SpectraTreeTab Class Reference

Hierarchical visualization and selection of spectra. More...

#include <OpenMS/VISUAL/SpectraTreeTab.h>

Inheritance diagram for SpectraTreeTab:

Signals
void	spectrumSelected (int)
void	chromsSelected (std::vector< int > indices)
void	spectrumDoubleClicked (int)
void	chromsDoubleClicked (std::vector< int > indices)
void	showSpectrumAsNew1D (int)
void	showChromatogramsAsNew1D (std::vector< int > indices)
void	showSpectrumMetaData (int)

Public Member Functions
	SpectraTreeTab (QWidget *parent=nullptr)
	Constructor.
	~SpectraTreeTab () override=default
	Destructor.
bool	hasData (const LayerDataBase *layer) override
	docu in base class
void	updateEntries (LayerDataBase *cl) override
	refresh the table using data from cl
void	clear () override
	remove all visible data
bool	getSelectedScan (MSExperiment &exp, LayerDataBase::DataType &current_type) const

Static Public Member Functions
static std::vector< int >	getParentIndices (const MSExperiment &exp)
	Determines under which spectrum each spectrum of exp is listed in the tree.

Private Slots
void	populateSearchBox_ ()
	fill the search-combo-box with current column header names
void	spectrumSearchText_ ()
	searches for rows containing a search text (from spectra_search_box_); called when text search box is used
void	itemSelectionChange_ (QTreeWidgetItem *, QTreeWidgetItem *)
	emits spectrumSelected() for PEAK or chromsSelected() for CHROM data
void	searchAndShow_ ()
	searches using text box and plots the spectrum
void	itemDoubleClicked_ (QTreeWidgetItem *)
	called upon double click on an item; emits spectrumDoubleClicked() or chromsDoubleClicked() after some checking
void	spectrumContextMenu_ (const QPoint &)
	Display context menu; allows to open metadata window.

Private Attributes
QLineEdit *	spectra_search_box_ = nullptr
QComboBox *	spectra_combo_box_ = nullptr
TreeView *	spectra_treewidget_ = nullptr
LayerDataBase *	layer_ = nullptr
std::map< size_t, std::map< Precursor, std::vector< Size >, Precursor::MZLess > >	map_precursor_to_chrom_idx_cache_
	cache to store mapping of chromatogram precursors to chromatogram indices
const PeakMap *	last_peakmap_ = nullptr
	remember the last PeakMap that we used to fill the spectra list (and avoid rebuilding it)

Detailed Description

Hierarchical visualization and selection of spectra.

Constructor & Destructor Documentation

SpectraTreeTab()

SpectraTreeTab

(

QWidget *

parent = nullptr

)

Constructor.

~SpectraTreeTab()

~SpectraTreeTab ( )

overridedefault

Destructor.

Member Function Documentation

chromsDoubleClicked

void chromsDoubleClicked ( std::vector< int >  indices )

signal

chromsSelected

void chromsSelected ( std::vector< int >  indices )

signal

clear()

void clear ( )

overridevirtual

remove all visible data

Implements DataTabBase.

getParentIndices()

static std::vector< int > getParentIndices ( const MSExperiment &  exp )

static

Determines under which spectrum each spectrum of exp is listed in the tree.

A spectrum of MS level n is listed under the spectrum its (first) precursor refers to (the mzML 'spectrumRef', stored as meta value 'spectrum_ref' of the Precursor), if that is a preceding spectrum of MS level n-1. This holds even if other spectra were acquired in between, e.g. for SPS-MS3 scans, which are usually interleaved with the next MS2 scans. Without such a reference, a spectrum is listed under the closest preceding spectrum of MS level n-1, unless a spectrum of an even lower MS level came in between.

Parameters

[in]

exp

The spectra

Returns

For each spectrum, the index of the spectrum it is listed under, or -1 for a top-level entry

getSelectedScan()

bool getSelectedScan	(	MSExperiment &	exp,
		LayerDataBase::DataType &	current_type
	)		const

Return a copy of the currently selected spectrum/chrom (for drag'n'drop to new window) and store it either as Spectrum or Chromatogram in exp (all other data is cleared) If no spectrum/chrom is selected, false is returned and exp is empty

Parameters

[out]	exp	The currently active spec/chrom
[in]	current_type	Either DT_PEAK or DT_CHROMATOGRAM, depending on what is currently shown

Returns

true if a spec/chrom is currently active

Referenced by TOPPViewBase::copyLayer().

hasData()

bool hasData ( const LayerDataBase *  layer )

overridevirtual

docu in base class

Implements DataTabBase.

itemDoubleClicked_

void itemDoubleClicked_ ( QTreeWidgetItem *  )

privateslot

called upon double click on an item; emits spectrumDoubleClicked() or chromsDoubleClicked() after some checking

itemSelectionChange_

void itemSelectionChange_ ( QTreeWidgetItem *  , QTreeWidgetItem *    )

privateslot

emits spectrumSelected() for PEAK or chromsSelected() for CHROM data

populateSearchBox_

void populateSearchBox_ ( )

privateslot

fill the search-combo-box with current column header names

searchAndShow_

void searchAndShow_ ( )

privateslot

searches using text box and plots the spectrum

showChromatogramsAsNew1D

void showChromatogramsAsNew1D ( std::vector< int >  indices )

signal

showSpectrumAsNew1D

void showSpectrumAsNew1D ( int  )

signal

showSpectrumMetaData

void showSpectrumMetaData ( int  )

signal

spectrumContextMenu_

void spectrumContextMenu_ ( const QPoint &  )

privateslot

Display context menu; allows to open metadata window.

spectrumDoubleClicked

void spectrumDoubleClicked ( int  )

signal

spectrumSearchText_

void spectrumSearchText_ ( )

privateslot

searches for rows containing a search text (from spectra_search_box_); called when text search box is used

spectrumSelected

void spectrumSelected ( int  )

signal

updateEntries()

void updateEntries ( LayerDataBase *  cl )

overridevirtual

refresh the table using data from cl

Implements DataTabBase.

Member Data Documentation

last_peakmap_

const PeakMap* last_peakmap_ = nullptr

private

remember the last PeakMap that we used to fill the spectra list (and avoid rebuilding it)

layer_

LayerDataBase* layer_ = nullptr

private

map_precursor_to_chrom_idx_cache_

std::map<size_t, std::map<Precursor, std::vector<Size>, Precursor::MZLess> > map_precursor_to_chrom_idx_cache_

private

cache to store mapping of chromatogram precursors to chromatogram indices

spectra_combo_box_

QComboBox* spectra_combo_box_ = nullptr

private

spectra_search_box_

QLineEdit* spectra_search_box_ = nullptr

private

spectra_treewidget_

TreeView* spectra_treewidget_ = nullptr

private