide mass unit

void setPeptideMassUnit ( UInt  peptide_mass_unit  ) 

sets the peptide mass unit

UInt getOutputLines (  )  const

return the number of peptides to be displayed

void setOutputLines ( UInt  output_lines  ) 

sets the number of peptides to be displayed

UInt 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

UInt setEnzyme ( String  enzyme_name  ) 

sets the enzyme used for cleavage (by means of the number from a list of enzymes)

UInt getMaxAAPerModPerPeptide (  )  const

returns the maximum number of amino acids containing the same modification in a peptide

void setMaxAAPerModPerPeptide ( UInt  max_aa_per_mod_per_peptide  ) 

sets the maximum number of amino acids containing the same modification in a peptide

UInt getMaxModsPerPeptide (  )  const

returns the maximum number of modifications that are allowed in a peptide

void setMaxModsPerPeptide ( UInt  max_mods_per_peptide  ) 

set the maximum number of modifications that are allowed in a peptide

UInt getNucleotideReadingFrame (  )  const

returns the nucleotide reading frame

void setNucleotideReadingFrame ( UInt  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.

UInt getMaxInternalCleavageSites (  )  const

returns the maximum number of internal cleavage sites

void setMaxInternalCleavageSites ( UInt  max_internal_cleavage_sites  ) 

sets the maximum number of internal cleavage sites

UInt getMatchPeakCount (  )  const

returns the number of top abundant peaks to match with theoretical ones

void setMatchPeakCount ( UInt  match_peak_count  ) 

sets the number of top abundant peaks to with theoretical ones

UInt getMatchPeakAllowedError (  )  const

returns the number of top abundant peaks that are allowed not to match with a theoretical peak

void setMatchPeakAllowedError ( UInt  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  ) 

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 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 
) throw (Exception::FileNotReadable, Exception::FileNotFound, Exception::ParseError)

retrieves the name, mass change, affected residues, type and position for all modifications from a string

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

returns the enzyme list

void setStandardEnzymeInfo_ (  )  [protected]

returns some standard enzymes (used to initialize the enzyme list)


Member Data Documentation

const String aas_single_letter_ [static, protected]

the amino acids in one-letter-code

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

String database_ [protected]

database used

String snd_database_ [protected]

second database used

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)

String ion_series_weights_ [protected]

weights for the a-; b-; c-; d-; v-; w-; x-; y- and z-ion series; space delimited

String partial_sequence_ [protected]

space-delimited list of sequence parts that have to occur in the theortical spectra

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

String protein_mass_filter_ [protected]

Real precursor_mass_tolerance_ [protected]

tolerance for matching a theoretical to an experimental peptide

Real peak_mass_tolerance_ [protected]

tolerance for matching a theoretical to an experimental peak

Real match_peak_tolerance_ [protected]

minimum distance between two experimental peaks

Real ion_cutoff_percentage_ [protected]

cutoff of the ratio matching theoretical peaks/theoretical peaks

UInt peptide_mass_unit_ [protected]

peptide mass unit (0 = amu; 1 = mmu; 2 = ppm)

UInt output_lines_ [protected]

number of peptides to be displayed

UInt enzyme_number_ [protected]

number of the enzyme used for cleavage

UInt max_AA_per_mod_per_peptide_ [protected]

maximum number of amino acids containing the same modification in a peptide

UInt max_mods_per_peptide_ [protected]

maximum number of modifications per peptide

UInt nucleotide_reading_frame_ [protected]

nucleotide reading frame:

UInt 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.

UInt match_peak_count_ [protected]

number of the top abundant peaks to match with theoretical one

UInt match_peak_allowed_error_ [protected]

number of peaks that may lack this test

bool show_fragment_ions_ [protected]

wether to display fragment ions

bool print_duplicate_references_ [protected]

whether all proteins containing a found peptide should be displayed

bool remove_precursor_near_peaks_ [protected]

whether peaks near (15 amu) the precursor peak are removed

bool mass_type_parent_ [protected]

mass type of the parent peak (0 - monoisotopic; 1 - average)

bool mass_type_fragment_ [protected]

mass type of fragment peaks (0 - monoisotopic; 1 - average)

bool normalize_xcorr_ [protected]

whether to display normalized xcorr values

bool residues_in_upper_case_ [protected]

whether residues are in upper case

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


The documentation for this class was generated from the following file:
Generated Tue Apr 1 15:36:45 2008 -- using doxygen 1.5.4 OpenMS / TOPP 1.1