35 #ifndef OPENMS_ANALYSIS_XLMS_OPXLDATASTRUCTS 36 #define OPENMS_ANALYSIS_XLMS_OPXLDATASTRUCTS 61 NUMBER_OF_CROSS_LINK_TYPES
85 if (!beta.
empty())
return CROSS;
87 if (cross_link_position.second == -1)
return MONO;
94 return alpha == other.
alpha &&
157 return score < other.
score;
165 score == other.
score &&
166 rank == other.
rank &&
169 wTIC == other.
wTIC &&
298 for (
Size i = 0; i != size; ++i)
The AASeqWithMassComparator is a comparator for AASeqWithMass objects.
Definition: OPXLDataStructs.h:266
Size matched_xlink_alpha
Definition: OPXLDataStructs.h:138
std::vector< double > xcorrc
Definition: OPXLDataStructs.h:134
double percTIC
Definition: OPXLDataStructs.h:128
double wTIC
Definition: OPXLDataStructs.h:129
A more convenient string class.
Definition: String.h:57
ProteinProteinCrossLinkType
The ProteinProteinCrossLinkType enum enumerates possible types of Protein-Protein cross-linking react...
Definition: OPXLDataStructs.h:56
double HyperXlink
Definition: OPXLDataStructs.h:141
void addSpectrum(const MSSpectrum &spectrum)
adds a spectrum to the list
Definition: MSExperiment.h:831
ResidueModification::TermSpecificity term_spec_alpha
Definition: OPXLDataStructs.h:80
unsigned int beta_index
Definition: OPXLDataStructs.h:207
MSExperiment spectra_xlink_peaks
Definition: OPXLDataStructs.h:292
The XLPrecursorComparator is a comparator for XLPrecursors, that allows direct comparison of the XLPr...
Definition: OPXLDataStructs.h:216
std::vector< PeptideHit::PeakAnnotation > frag_annotations
Definition: OPXLDataStructs.h:151
double HyperAlpha
Definition: OPXLDataStructs.h:142
Representation of a peptide/protein sequence.
Definition: AASequence.h:108
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
double HyperCommon
Definition: OPXLDataStructs.h:140
std::vector< double > xcorrx
Definition: OPXLDataStructs.h:132
double PScoreBoth
Definition: OPXLDataStructs.h:149
double xcorrx_max
Definition: OPXLDataStructs.h:133
The CrossLinkSpectrumMatch struct represents a PSM between a ProteinProteinCrossLink and a spectrum i...
Definition: OPXLDataStructs.h:111
ProteinProteinCrossLinkType getType() const
Definition: OPXLDataStructs.h:83
Size matched_common_alpha
Definition: OPXLDataStructs.h:136
double HyperBoth
Definition: OPXLDataStructs.h:144
ResidueModification::TermSpecificity term_spec_beta
Definition: OPXLDataStructs.h:81
double xcorrc_max
Definition: OPXLDataStructs.h:135
Size scan_index_heavy
Definition: OPXLDataStructs.h:118
PreprocessedPairSpectra(Size size)
Definition: OPXLDataStructs.h:296
AASequence peptide_seq
Definition: OPXLDataStructs.h:257
double pre_score
counts, scores and other data for xQuest-like output
Definition: OPXLDataStructs.h:127
Definition: OPXLDataStructs.h:48
The PreprocessedPairSpectra struct represents the result of comparing a light and a heavy labeled spe...
Definition: OPXLDataStructs.h:288
bool operator==(const ProteinProteinCrossLink &other) const
Definition: OPXLDataStructs.h:92
The ProteinProteinCrossLink struct represents a cross-link between two peptides in OpenPepXL...
Definition: OPXLDataStructs.h:73
bool operator==(const CrossLinkSpectrumMatch &other) const
Definition: OPXLDataStructs.h:160
double score
final score
Definition: OPXLDataStructs.h:121
TermSpecificity
Position where the modification is allowed to occur.
Definition: ResidueModification.h:96
Size matched_xlink_beta
Definition: OPXLDataStructs.h:139
double PScoreBeta
Definition: OPXLDataStructs.h:148
bool operator<(const CrossLinkSpectrumMatch &other) const
Definition: OPXLDataStructs.h:155
std::pair< SignedSize, SignedSize > cross_link_position
Definition: OPXLDataStructs.h:77
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:82
double peptide_mass
Definition: OPXLDataStructs.h:256
double match_odds
Definition: OPXLDataStructs.h:131
bool empty() const
check if sequence is empty
MSExperiment spectra_common_peaks
Definition: OPXLDataStructs.h:291
double HyperBeta
Definition: OPXLDataStructs.h:143
MSSpectrum PeakSpectrum
Spectrum consisting of raw data points or peaks.
Definition: StandardTypes.h:53
double PScoreCommon
Definition: OPXLDataStructs.h:145
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:128
double cross_linker_mass
Definition: OPXLDataStructs.h:78
unsigned int alpha_index
Definition: OPXLDataStructs.h:206
MSExperiment spectra_all_peaks
Definition: OPXLDataStructs.h:293
double PScoreAlpha
Definition: OPXLDataStructs.h:147
The XLPrecursor struct represents a cross-link candidate in the process of filtering candidates by pr...
Definition: OPXLDataStructs.h:203
double int_sum
Definition: OPXLDataStructs.h:130
Size peptide_id_index
Definition: OPXLDataStructs.h:153
Size matched_common_beta
Definition: OPXLDataStructs.h:137
The AASeqWithMass struct represents a normal peptide with its precomputed mass.
Definition: OPXLDataStructs.h:254
AASequence alpha
Definition: OPXLDataStructs.h:75
PeptidePosition position
Definition: OPXLDataStructs.h:258
ProteinProteinCrossLink cross_link
structure of the cross-link
Definition: OPXLDataStructs.h:114
float precursor_mass
Definition: OPXLDataStructs.h:205
PeptidePosition
The PeptidePosition enum.
Definition: OPXLDataStructs.h:237
Size scan_index_light
reference to pair of spectra
Definition: OPXLDataStructs.h:117
AASequence beta
Definition: OPXLDataStructs.h:76
double PScoreXlink
Definition: OPXLDataStructs.h:146
String cross_linker_name
Definition: OPXLDataStructs.h:79
Size rank
rank among the matches to the same spectrum
Definition: OPXLDataStructs.h:124