45 #pragma clang diagnostic push 46 #pragma clang diagnostic ignored "-Wnon-virtual-dtor" 72 virtual bool isNull()
const = 0;
73 virtual void setNull(
bool b) = 0;
74 virtual String toCellString()
const = 0;
75 virtual void fromCellString(
const String&) = 0;
84 virtual bool isNaN()
const = 0;
85 virtual void setNaN() = 0;
86 virtual bool isInf()
const = 0;
87 virtual void setInf() = 0;
99 bool isNull()
const override;
101 void setNull(
bool b)
override;
116 bool isNull()
const override;
118 void setNull(
bool b)
override;
120 bool isNaN()
const override;
122 void setNaN()
override;
124 bool isInf()
const override;
126 void setInf()
override;
142 void set(
const double& value);
146 String toCellString()
const override;
148 void fromCellString(
const String& s)
override;
162 bool isNull()
const override;
164 void setNull(
bool b)
override;
166 String toCellString()
const override;
168 void fromCellString(
const String& s)
override;
170 std::vector<MzTabDouble>
get()
const;
172 void set(
const std::vector<MzTabDouble>& entries);
188 void set(
const Int& value);
192 String toCellString()
const override;
194 void fromCellString(
const String& s)
override;
206 bool isNull()
const override;
208 void setNull(
bool b)
override;
210 String toCellString()
const override;
212 void fromCellString(
const String& s)
override;
214 std::vector<MzTabInteger>
get()
const;
216 void set(
const std::vector<MzTabInteger>& entries);
232 void set(
const bool& value);
236 String toCellString()
const override;
238 void fromCellString(
const String& s)
override;
254 void set(
const String& value);
258 bool isNull()
const override;
260 void setNull(
bool b)
override;
262 String toCellString()
const override;
264 void fromCellString(
const String& s)
override;
278 bool isNull()
const override;
280 void setNull(
bool b)
override;
282 void setCVLabel(
const String& CV_label);
284 void setAccession(
const String& accession);
286 void setName(
const String& name);
288 void setValue(
const String& value);
290 String getCVLabel()
const;
292 String getAccession()
const;
298 String toCellString()
const override;
300 void fromCellString(
const String& s)
override;
316 bool isNull()
const override;
318 void setNull(
bool b)
override;
320 String toCellString()
const override;
322 void fromCellString(
const String& s)
override;
324 std::vector<MzTabParameter>
get()
const;
326 void set(
const std::vector<MzTabParameter>& parameters);
341 void setSeparator(
char sep);
343 bool isNull()
const override;
345 void setNull(
bool b)
override;
347 String toCellString()
const override;
349 void fromCellString(
const String& s)
override;
351 std::vector<MzTabString>
get()
const;
353 void set(
const std::vector<MzTabString>& entries);
368 bool isNull()
const override;
370 void setNull(
bool b)
override;
373 void setPositionsAndParameters(
const std::vector<std::pair<Size, MzTabParameter> >& ppp);
375 std::vector<std::pair<Size, MzTabParameter> > getPositionsAndParameters()
const;
377 void setModificationIdentifier(
const MzTabString& mod_id);
381 String toCellString()
const override;
383 void fromCellString(
const String& s)
override;
396 bool isNull()
const override;
398 void setNull(
bool b)
override;
400 String toCellString()
const override;
402 void fromCellString(
const String& s)
override;
404 std::vector<MzTabModification>
get()
const;
406 void set(
const std::vector<MzTabModification>& entries);
421 bool isNull()
const override;
423 void setNull(
bool b)
override;
425 void setMSFile(
Size index);
427 void setSpecRef(
String spec_ref);
429 String getSpecRef()
const;
431 Size getMSFile()
const;
433 void setSpecRefFile(
const String& spec_ref);
435 String toCellString()
const override;
437 void fromCellString(
const String& s)
override;
545 std::map<Size, MzTabString>
uri;
557 std::map<Size, MzTabMSRunMetaData>
ms_run;
561 std::map<Size, MzTabSampleMetaData>
sample;
563 std::map<Size, MzTabAssayMetaData>
assay;
567 std::map<Size, MzTabCVMetaData>
cv;
603 std::vector<MzTabOptionalColumnEntry>
opt_;
629 std::vector<MzTabOptionalColumnEntry>
opt_;
655 std::vector<MzTabOptionalColumnEntry>
opt_;
685 std::vector<MzTabOptionalColumnEntry>
opt_;
724 void setCommentRows(
const std::map<Size, String>& com);
726 void setEmptyRows(
const std::vector<Size>& empty);
728 const std::vector<Size>& getEmptyRows()
const;
730 const std::map<Size, String>& getCommentRows()
const;
737 std::vector<String> getProteinOptionalColumnNames()
const;
740 std::vector<String> getPeptideOptionalColumnNames()
const;
743 std::vector<String> getPSMOptionalColumnNames()
const;
746 std::vector<String> getSmallMoleculeOptionalColumnNames()
const;
760 #pragma clang diagnostic pop
MzTabSpectraRef spectra_ref
Definition: MzTab.h:624
MzTabSpectraRef spectra_ref
Definition: MzTab.h:676
MzTabDoubleList retention_time
Definition: MzTab.h:645
MzTabString uri
Definition: MzTab.h:596
std::map< Size, MzTabDouble > protein_abundance_assay
Definition: MzTab.h:599
MzTabMetaData meta_data_
Definition: MzTab.h:749
MzTabString database
Definition: MzTab.h:612
A more convenient string class.
Definition: String.h:57
MzTabString accession
Definition: MzTab.h:610
MzTabDouble calc_mass_to_charge
Definition: MzTab.h:667
MzTabString sequence
Definition: MzTab.h:609
std::map< Size, std::map< Size, MzTabDouble > > search_engine_score_ms_run
Definition: MzTab.h:616
MzTabString sequence
Definition: MzTab.h:635
MzTabParameterList search_engine
Definition: MzTab.h:587
std::vector< MzTabOptionalColumnEntry > opt_
Definition: MzTab.h:655
std::map< Size, MzTabDouble > best_search_engine_score
Definition: MzTab.h:678
MzTabString inchi_key
Definition: MzTab.h:664
MzTabString database
Definition: MzTab.h:639
MzTabString post
Definition: MzTab.h:652
std::vector< MzTabOptionalColumnEntry > opt_
Definition: MzTab.h:629
MzTabString end
Definition: MzTab.h:654
MzTabString database
Definition: MzTab.h:585
Size ms_run_
Definition: MzTab.h:440
String value_
Definition: MzTab.h:267
MzTabString modifications
Definition: MzTab.h:680
MzTabString database_version
Definition: MzTab.h:586
String CV_label_
Definition: MzTab.h:303
MzTabParameterList search_engine
Definition: MzTab.h:614
MzTabStringList identifier
Definition: MzTab.h:661
std::map< Size, MzTabDouble > best_search_engine_score
Definition: MzTab.h:615
std::vector< MzTabSmallMoleculeSectionRow > MzTabSmallMoleculeSectionRows
Definition: MzTab.h:691
std::map< Size, MzTabDouble > protein_abundance_stdev_study_variable
Definition: MzTab.h:601
std::vector< MzTabModification > entries_
Definition: MzTab.h:409
MzTabCellStateType state_
Definition: MzTab.h:129
std::vector< MzTabOptionalColumnEntry > opt_
Definition: MzTab.h:685
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
std::map< Size, MzTabDouble > peptide_abundance_study_variable
Definition: MzTab.h:626
char sep_
Definition: MzTab.h:357
Int value_
Definition: MzTab.h:197
std::map< Size, MzTabDouble > protein_abundance_std_error_study_variable
Definition: MzTab.h:602
std::map< Size, MzTabDouble > smallmolecule_abundance_assay
Definition: MzTab.h:681
MzTabString uri
Definition: MzTab.h:675
std::vector< MzTabProteinSectionRow > MzTabProteinSectionRows
Definition: MzTab.h:688
MzTabDoubleList retention_time
Definition: MzTab.h:669
std::map< Size, MzTabDouble > peptide_abundance_stdev_study_variable
Definition: MzTab.h:627
MzTabBoolean unique
Definition: MzTab.h:611
double value_
Definition: MzTab.h:151
MzTabInteger reliability
Definition: MzTab.h:617
MzTabModificationList modifications
Definition: MzTab.h:644
MzTabCellStateType
Data model of MzTab files. Please see the official MzTab specification at https://code.google.com/p/mztab/.
Definition: MzTab.h:58
std::vector< MzTabInteger > entries_
Definition: MzTab.h:219
MzTabString description
Definition: MzTab.h:665
MzTabString accession
Definition: MzTab.h:581
std::map< Size, MzTabInteger > num_peptides_distinct_ms_run
Definition: MzTab.h:592
MzTabString accession
Definition: MzTab.h:637
MzTabModificationList modifications
Definition: MzTab.h:595
MzTabDouble mass_to_charge
Definition: MzTab.h:622
String accession_
Definition: MzTab.h:304
std::map< Size, MzTabDouble > peptide_abundance_assay
Definition: MzTab.h:625
MzTabString species
Definition: MzTab.h:671
MzTabString uri
Definition: MzTab.h:649
MzTabPeptideSectionRows peptide_data_
Definition: MzTab.h:751
MzTabProteinSectionRows protein_data_
Definition: MzTab.h:750
String spec_ref_
Definition: MzTab.h:441
bool value_
Definition: MzTab.h:241
MzTabDoubleList retention_time_window
Definition: MzTab.h:620
MzTabInteger reliability
Definition: MzTab.h:590
std::map< Size, MzTabDouble > smallmolecule_abundance_std_error_study_variable
Definition: MzTab.h:684
MzTabString description
Definition: MzTab.h:582
std::map< Size, MzTabDouble > smallmolecule_abundance_stdev_study_variable
Definition: MzTab.h:683
std::vector< MzTabDouble > entries_
Definition: MzTab.h:175
MzTabString pre
Definition: MzTab.h:651
std::map< Size, std::map< Size, MzTabDouble > > search_engine_score_ms_run
Definition: MzTab.h:589
MzTabInteger taxid
Definition: MzTab.h:670
MzTabDoubleList retention_time
Definition: MzTab.h:619
std::vector< MzTabParameter > parameters_
Definition: MzTab.h:329
MzTabString species
Definition: MzTab.h:584
MzTabDouble protein_coverage
Definition: MzTab.h:598
MzTabModificationList modifications
Definition: MzTab.h:618
MzTabStringList go_terms
Definition: MzTab.h:597
MzTabString mod_identifier_
Definition: MzTab.h:387
std::vector< MzTabPeptideSectionRow > MzTabPeptideSectionRows
Definition: MzTab.h:689
std::map< Size, MzTabDouble > protein_abundance_study_variable
Definition: MzTab.h:600
MzTabDouble calc_mass_to_charge
Definition: MzTab.h:648
std::map< Size, std::map< Size, MzTabDouble > > search_engine_score_ms_run
Definition: MzTab.h:679
MzTabStringList ambiguity_members
Definition: MzTab.h:594
MzTabInteger charge
Definition: MzTab.h:646
MzTabString start
Definition: MzTab.h:653
std::map< Size, MzTabDouble > peptide_abundance_std_error_study_variable
Definition: MzTab.h:628
std::map< Size, MzTabDouble > smallmolecule_abundance_study_variable
Definition: MzTab.h:682
std::map< Size, MzTabDouble > best_search_engine_score
Definition: MzTab.h:588
MzTabDouble exp_mass_to_charge
Definition: MzTab.h:666
std::vector< Size > empty_rows_
Definition: MzTab.h:754
MzTabParameterList search_engine
Definition: MzTab.h:677
MzTabPSMSectionRows psm_data_
Definition: MzTab.h:752
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
bool null_
Definition: MzTab.h:104
MzTabInteger PSM_ID
Definition: MzTab.h:636
String name_
Definition: MzTab.h:305
MzTabString database
Definition: MzTab.h:672
std::vector< std::pair< Size, MzTabParameter > > pos_param_pairs_
Definition: MzTab.h:386
MzTabString uri
Definition: MzTab.h:623
std::vector< MzTabString > entries_
Definition: MzTab.h:356
std::map< Size, MzTabDouble > search_engine_score
Definition: MzTab.h:642
MzTabInteger reliability
Definition: MzTab.h:674
std::vector< MzTabPSMSectionRow > MzTabPSMSectionRows
Definition: MzTab.h:690
MzTabInteger charge
Definition: MzTab.h:621
MzTabInteger taxid
Definition: MzTab.h:583
MzTabSpectraRef spectra_ref
Definition: MzTab.h:650
std::vector< MzTabOptionalColumnEntry > opt_
Definition: MzTab.h:603
MzTabBoolean unique
Definition: MzTab.h:638
std::map< Size, MzTabInteger > num_psms_ms_run
Definition: MzTab.h:591
MzTabString database_version
Definition: MzTab.h:673
std::map< Size, MzTabInteger > num_peptides_unique_ms_run
Definition: MzTab.h:593
MzTabString chemical_formula
Definition: MzTab.h:662
MzTabString database_version
Definition: MzTab.h:613
int Int
Signed integer type.
Definition: Types.h:102
MzTabDouble charge
Definition: MzTab.h:668
String value_
Definition: MzTab.h:306
MzTabString database_version
Definition: MzTab.h:640
MzTabDouble exp_mass_to_charge
Definition: MzTab.h:647
std::map< Size, String > comment_rows_
Definition: MzTab.h:755
MzTabParameterList search_engine
Definition: MzTab.h:641
MzTabInteger reliability
Definition: MzTab.h:643
MzTabSmallMoleculeSectionRows small_molecule_data_
Definition: MzTab.h:753
MzTabString smiles
Definition: MzTab.h:663
std::pair< String, MzTabString > MzTabOptionalColumnEntry
Definition: MzTab.h:575
Data model of MzTab files. Please see the official MzTab specification at https://code.google.com/p/mztab/.
Definition: MzTab.h:699