This class can convert TraML and TSV files into each other. More...
#include <OpenMS/ANALYSIS/OPENSWATH/TransitionTSVReader.h>
Classes | |
struct | TSVTransition |
Public Member Functions | |
void | convertTargetedExperimentToTSV (const char *filename, OpenMS::TargetedExperiment &targeted_exp) |
Write out a targeted experiment (TraML structure) into a tsv file. More... | |
void | convertTSVToTargetedExperiment (const char *filename, OpenMS::TargetedExperiment &targeted_exp) |
Read in a tsv file and construct a targeted experiment (TraML structure) More... | |
void | validateTargetedExperiment (OpenMS::TargetedExperiment &targeted_exp) |
Validate a TargetedExperiment (check that all ids are unique) More... | |
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ProgressLogger () | |
Constructor. More... | |
~ProgressLogger () | |
Destructor. More... | |
void | setLogType (LogType type) const |
Sets the progress log that should be used. The default type is NONE! More... | |
LogType | getLogType () const |
Returns the type of progress log being used. More... | |
void | startProgress (SignedSize begin, SignedSize end, const String &label) const |
Initializes the progress display. More... | |
void | setProgress (SignedSize value) const |
Sets the current progress. More... | |
void | endProgress () const |
Ends the progress display. More... | |
Private Types | |
typedef std::vector < OpenMS::TargetedExperiment::Protein > | ProteinVectorType |
typedef std::vector < OpenMS::TargetedExperiment::Peptide > | PeptideVectorType |
typedef std::vector < OpenMS::ReactionMonitoringTransition > | TransitionVectorType |
Private Member Functions | |
void | readTSVInput_ (const char *filename, std::vector< TSVTransition > &transition_list) |
read TSV input with columns in defined order More... | |
void | getTSVHeader (std::string &line, char &delimiter, std::vector< std::string > header, std::map< std::string, int > &header_dict) |
determine separater in a CSV file and check for correct headers More... | |
void | readUnstructuredTSVInput_ (const char *filename, std::vector< TSVTransition > &transition_list) |
read tab or comma separated input with columns defined by their column headers only More... | |
void | cleanUpTransition (TSVTransition &mytransition) |
do post-processing on read input data (removing quotes etc) More... | |
void | TSVToTargetedExperiment_ (std::vector< TSVTransition > &transition_list, OpenMS::TargetedExperiment &exp) |
store a list of TSVTransition objects properly in a TargetedExperiment More... | |
void | createTransition_ (std::vector< TSVTransition >::iterator &tr_it, OpenMS::ReactionMonitoringTransition &rm_trans) |
void | createProtein_ (std::vector< TSVTransition >::iterator &tr_it, OpenMS::TargetedExperiment::Protein &protein) |
void | createPeptide_ (std::vector< TSVTransition >::iterator &tr_it, OpenMS::TargetedExperiment::Peptide &peptide) |
void | add_modification_ (std::vector< TargetedExperiment::Peptide::Modification > &mods, int location, ResidueModification &rmod, const String &name) |
void | writeTSVOutput_ (const char *filename, OpenMS::TargetedExperiment &targeted_exp) |
write a TargetedExperiment to a file More... | |
Static Private Attributes | |
static const char * | strarray [] |
static const std::vector < std::string > | header_names |
Additional Inherited Members | |
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enum | LogType { CMD, GUI, NONE } |
Possible log types. More... | |
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LogType | type_ |
SignedSize | begin_ |
SignedSize | end_ |
SignedSize | value_ |
QProgressDialog * | dlg_ |
StopWatch | stop_watch_ |
time_t | last_invoke_ |
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static int | recursion_depth_ |
This class can convert TraML and TSV files into each other.
The TSV are tab-separated and need to have the following columns:
PrecursorMz (float) ProductMz (float) Tr_calibrated (float) transition_name (free text, needs to be unique for each transition [in this file]) CE (float) LibraryIntensity (float) transition_group_id (free text, designates the transition group [e.g. peptide] to which this transition belongs) decoy (1==decoy, 0== no decoy; determines whether the transition is a decoy transition or not) PeptideSequence (free text, sequence only (no modifications) ) ProteinName (free text) Annotation (free text, e.g. y7) FullUniModPeptideName (free text, should contain modifications*) MissedCleavages Replicates NrModifications PrecursorCharge (integer) Labelgroup (free text, e.g. heavy or light)
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do post-processing on read input data (removing quotes etc)
void convertTargetedExperimentToTSV | ( | const char * | filename, |
OpenMS::TargetedExperiment & | targeted_exp | ||
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Write out a targeted experiment (TraML structure) into a tsv file.
void convertTSVToTargetedExperiment | ( | const char * | filename, |
OpenMS::TargetedExperiment & | targeted_exp | ||
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Read in a tsv file and construct a targeted experiment (TraML structure)
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determine separater in a CSV file and check for correct headers
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read TSV input with columns in defined order
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read tab or comma separated input with columns defined by their column headers only
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store a list of TSVTransition objects properly in a TargetedExperiment
void validateTargetedExperiment | ( | OpenMS::TargetedExperiment & | targeted_exp | ) |
Validate a TargetedExperiment (check that all ids are unique)
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write a TargetedExperiment to a file
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OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:27 using doxygen 1.8.5 |