Filtering for SILAC data. More...
#include <OpenMS/FILTERING/DATAREDUCTION/SILACFiltering.h>
Classes | |
struct | BlacklistEntry |
structure for blacklist More... | |
class | SpectrumInterpolation |
Wrapper class for spectrum interpolation. More... | |
Public Types | |
typedef std::vector< SILACFilter > | Filters |
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enum | LogType { CMD, GUI, NONE } |
Possible log types. More... | |
Public Member Functions | |
SILACFiltering (MSExperiment< Peak1D > &exp, const PeakWidthEstimator::Result &, const DoubleReal intensity_cutoff, const String debug_filebase_="") | |
detailed constructor More... | |
void | addFilter (SILACFilter &filter) |
adds a new filter to the filtering More... | |
void | filterDataPoints () |
starts the filtering based on the added filters 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... | |
Public Attributes | |
Filters | filters_ |
holds all filters used in the filtering More... | |
const PeakWidthEstimator::Result | peak_width |
peak-width equation More... | |
std::multimap< DoubleReal, BlacklistEntry > | blacklist |
holds the range that is blacklisted for other filters and the filter that generated the blacklist entry More... | |
Private Member Functions | |
void | pickSeeds_ () |
pick data seeds More... | |
void | filterSeeds_ () |
apply filtering to picked data seeds More... | |
Private Attributes | |
DoubleReal | intensity_cutoff_ |
minimal intensity of SILAC features More... | |
MSExperiment< Peak1D > & | exp_ |
raw data More... | |
MSExperiment< Peak1D > | picked_exp_ |
picked data More... | |
MSExperiment< Peak1D > | picked_exp_seeds_ |
picked data seeds More... | |
const String | debug_filebase_ |
Additional Inherited Members | |
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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_ |
Filtering for SILAC data.
This filtering can be used to extract SILAC features from an MS experiment. Several SILACFilters can be added to the filtering to search for specific SILAC patterns.
typedef std::vector<SILACFilter> Filters |
SILACFiltering | ( | MSExperiment< Peak1D > & | exp, |
const PeakWidthEstimator::Result & | , | ||
const DoubleReal | intensity_cutoff, | ||
const String | debug_filebase_ = "" |
||
) |
detailed constructor
exp | raw data |
intensity_cutoff | minimal intensity of SILAC features |
void addFilter | ( | SILACFilter & | filter | ) |
adds a new filter to the filtering
filter | filter to add |
void filterDataPoints | ( | ) |
starts the filtering based on the added filters
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private |
apply filtering to picked data seeds
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private |
pick data seeds
std::multimap<DoubleReal, BlacklistEntry> blacklist |
holds the range that is blacklisted for other filters and the filter that generated the blacklist entry
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private |
Filename base for debugging output
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private |
raw data
Filters filters_ |
holds all filters used in the filtering
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private |
minimal intensity of SILAC features
const PeakWidthEstimator::Result peak_width |
peak-width equation
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private |
picked data
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private |
picked data seeds
OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:30 using doxygen 1.8.5 |