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// --------------------------------------------------------------------------
// OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2013.
//
// This software is released under a three-clause BSD license:
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
// * Neither the name of any author or any participating institution
// may be used to endorse or promote products derived from this software
// without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer:Timo Sachsenberg $
// $Authors: Marc Sturm $
// --------------------------------------------------------------------------
#include <OpenMS/VISUAL/VISUALIZER/ProteinIdentificationVisualizer.h>
#include <OpenMS/DATASTRUCTURES/DateTime.h>
#include <OpenMS/VISUAL/MetaDataBrowser.h>
//QT
#include <QtGui/QLineEdit>
#include <QtGui/QValidator>
#include <QtGui/QPushButton>
#include <QtGui/QComboBox>
// STL
#include <iostream>
using namespace std;
namespace OpenMS
{
ProteinIdentificationVisualizer::ProteinIdentificationVisualizer(bool editable, QWidget * parent, MetaDataBrowser * caller) :
BaseVisualizerGUI(editable, parent),
BaseVisualizer<ProteinIdentification>()
{
pidv_caller_ = caller;
addLineEdit_(identifier_, "Identifier<br>(of corresponding PeptideIdentifications)");
addSeparator_();
addLineEdit_(engine_, "Search engine");
addLineEdit_(engine_version_, "Search engine version");
addLineEdit_(identification_date_, "Date of search");
addLineEdit_(score_type_, "Score type");
addBooleanComboBox_(higher_better_, "Higher score is better");
addDoubleLineEdit_(identification_threshold_, "Protein significance threshold");
addSeparator_();
addLabel_("Search Parameters:");
addLineEdit_(db_, "Database name");
addLineEdit_(db_version_, "Database version");
addLineEdit_(taxonomy_, "Taxonomy restriction");
addLineEdit_(charges_, "Allowed charges");
addIntLineEdit_(missed_cleavages_, "Missed Cleavages");
addDoubleLineEdit_(peak_tolerance_, "Fragment ion mass tolerance");
addDoubleLineEdit_(precursor_tolerance_, "Precursor ion mass tolerance");
addComboBox_(mass_type_, "Mass type");
addComboBox_(enzyme_, "Digestion enzyme");
addSeparator_();
addLabel_("Show protein hits with score equal or better than a threshold.");
QPushButton * button;
addLineEditButton_("Score threshold", filter_threshold_, button, "Filter");
connect(button, SIGNAL(clicked()), this, SLOT(updateTree_()));
finishAdding_();
}
void ProteinIdentificationVisualizer::load(ProteinIdentification & s, int tree_item_id)
{
ptr_ = &s;
temp_ = s;
// id of the item in the tree
tree_id_ = tree_item_id;
identification_date_->setText(temp_.getDateTime().get().toQString());
identification_threshold_->setText(QString::number(temp_.getSignificanceThreshold()));
identifier_->setText(temp_.getIdentifier().toQString());
engine_->setText(temp_.getSearchEngine().toQString());
engine_version_->setText(temp_.getSearchEngineVersion().toQString());
score_type_->setText(temp_.getScoreType().toQString());
higher_better_->setCurrentIndex(temp_.isHigherScoreBetter());
db_->setText(temp_.getSearchParameters().db.toQString());
db_version_->setText(temp_.getSearchParameters().db_version.toQString());
taxonomy_->setText(temp_.getSearchParameters().taxonomy.toQString());
charges_->setText(temp_.getSearchParameters().charges.toQString());
missed_cleavages_->setText(QString::number(temp_.getSearchParameters().missed_cleavages));
peak_tolerance_->setText(QString::number(temp_.getSearchParameters().peak_mass_tolerance));
precursor_tolerance_->setText(QString::number(temp_.getSearchParameters().precursor_tolerance));
if (!isEditable())
{
fillComboBox_(mass_type_, &ProteinIdentification::NamesOfPeakMassType[temp_.getSearchParameters().mass_type], 1);
fillComboBox_(enzyme_, &ProteinIdentification::NamesOfDigestionEnzyme[temp_.getSearchParameters().enzyme], 1);
}
else
{
fillComboBox_(mass_type_, ProteinIdentification::NamesOfPeakMassType, ProteinIdentification::SIZE_OF_PEAKMASSTYPE);
fillComboBox_(enzyme_, ProteinIdentification::NamesOfDigestionEnzyme, ProteinIdentification::SIZE_OF_DIGESTIONENZYME);
enzyme_->setCurrentIndex(temp_.getSearchParameters().enzyme);
mass_type_->setCurrentIndex(temp_.getSearchParameters().mass_type);
}
}
void ProteinIdentificationVisualizer::updateTree_()
{
if (filter_threshold_->text() != "")
{
pidv_caller_->filterHits_(filter_threshold_->text().toDouble(), temp_.isHigherScoreBetter(), tree_id_);
}
else
{
pidv_caller_->showAllHits_(tree_id_);
}
}
void ProteinIdentificationVisualizer::store()
{
ptr_->setSearchEngine(engine_->text());
ptr_->setSearchEngineVersion(engine_version_->text());
ptr_->setIdentifier(identifier_->text());
ptr_->setSignificanceThreshold(identification_threshold_->text().toFloat());
ptr_->setScoreType(score_type_->text());
ptr_->setHigherScoreBetter(higher_better_->currentIndex());
//date
DateTime date;
try
{
date.set(identification_date_->text());
ptr_->setDateTime(date);
}
catch (exception & /*e*/)
{
if (date.isNull())
{
std::string status = "Format of date in PROTEINIDENTIFICATION is not correct.";
emit sendStatus(status);
}
}
//search parameters
ProteinIdentification::SearchParameters tmp = ptr_->getSearchParameters();
tmp.db = db_->text();
tmp.db_version = db_version_->text();
tmp.taxonomy = taxonomy_->text();
tmp.charges = charges_->text();
tmp.missed_cleavages = missed_cleavages_->text().toInt();
tmp.peak_mass_tolerance = peak_tolerance_->text().toFloat();
tmp.precursor_tolerance = precursor_tolerance_->text().toFloat();
tmp.enzyme = (ProteinIdentification::DigestionEnzyme)(enzyme_->currentIndex());
tmp.mass_type = (ProteinIdentification::PeakMassType)(mass_type_->currentIndex());
ptr_->setSearchParameters(tmp);
temp_ = (*ptr_);
}
void ProteinIdentificationVisualizer::undo_()
{
load(*ptr_, tree_id_);
}
}
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