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... | |
|  Public Member Functions inherited from ProgressLogger | |
| 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 | |
|  Public Types inherited from ProgressLogger | |
| enum | LogType { CMD, GUI, NONE } | 
| Possible log types.  More... | |
|  Protected Attributes inherited from ProgressLogger | |
| LogType | type_ | 
| SignedSize | begin_ | 
| SignedSize | end_ | 
| SignedSize | value_ | 
| QProgressDialog * | dlg_ | 
| StopWatch | stop_watch_ | 
| time_t | last_invoke_ | 
|  Static Protected Attributes inherited from ProgressLogger | |
| 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)
| 
 | private | 
| 
 | private | 
| 
 | private | 
| 
 | private | 
| 
 | private | 
do post-processing on read input data (removing quotes etc)
| void convertTargetedExperimentToTSV | ( | const char * | filename, | 
| OpenMS::TargetedExperiment & | targeted_exp | ||
| ) | 
Write out a targeted experiment (TraML structure) into a tsv file.
| void convertTSVToTargetedExperiment | ( | const char * | filename, | 
| OpenMS::TargetedExperiment & | targeted_exp | ||
| ) | 
Read in a tsv file and construct a targeted experiment (TraML structure)
| 
 | private | 
| 
 | private | 
| 
 | private | 
| 
 | private | 
determine separater in a CSV file and check for correct headers
| 
 | private | 
read TSV input with columns in defined order
| 
 | private | 
read tab or comma separated input with columns defined by their column headers only
| 
 | private | 
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)
| 
 | private | 
write a TargetedExperiment to a file
| 
 | staticprivate | 
| 
 | staticprivate | 
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:27 using doxygen 1.8.5 |