cMainWindow::cMainWindow() {
@@ -22,6 +23,7 @@ cMainWindow::cMainWindow() {
// items in the menu
menuFile = new QMenu(tr("&File"), this);
menuSearch = new QMenu(tr("&Search"), this);
+ menuTools = new QMenu(tr("&Tools"), this);
menuView = new QMenu(tr("&View"), this);
menuHelp = new QMenu(tr("&Help"), this);
@@ -36,6 +38,8 @@ cMainWindow::cMainWindow() {
actionStop = new QAction(tr("&Stop"), this);
actionStop->setEnabled(false);
actionProperties = new QAction(tr("&Settings..."), this);
+ actionBricksDatabase = new QAction(tr("&Building Blocks Editor"), this);
+ actionSequenceDatabase = new QAction(tr("&Sequence Database Editor"), this);
actionGraph = new QAction(tr("&Graph"), this);
actionLog = new QAction(tr("&Log Window"), this);
actionHTMLDocumentation = new QAction(tr("&HTML Documentation"), this);
@@ -48,7 +52,10 @@ cMainWindow::cMainWindow() {
splitter = new QSplitter(this);
about = new cAboutWidget(this);
+
graph = new cGraphWidget();
+ bricksdatabasewidget = new cBricksDatabaseWidget();
+ sequencedatabasewidget = new cSequenceDatabaseWidget();
parameterswidget = new cParametersWidget();
// additional key shortcuts
@@ -65,6 +72,8 @@ cMainWindow::cMainWindow() {
connect(actionRun, SIGNAL(triggered()), this, SLOT(run()));
connect(actionStop, SIGNAL(triggered()), this, SLOT(stop()));
connect(actionProperties, SIGNAL(triggered()), this, SLOT(showProperties()));
+ connect(actionBricksDatabase, SIGNAL(triggered()), this, SLOT(showBricksDatabase()));
+ connect(actionSequenceDatabase, SIGNAL(triggered()), this, SLOT(showSequenceDatabase()));
connect(actionGraph, SIGNAL(triggered()), this, SLOT(showGraph()));
connect(actionLog, SIGNAL(triggered()), this, SLOT(showHideLog()));
connect(actionHTMLDocumentation, SIGNAL(triggered()), this, SLOT(showHTMLDocumentation()));
@@ -84,7 +93,10 @@ cMainWindow::cMainWindow() {
menuSearch->addAction(actionStop);
menuSearch->addSeparator();
menuSearch->addAction(actionProperties);
+ menuTools->addAction(actionBricksDatabase);
+ menuTools->addAction(actionSequenceDatabase);
menuView->addAction(actionGraph);
+ menuView->addSeparator();
menuView->addAction(actionLog);
menuHelp->addAction(actionHTMLDocumentation);
menuHelp->addAction(actionPDFManual);
@@ -94,6 +106,7 @@ cMainWindow::cMainWindow() {
// add items to the main menu
menuBar->addMenu(menuFile);
menuBar->addMenu(menuSearch);
+ menuBar->addMenu(menuTools);
menuBar->addMenu(menuView);
menuBar->addMenu(menuHelp);
@@ -110,6 +123,8 @@ cMainWindow::cMainWindow() {
about->hide();
graph->hide();
+ bricksdatabasewidget->hide();
+ sequencedatabasewidget->hide();
parameterswidget->hide();
splitter->setOrientation(Qt::Vertical);
@@ -127,6 +142,7 @@ cMainWindow::cMainWindow() {
resultsbasecolumncount = 8;
resultsspecificcolumncount = 0;
+ dbsearchspecificcolumncount = 0;
resultsDetails.clear();
@@ -161,6 +177,18 @@ void cMainWindow::showAbout() {
}
+void cMainWindow::showBricksDatabase() {
+ bricksdatabasewidget->show();
+ bricksdatabasewidget->activateWindow();
+}
+
+
+void cMainWindow::showSequenceDatabase() {
+ sequencedatabasewidget->show();
+ sequencedatabasewidget->activateWindow();
+}
+
+
void cMainWindow::showGraph() {
graph->show();
graph->activateWindow();
@@ -214,7 +242,7 @@ void cMainWindow::enableRunButtonAndSettings(bool enable) {
actionRun->setEnabled(enable);
actionProperties->setEnabled(enable);
- parameterswidget->hide();
+ parameterswidget->close();
}
@@ -240,61 +268,89 @@ void cMainWindow::sendTheoreticalSpectrum(cTheoreticalSpectrum theoreticalspectr
results->setItem(row, 1, new QTableWidgetItem());
results->item(row, 1)->setData(Qt::DisplayRole, results->rowCount());
- results->setItem(row, 2, new QTableWidgetItem(stripHTML(theoreticalspectrum.getAcronymPeptideNameWithHTMLReferences()).c_str()));
- results->setItem(row, 3, new QTableWidgetItem());
- results->item(row, 3)->setData(Qt::DisplayRole, theoreticalspectrum.getCandidate().getSummaryFormula(parameters).c_str());
+ if ((parameters.mode == denovoengine) || (parameters.mode == singlecomparison) || (parameters.mode == databasesearch)) {
- results->setItem(row, 4, new QTableWidgetItem());
- results->item(row, 4)->setData(Qt::DisplayRole, getNumberOfBricks(theoreticalspectrum.getCandidate().getComposition()));
+ if (parameters.mode == databasesearch) {
+ results->setItem(row, 2, new QTableWidgetItem(theoreticalspectrum.getCandidate().getName().c_str()));
+ }
- switch (parameters.peptidetype)
- {
- case linear:
- results->setItem(row, 5, new QTableWidgetItem(parameters.searchedmodifications[theoreticalspectrum.getCandidate().getStartModifID()].name.c_str()));
- results->setItem(row, 6, new QTableWidgetItem(parameters.searchedmodifications[theoreticalspectrum.getCandidate().getEndModifID()].name.c_str()));
- break;
- case branched:
- results->setItem(row, 5, new QTableWidgetItem(parameters.searchedmodifications[theoreticalspectrum.getCandidate().getStartModifID()].name.c_str()));
- results->setItem(row, 6, new QTableWidgetItem(parameters.searchedmodifications[theoreticalspectrum.getCandidate().getMiddleModifID()].name.c_str()));
- results->setItem(row, 7, new QTableWidgetItem(parameters.searchedmodifications[theoreticalspectrum.getCandidate().getEndModifID()].name.c_str()));
- break;
- case cyclic:
- results->setItem(row, 5, new QTableWidgetItem());
- results->item(row, 5)->setData(Qt::DisplayRole, theoreticalspectrum.getNumberOfMatchedBricks());
- break;
- case lasso:
- results->setItem(row, 5, new QTableWidgetItem(parameters.searchedmodifications[theoreticalspectrum.getCandidate().getMiddleModifID()].name.c_str()));
- break;
- case linearpolysaccharide:
- results->setItem(row, 5, new QTableWidgetItem(parameters.searchedmodifications[theoreticalspectrum.getCandidate().getStartModifID()].name.c_str()));
- results->setItem(row, 6, new QTableWidgetItem(parameters.searchedmodifications[theoreticalspectrum.getCandidate().getEndModifID()].name.c_str()));
- break;
- default:
- break;
- }
+ results->setItem(row, 2 + dbsearchspecificcolumncount, new QTableWidgetItem(stripHTML(theoreticalspectrum.getAcronymPeptideNameWithHTMLReferences()).c_str()));
+
+ results->setItem(row, 3 + dbsearchspecificcolumncount, new QTableWidgetItem());
+ results->item(row, 3 + dbsearchspecificcolumncount)->setData(Qt::DisplayRole, theoreticalspectrum.getCandidate().getSummaryFormula(parameters, parameters.peptidetype).c_str());
+
+ results->setItem(row, 4 + dbsearchspecificcolumncount, new QTableWidgetItem());
+ results->item(row, 4 + dbsearchspecificcolumncount)->setData(Qt::DisplayRole, getNumberOfBricks(theoreticalspectrum.getCandidate().getComposition()));
+
+ switch (parameters.peptidetype)
+ {
+ case linear:
+ results->setItem(row, 5 + dbsearchspecificcolumncount, new QTableWidgetItem(parameters.searchedmodifications[theoreticalspectrum.getCandidate().getStartModifID()].name.c_str()));
+ results->setItem(row, 6 + dbsearchspecificcolumncount, new QTableWidgetItem(parameters.searchedmodifications[theoreticalspectrum.getCandidate().getEndModifID()].name.c_str()));
+ break;
+ case branched:
+ results->setItem(row, 5 + dbsearchspecificcolumncount, new QTableWidgetItem(parameters.searchedmodifications[theoreticalspectrum.getCandidate().getStartModifID()].name.c_str()));
+ results->setItem(row, 6 + dbsearchspecificcolumncount, new QTableWidgetItem(parameters.searchedmodifications[theoreticalspectrum.getCandidate().getMiddleModifID()].name.c_str()));
+ results->setItem(row, 7 + dbsearchspecificcolumncount, new QTableWidgetItem(parameters.searchedmodifications[theoreticalspectrum.getCandidate().getEndModifID()].name.c_str()));
+ break;
+ case cyclic:
+ results->setItem(row, 5 + dbsearchspecificcolumncount, new QTableWidgetItem());
+ results->item(row, 5 + dbsearchspecificcolumncount)->setData(Qt::DisplayRole, theoreticalspectrum.getNumberOfMatchedBricks());
+ break;
+ case lasso:
+ results->setItem(row, 5 + dbsearchspecificcolumncount, new QTableWidgetItem(parameters.searchedmodifications[theoreticalspectrum.getCandidate().getMiddleModifID()].name.c_str()));
+ break;
+ case linearpolysaccharide:
+ results->setItem(row, 5 + dbsearchspecificcolumncount, new QTableWidgetItem(parameters.searchedmodifications[theoreticalspectrum.getCandidate().getStartModifID()].name.c_str()));
+ results->setItem(row, 6 + dbsearchspecificcolumncount, new QTableWidgetItem(parameters.searchedmodifications[theoreticalspectrum.getCandidate().getEndModifID()].name.c_str()));
+ break;
+ case other:
+ default:
+ break;
+ }
- results->setItem(row, 5 + resultsspecificcolumncount, new QTableWidgetItem());
- results->item(row, 5 + resultsspecificcolumncount)->setData(Qt::DisplayRole, theoreticalspectrum.getNumberOfMatchedPeaks());
+ results->setItem(row, 5 + dbsearchspecificcolumncount + resultsspecificcolumncount, new QTableWidgetItem());
+ results->item(row, 5 + dbsearchspecificcolumncount + resultsspecificcolumncount)->setData(Qt::DisplayRole, theoreticalspectrum.getNumberOfMatchedPeaks());
- results->setItem(row, 6 + resultsspecificcolumncount, new QTableWidgetItem());
- results->item(row, 6 + resultsspecificcolumncount)->setData(Qt::DisplayRole, theoreticalspectrum.getRatioOfMatchedPeaks()*100);
+ results->setItem(row, 6 + dbsearchspecificcolumncount + resultsspecificcolumncount, new QTableWidgetItem());
+ results->item(row, 6 + dbsearchspecificcolumncount + resultsspecificcolumncount)->setData(Qt::DisplayRole, theoreticalspectrum.getRatioOfMatchedPeaks()*100);
- results->setItem(row, 7 + resultsspecificcolumncount, new QTableWidgetItem());
- results->item(row, 7 + resultsspecificcolumncount)->setData(Qt::DisplayRole, theoreticalspectrum.getWeightedIntensityScore());
+ results->setItem(row, 7 + dbsearchspecificcolumncount + resultsspecificcolumncount, new QTableWidgetItem());
+ results->item(row, 7 + dbsearchspecificcolumncount + resultsspecificcolumncount)->setData(Qt::DisplayRole, theoreticalspectrum.getWeightedIntensityScore());
- for (int i = 0; i < (int)parameters.fragmentionsfortheoreticalspectra.size(); i++) {
- results->setItem(row, resultsbasecolumncount + resultsspecificcolumncount + i, new QTableWidgetItem());
- results->item(row, resultsbasecolumncount + resultsspecificcolumncount + i)->setData(Qt::DisplayRole, theoreticalspectrum.getNumberOfMatchedPeaks(parameters.fragmentionsfortheoreticalspectra[i]));
- }
+ for (int i = 0; i < (int)parameters.fragmentionsfortheoreticalspectra.size(); i++) {
+ results->setItem(row, resultsbasecolumncount + dbsearchspecificcolumncount + resultsspecificcolumncount + i, new QTableWidgetItem());
+ results->item(row, resultsbasecolumncount + dbsearchspecificcolumncount + resultsspecificcolumncount + i)->setData(Qt::DisplayRole, theoreticalspectrum.getNumberOfMatchedPeaks(parameters.fragmentionsfortheoreticalspectra[i]));
+ }
- if (theoreticalspectrum.isValid()) {
- results->item(row, 0)->setData(Qt::DisplayRole, "*");
- for (int i = 0; i < results->columnCount(); i++) {
- results->item(row, i)->setBackground(Qt::yellow);
+ if ((parameters.peptidetype == cyclic) && parameters.enablescrambling) {
+ results->setItem(row, results->columnCount() - 1, new QTableWidgetItem());
+ results->item(row, results->columnCount() - 1)->setData(Qt::DisplayRole, theoreticalspectrum.getNumberOfScrambledPeaks());
+ }
+
+ if (theoreticalspectrum.isValid()) {
+ results->item(row, 0)->setData(Qt::DisplayRole, "*");
+ for (int i = 0; i < results->columnCount(); i++) {
+ results->item(row, i)->setBackground(Qt::yellow);
+ }
}
+
+ }
+
+
+ if (parameters.mode == dereplication) {
+ results->setItem(row, 2, new QTableWidgetItem());
+ results->item(row, 2)->setData(Qt::DisplayRole, theoreticalspectrum.getNumberOfMatchedPeaks());
+
+ results->setItem(row, 3, new QTableWidgetItem());
+ results->item(row, 3)->setData(Qt::DisplayRole, theoreticalspectrum.getRatioOfMatchedPeaks()*100);
+
+ results->setItem(row, 4, new QTableWidgetItem());
+ results->item(row, 4)->setData(Qt::DisplayRole, theoreticalspectrum.getWeightedIntensityScore());
}
+
cSpectrumDetailWidget sd;
sd.initialize(¶meters, theoreticalspectrum);
sd.setWindowTitle(("Theoretical Spectrum No. " + to_string(row+1)).c_str());
@@ -326,52 +382,88 @@ void cMainWindow::prepareColumns() {
case linearpolysaccharide:
resultsspecificcolumncount = 2;
break;
+ case other:
default:
break;
}
- string s;
- results->setColumnCount(resultsbasecolumncount + resultsspecificcolumncount + (int)parameters.fragmentionsfortheoreticalspectra.size());
+ if (parameters.mode == databasesearch) {
+ dbsearchspecificcolumncount = 1;
+ }
+ else {
+ dbsearchspecificcolumncount = 0;
+ }
- results->setHorizontalHeaderItem(0, new QTableWidgetItem("*"));
- results->setHorizontalHeaderItem(1, new QTableWidgetItem("Result ID"));
- results->setHorizontalHeaderItem(2, new QTableWidgetItem("Peptide Sequence"));
- results->setHorizontalHeaderItem(3, new QTableWidgetItem("Neutral Formula"));
- results->setHorizontalHeaderItem(4, new QTableWidgetItem("Number of Bricks"));
- switch (parameters.peptidetype)
- {
- case linear:
- results->setHorizontalHeaderItem(5, new QTableWidgetItem("N-terminal Modification"));
- results->setHorizontalHeaderItem(6, new QTableWidgetItem("C-terminal Modification"));
- break;
- case branched:
- results->setHorizontalHeaderItem(5, new QTableWidgetItem("N-terminal Modification"));
- results->setHorizontalHeaderItem(6, new QTableWidgetItem("Branch Modification"));
- results->setHorizontalHeaderItem(7, new QTableWidgetItem("C-terminal Modification"));
- break;
- case cyclic:
- results->setHorizontalHeaderItem(5, new QTableWidgetItem("Matched Bricks"));
- break;
- case lasso:
- results->setHorizontalHeaderItem(5, new QTableWidgetItem("Branch Modification"));
- break;
- case linearpolysaccharide:
- results->setHorizontalHeaderItem(5, new QTableWidgetItem("N-terminal Modification"));
- results->setHorizontalHeaderItem(6, new QTableWidgetItem("C-terminal Modification"));
- break;
- default:
- break;
- }
+ if ((parameters.mode == denovoengine) || (parameters.mode == singlecomparison) || (parameters.mode == databasesearch)) {
+
+ results->setColumnCount(resultsbasecolumncount + dbsearchspecificcolumncount + resultsspecificcolumncount + (int)parameters.fragmentionsfortheoreticalspectra.size());
+
+ if ((parameters.peptidetype == cyclic) && parameters.enablescrambling) {
+ results->setColumnCount(results->columnCount() + 1);
+ }
+
+ results->setHorizontalHeaderItem(0, new QTableWidgetItem("*"));
+ results->setHorizontalHeaderItem(1, new QTableWidgetItem("Result ID"));
+ if (parameters.mode == databasesearch) {
+ results->setHorizontalHeaderItem(2, new QTableWidgetItem("Name"));
+ }
+ results->setHorizontalHeaderItem(2 + dbsearchspecificcolumncount, new QTableWidgetItem("Peptide Sequence"));
+ results->setHorizontalHeaderItem(3 + dbsearchspecificcolumncount, new QTableWidgetItem("Summary Formula"));
+ results->setHorizontalHeaderItem(4 + dbsearchspecificcolumncount, new QTableWidgetItem("Number of Bricks"));
+
+ switch (parameters.peptidetype)
+ {
+ case linear:
+ results->setHorizontalHeaderItem(5 + dbsearchspecificcolumncount, new QTableWidgetItem("N-terminal Modification"));
+ results->setHorizontalHeaderItem(6 + dbsearchspecificcolumncount, new QTableWidgetItem("C-terminal Modification"));
+ break;
+ case branched:
+ results->setHorizontalHeaderItem(5 + dbsearchspecificcolumncount, new QTableWidgetItem("N-terminal Modification"));
+ results->setHorizontalHeaderItem(6 + dbsearchspecificcolumncount, new QTableWidgetItem("Branch Modification"));
+ results->setHorizontalHeaderItem(7 + dbsearchspecificcolumncount, new QTableWidgetItem("C-terminal Modification"));
+ break;
+ case cyclic:
+ results->setHorizontalHeaderItem(5 + dbsearchspecificcolumncount, new QTableWidgetItem("Matched Bricks"));
+ break;
+ case lasso:
+ results->setHorizontalHeaderItem(5 + dbsearchspecificcolumncount, new QTableWidgetItem("Branch Modification"));
+ break;
+ case linearpolysaccharide:
+ results->setHorizontalHeaderItem(5 + dbsearchspecificcolumncount, new QTableWidgetItem("N-terminal Modification"));
+ results->setHorizontalHeaderItem(6 + dbsearchspecificcolumncount, new QTableWidgetItem("C-terminal Modification"));
+ break;
+ case other:
+ default:
+ break;
+ }
- results->setHorizontalHeaderItem(5 + resultsspecificcolumncount, new QTableWidgetItem("Matched Peaks"));
- results->setHorizontalHeaderItem(6 + resultsspecificcolumncount, new QTableWidgetItem("Ratio of Matched Peaks [%]"));
- results->setHorizontalHeaderItem(7 + resultsspecificcolumncount, new QTableWidgetItem("Sum of Relative Intensities"));
+ results->setHorizontalHeaderItem(5 + dbsearchspecificcolumncount + resultsspecificcolumncount, new QTableWidgetItem("Matched Peaks"));
+ results->setHorizontalHeaderItem(6 + dbsearchspecificcolumncount + resultsspecificcolumncount, new QTableWidgetItem("Ratio of Matched Peaks [%]"));
+ results->setHorizontalHeaderItem(7 + dbsearchspecificcolumncount + resultsspecificcolumncount, new QTableWidgetItem("Sum of Relative Intensities"));
+
+ for (int i = 0; i < (int)parameters.fragmentionsfortheoreticalspectra.size(); i++) {
+ results->setHorizontalHeaderItem(resultsbasecolumncount + dbsearchspecificcolumncount + resultsspecificcolumncount + i, new QTableWidgetItem(parameters.fragmentdefinitions[(fragmentIonType)parameters.fragmentionsfortheoreticalspectra[i]].name.c_str()));
+ }
+
+ if ((parameters.peptidetype == cyclic) && parameters.enablescrambling) {
+ results->setHorizontalHeaderItem(results->columnCount() - 1, new QTableWidgetItem("Scrambled Peaks"));
+ }
+
+ }
+
- for (int i = 0; i < (int)parameters.fragmentionsfortheoreticalspectra.size(); i++) {
- results->setHorizontalHeaderItem(resultsbasecolumncount + resultsspecificcolumncount + i, new QTableWidgetItem(parameters.fragmentdefinitions[(fragmentIonType)parameters.fragmentionsfortheoreticalspectra[i]].name.c_str()));
+ if (parameters.mode == dereplication) {
+ results->setColumnCount(5);
+ results->setHorizontalHeaderItem(0, new QTableWidgetItem("*"));
+ results->setHorizontalHeaderItem(1, new QTableWidgetItem("Result ID"));
+ results->setHorizontalHeaderItem(2, new QTableWidgetItem("Matched Peaks"));
+ results->setHorizontalHeaderItem(3, new QTableWidgetItem("Ratio of Matched Peaks [%]"));
+ results->setHorizontalHeaderItem(4, new QTableWidgetItem("Sum of Relative Intensities"));
}
+
+
results->resizeColumnsToContents();
resultsheadersort.resize(results->columnCount());
@@ -556,7 +648,7 @@ void cMainWindow::exportToHTML() {
out << "\n" << parameters.printToString().c_str() << "
";
- if (parameters.mode == 0) {
+ if (parameters.mode == denovoengine) {
out << "De Novo Graph
\n";
@@ -600,6 +692,12 @@ void cMainWindow::saveResultsFile() {
if (outfile.is_open()) {
int size;
+ // write the application name and version
+ QString appinfo = appname + " " + appversion;
+ size = (int)appinfo.toStdString().size();
+ outfile.write((char *)&size, sizeof(int));
+ outfile.write(appinfo.toStdString().c_str(), size);
+
// store graph window
graph->store(outfile);
@@ -643,6 +741,23 @@ void cMainWindow::openResultsFile() {
string s;
cTheoreticalSpectrum theoreticalspectrum;
+ // read the application name and version
+ infile.read((char *)&size, sizeof(int));
+ s.resize(size);
+ infile.read(&s[0], s.size());
+ QString appinfo = appname + " " + appversion;
+ if (appinfo.toStdString().compare(s) != 0) {
+ QMessageBox msgBox;
+ QString errstr = "The results file cannot be read because it was created by different version ";
+ errstr += s.c_str();
+ errstr += ".";
+ msgBox.setText(errstr);
+ msgBox.exec();
+
+ infile.close();
+ return;
+ }
+
deleteResults();
resultsDetails.clear();
@@ -696,6 +811,7 @@ cMainWindow::~cMainWindow() {
delete menuFile;
delete menuSearch;
+ delete menuTools;
delete menuView;
delete menuHelp;
@@ -706,6 +822,8 @@ cMainWindow::~cMainWindow() {
delete actionQuit;
delete actionProperties;
delete actionRun;
+ delete actionBricksDatabase;
+ delete actionSequenceDatabase;
delete actionGraph;
delete actionLog;
delete actionHTMLDocumentation;
@@ -718,6 +836,8 @@ cMainWindow::~cMainWindow() {
delete about;
delete graph;
+ delete bricksdatabasewidget;
+ delete sequencedatabasewidget;
delete parameterswidget;
}
diff --git a/CycloBranch/gui/cMainWindow.h b/CycloBranch/gui/cMainWindow.h
index 779a713..6a780ee 100644
--- a/CycloBranch/gui/cMainWindow.h
+++ b/CycloBranch/gui/cMainWindow.h
@@ -16,6 +16,8 @@
#include "gui/cGraphWidget.h"
#include "gui/cParametersWidget.h"
#include "gui/cSpectrumDetailWidget.h"
+#include "gui/cBricksDatabaseWidget.h"
+#include "gui/cSequenceDatabaseWidget.h"
#include "gui/cMainThread.h"
// forward declaration
@@ -54,6 +56,7 @@ class cMainWindow : public QMainWindow
// items in the menu
QMenu* menuFile;
QMenu* menuSearch;
+ QMenu* menuTools;
QMenu* menuView;
QMenu* menuHelp;
@@ -66,6 +69,8 @@ class cMainWindow : public QMainWindow
QAction* actionRun;
QAction* actionStop;
QAction* actionProperties;
+ QAction* actionBricksDatabase;
+ QAction* actionSequenceDatabase;
QAction* actionGraph;
QAction* actionLog;
QAction* actionHTMLDocumentation;
@@ -82,10 +87,13 @@ class cMainWindow : public QMainWindow
cAboutWidget* about;
cGraphWidget* graph;
+ cBricksDatabaseWidget* bricksdatabasewidget;
+ cSequenceDatabaseWidget* sequencedatabasewidget;
cParametersWidget* parameterswidget;
int resultsbasecolumncount;
int resultsspecificcolumncount;
+ int dbsearchspecificcolumncount;
vector resultsheadersort;
@@ -103,6 +111,10 @@ private slots:
void showAbout();
+ void showBricksDatabase();
+
+ void showSequenceDatabase();
+
void showGraph();
void showProperties();
diff --git a/CycloBranch/gui/cParametersWidget.cpp b/CycloBranch/gui/cParametersWidget.cpp
index f5b17b8..6848117 100644
--- a/CycloBranch/gui/cParametersWidget.cpp
+++ b/CycloBranch/gui/cParametersWidget.cpp
@@ -16,6 +16,7 @@
#include
#include
#include
+#include
cParametersWidget::cParametersWidget() {
@@ -25,6 +26,7 @@ cParametersWidget::cParametersWidget() {
oldsettingsfile = "";
peaklistfilename = "";
brickdatabasefilename = "";
+ sequencedatabasefilename = "";
stdbuttons = new QDialogButtonBox(QDialogButtonBox::Ok | QDialogButtonBox::Apply | QDialogButtonBox::Cancel);
stdbuttons->button(QDialogButtonBox::Ok)->setToolTip("Accept changes and hide window.");
@@ -54,6 +56,7 @@ cParametersWidget::cParametersWidget() {
peptidetype->addItem(tr("Branched"));
peptidetype->addItem(tr("Lasso"));
peptidetype->addItem(tr("Linear polysaccharide (beta version)"));
+ //peptidetype->addItem(tr("Other"));
peaklistformlayout->addRow(tr("Peptide Type: "), peptidetype);
peaklistline = new QLineEdit();
@@ -201,9 +204,11 @@ cParametersWidget::cParametersWidget() {
applicationformlayout = new QFormLayout();
mode = new QComboBox();
- mode->setToolTip("De Novo Search Engine (identification mode) - the default mode of the application.\nCompare Spectrum of Searched Sequence with Peaklist (annotation mode) - a theoretical spectrum is generated for an input \"Searched Peptide Sequence\" and it is compared with the peaklist.");
+ mode->setToolTip("De Novo Search Engine (identification mode) - the default mode of the application.\nCompare Peaklist with Spectrum of Searched Sequence (annotation mode) - a theoretical spectrum is generated for an input \"Searched Peptide Sequence\" and it is compared with the peaklist.\nCompare Peaklist with Database - MS/MS data (identification mode) - the peaklist is compared with theoretical spectra generated from a database of sequences.\nCompare Peaklist with Database - MS data (identification mode) - the peaklist is compared with theoretical peaks generated from a database of sequences.");
mode->addItem(tr("De Novo Search Engine"));
- mode->addItem(tr("Compare Spectrum of Searched Sequence with Peaklist"));
+ mode->addItem(tr("Compare Peaklist with Spectrum of Searched Sequence"));
+ mode->addItem(tr("Compare Peaklist with Database - MS/MS data"));
+ mode->addItem(tr("Compare Peaklist with Database - MS data"));
applicationformlayout->addRow(tr("Mode: "), mode);
maximumnumberofthreads = new QSpinBox();
@@ -215,8 +220,8 @@ cParametersWidget::cParametersWidget() {
scoretype = new QComboBox();
scoretype->setToolTip("A score for peptide-spectrum matches.");
scoretype->addItem(tr("Number of b-ions"));
- scoretype->addItem(tr("Number of b-ions + water loss b-ions"));
- scoretype->addItem(tr("Number of b-ions + ammonia loss b-ions"));
+ scoretype->addItem(tr("Number of b-ions + dehydrated b-ions"));
+ scoretype->addItem(tr("Number of b-ions + deamidated b-ions"));
scoretype->addItem(tr("Number of y-ions + b-ions (not for cyclic peptides)"));
scoretype->addItem(tr("Number of y-ions (not for cyclic peptides)"));
scoretype->addItem(tr("Sum of relative intensities of matched peaks"));
@@ -240,7 +245,7 @@ cParametersWidget::cParametersWidget() {
applicationformlayout->addRow(tr("Fragment Ion Types in Theoretical Spectra: "), fragmentiontypes);
clearhitswithoutparent = new QCheckBox();
- clearhitswithoutparent->setToolTip("When checked, a hit of a peak is not considered when corresponding parent peak is not hit (e.g., a hit of a water loss b-ion is not considered as a hit when corresponding b-ion has not been hit).");
+ clearhitswithoutparent->setToolTip("When checked, a hit of a peak is not considered when corresponding parent peak is not hit (e.g., a hit of a dehydrated b-ion is not considered as a hit when corresponding b-ion has not been hit).");
applicationformlayout->addRow(tr("Remove Hits of Fragments without Hits of Parent Fragments: "), clearhitswithoutparent);
cyclicnterminus = new QCheckBox();
@@ -272,10 +277,25 @@ cParametersWidget::cParametersWidget() {
denovographgroupbox->setLayout(denovographformlayout);
+ databasesearchformlayout = new QFormLayout();
+
+ sequencedatabaseline = new QLineEdit();
+ sequencedatabaseline->setToolTip("Select the txt file containing a database of sequences.");
+ sequencedatabasebutton = new QPushButton("Select");
+ sequencedatabasebutton->setToolTip("Select the txt file containing a database of sequences.");
+ sequencedatabaselayout = new QHBoxLayout();
+ sequencedatabaselayout->addWidget(sequencedatabaseline);
+ sequencedatabaselayout->addWidget(sequencedatabasebutton);
+ databasesearchformlayout->addRow(tr("Sequence Database File: "), sequencedatabaselayout);
+
+ databasesearchgroupbox = new QGroupBox("Database Search");
+ databasesearchgroupbox->setLayout(databasesearchformlayout);
+
+
searchedsequenceformlayout = new QFormLayout();
searchedsequence = new QLineEdit();
- searchedsequence->setToolTip("A peptide sequence which you are searching for or a peptide sequence tag.\nA peptide sequence must be entered when \"Mode\" is set up to \"Compare Spectrum of Searched Sequence with Peaklist\".\nOtherwise, it is similar to the option \"Peptide Sequence Tag\" with a difference that a peptide sequence candidate is not removed from the search but it is just highlighted in an output report of peptide sequence candidates.");
+ searchedsequence->setToolTip("A peptide sequence which you are searching for or a peptide sequence tag.\nA peptide sequence must be entered when \"Mode\" is set up to \"Compare Peaklist with Spectrum of Searched Sequence\".\nOtherwise, it is similar to the option \"Peptide Sequence Tag\" with a difference that a peptide sequence candidate is not removed from the search but it is just highlighted in an output report of peptide sequence candidates.");
searchedsequence->setMaxLength(1024*1024);
searchedsequenceformlayout->addRow(tr("Sequence: "), searchedsequence);
@@ -303,6 +323,7 @@ cParametersWidget::cParametersWidget() {
vlayout2 = new QVBoxLayout();
vlayout2->addWidget(applicationgroupbox);
vlayout2->addWidget(denovographgroupbox);
+ vlayout2->addWidget(databasesearchgroupbox);
vlayout2->addWidget(searchedsequencegroupbox);
vlayout2->addStretch(1);
@@ -334,6 +355,7 @@ cParametersWidget::cParametersWidget() {
connect(peptidetype, SIGNAL(currentIndexChanged(int)), this, SLOT(updateSettingsWhenPeptideTypeChanged(int)));
connect(mode, SIGNAL(currentIndexChanged(int)), this, SLOT(updateSettingsWhenModeChanged(int)));
connect(fragmentiontypes, SIGNAL(resetReleased()), this, SLOT(resetFragmentIonTypes()));
+ connect(sequencedatabasebutton, SIGNAL(released()), this, SLOT(sequenceDatabaseButtonReleased()));
updateSettingsWhenPeptideTypeChanged(peptidetype->currentIndex());
@@ -346,6 +368,7 @@ cParametersWidget::cParametersWidget() {
lastdirsavesettings = "./Settings/";
lastdirselectpeaklist = "./PeakLists/";
lastdirselectbricksdatabase = "./BrickDatabases/";
+ lastdirselectsequencedatabase = "./SequenceDatabases/";
}
@@ -412,6 +435,12 @@ cParametersWidget::~cParametersWidget() {
delete denovographformlayout;
delete denovographgroupbox;
+ delete sequencedatabaseline;
+ delete sequencedatabasebutton;
+ delete sequencedatabaselayout;
+ delete databasesearchformlayout;
+ delete databasesearchgroupbox;
+
delete searchedsequence;
delete searchedsequenceNtermmodif;
delete searchedsequenceCtermmodif;
@@ -572,6 +601,8 @@ void cParametersWidget::loadSettings() {
blindedges->setCurrentIndex(settings.value("blindedges", 2).toInt());
+ sequencedatabaseline->setText(settings.value("sequencedatabase", "").toString());
+
searchedsequence->setText(settings.value("searchedsequence", "").toString());
searchedsequenceNtermmodif->setText(settings.value("searchedsequenceNtermmodif", "").toString());
searchedsequenceCtermmodif->setText(settings.value("searchedsequenceCtermmodif", "").toString());
@@ -651,6 +682,8 @@ void cParametersWidget::saveSettings() {
settings.setValue("blindedges", blindedges->currentIndex());
+ settings.setValue("sequencedatabase", sequencedatabaseline->text());
+
settings.setValue("searchedsequence", searchedsequence->text());
settings.setValue("searchedsequenceNtermmodif", searchedsequenceNtermmodif->text());
settings.setValue("searchedsequenceCtermmodif", searchedsequenceCtermmodif->text());
@@ -683,7 +716,7 @@ void cParametersWidget::peaklistButtonReleased() {
void cParametersWidget::brickDatabaseButtonReleased() {
- QString filename = QFileDialog::getOpenFileName(this, tr("Select Brick Database..."), lastdirselectbricksdatabase, tr("Text Files (*.txt)"));
+ QString filename = QFileDialog::getOpenFileName(this, tr("Select Building Blocks Database..."), lastdirselectbricksdatabase, tr("Text Files (*.txt)"));
lastdirselectbricksdatabase = filename;
if (filename.toStdString().compare("") != 0) {
@@ -693,6 +726,17 @@ void cParametersWidget::brickDatabaseButtonReleased() {
}
+void cParametersWidget::sequenceDatabaseButtonReleased() {
+ QString filename = QFileDialog::getOpenFileName(this, tr("Select Sequence Database..."), lastdirselectsequencedatabase, tr("Text Files (*.txt)"));
+ lastdirselectsequencedatabase = filename;
+
+ if (filename.toStdString().compare("") != 0) {
+ sequencedatabasefilename = filename.toStdString();
+ sequencedatabaseline->setText(filename);
+ }
+}
+
+
void cParametersWidget::modificationsInsertButtonReleased() {
modificationsTableInsertRow();
}
@@ -703,7 +747,31 @@ void cParametersWidget::modificationsRemoveButtonReleased() {
}
-void cParametersWidget::updateParameters() {
+bool cParametersWidget::updateParameters() {
+ QMessageBox msgBox;
+ QString errstr;
+
+ if (peaklistline->text().toStdString().compare("") == 0) {
+ errstr = "A peaklist must be specified.";
+ msgBox.setText(errstr);
+ msgBox.exec();
+ return false;
+ }
+
+ if ((brickdatabaseline->text().toStdString().compare("") == 0) && (((modeType)mode->currentIndex() == denovoengine) || ((modeType)mode->currentIndex() == singlecomparison) || ((modeType)mode->currentIndex() == databasesearch))) {
+ errstr = "A database of building blocks must be specified.";
+ msgBox.setText(errstr);
+ msgBox.exec();
+ return false;
+ }
+
+ if ((sequencedatabaseline->text().toStdString().compare("") == 0) && (((modeType)mode->currentIndex() == databasesearch) || ((modeType)mode->currentIndex() == dereplication))) {
+ errstr = "A sequence database must be specified.";
+ msgBox.setText(errstr);
+ msgBox.exec();
+ return false;
+ }
+
parameters.peptidetype = (peptideType)peptidetype->currentIndex();
parameters.peaklistfilename = peaklistline->text().toStdString();
parameters.precursormass = precursormass->value();
@@ -740,7 +808,7 @@ void cParametersWidget::updateParameters() {
i++;
}
- parameters.mode = mode->currentIndex();
+ parameters.mode = (modeType)mode->currentIndex();
parameters.maximumnumberofthreads = maximumnumberofthreads->value();
parameters.scoretype = (scoreType)scoretype->currentIndex();
parameters.hitsreported = hitsreported->value();
@@ -749,23 +817,30 @@ void cParametersWidget::updateParameters() {
parameters.fragmentionsfortheoreticalspectra.clear();
int start;
- switch ((peptideType)peptidetype->currentIndex())
- {
- case linear:
- case branched:
- start = b_ion;
- break;
- case cyclic:
- start = b_ion;
- break;
- case lasso:
- start = b_ion;
- break;
- case linearpolysaccharide:
- start = ms_nterminal_ion_hplus;
- break;
- default:
- break;
+
+ if ((modeType)mode->currentIndex() == dereplication) {
+ start = ms_hplus;
+ }
+ else {
+ switch ((peptideType)peptidetype->currentIndex())
+ {
+ case linear:
+ case branched:
+ start = b_ion;
+ break;
+ case cyclic:
+ start = b_ion;
+ break;
+ case lasso:
+ start = b_ion;
+ break;
+ case linearpolysaccharide:
+ start = ms_nterminal_ion_hplus;
+ break;
+ case other:
+ default:
+ break;
+ }
}
for (int i = 0; i < fragmentiontypes->getList()->count(); i++) {
@@ -783,6 +858,8 @@ void cParametersWidget::updateParameters() {
parameters.blindedges = blindedges->currentIndex();
+ parameters.sequencedatabasefilename = sequencedatabaseline->text().toStdString();
+
parameters.searchedsequence = searchedsequence->text().toStdString();
parameters.originalsearchedsequence = parameters.searchedsequence;
parameters.searchedsequenceNtermmodif = searchedsequenceNtermmodif->text().toStdString();
@@ -790,12 +867,15 @@ void cParametersWidget::updateParameters() {
parameters.searchedsequenceTmodif = searchedsequenceTmodif->text().toStdString();
oldsettingsfile = settingsfile;
+
+ return true;
}
void cParametersWidget::updateParametersAndHide() {
- updateParameters();
- hide();
+ if (updateParameters()) {
+ hide();
+ }
}
@@ -845,23 +925,29 @@ void cParametersWidget::restoreParameters() {
sequencetag->setText(parameters.sequencetag.c_str());
int start;
- switch (parameters.peptidetype)
- {
- case linear:
- case branched:
- start = b_ion;
- break;
- case cyclic:
- start = b_ion;
- break;
- case lasso:
- start = b_ion;
- break;
- case linearpolysaccharide:
- start = ms_nterminal_ion_hplus;
- break;
- default:
- break;
+ if (parameters.mode == dereplication) {
+ start = ms_hplus;
+ }
+ else {
+ switch (parameters.peptidetype)
+ {
+ case linear:
+ case branched:
+ start = b_ion;
+ break;
+ case cyclic:
+ start = b_ion;
+ break;
+ case lasso:
+ start = b_ion;
+ break;
+ case linearpolysaccharide:
+ start = ms_nterminal_ion_hplus;
+ break;
+ case other:
+ default:
+ break;
+ }
}
for (int i = 0; i < (int)parameters.fragmentionsfortheoreticalspectra.size(); i++) {
@@ -875,6 +961,8 @@ void cParametersWidget::restoreParameters() {
blindedges->setCurrentIndex(parameters.blindedges);
+ sequencedatabaseline->setText(parameters.sequencedatabasefilename.c_str());
+
searchedsequence->setText(parameters.searchedsequence.c_str());
searchedsequenceNtermmodif->setText(parameters.searchedsequenceNtermmodif.c_str());
searchedsequenceCtermmodif->setText(parameters.searchedsequenceCtermmodif.c_str());
@@ -943,6 +1031,7 @@ void cParametersWidget::updateSettingsWhenPeptideTypeChanged(int index) {
cycliccterminus->setDisabled(true);
enablescrambling->setDisabled(true);
break;
+ case other:
default:
break;
}
@@ -951,11 +1040,15 @@ void cParametersWidget::updateSettingsWhenPeptideTypeChanged(int index) {
void cParametersWidget::updateSettingsWhenModeChanged(int index) {
- switch (index)
+ switch ((modeType)index)
{
- case 0:
+ case denovoengine:
+ peptidetype->setDisabled(false);
precursormass->setDisabled(false);
+ precursorcharge->setDisabled(false);
precursormasserrortolerance->setDisabled(false);
+ brickdatabaseline->setDisabled(false);
+ brickdatabasebutton->setDisabled(false);
maximumbricksincombinationbegin->setDisabled(false);
maximumbricksincombinationmiddle->setDisabled(false);
maximumbricksincombinationend->setDisabled(false);
@@ -965,11 +1058,69 @@ void cParametersWidget::updateSettingsWhenModeChanged(int index) {
scoretype->setDisabled(false);
hitsreported->setDisabled(false);
sequencetag->setDisabled(false);
+ fragmentiontypes->setDisabled(false);
+ clearhitswithoutparent->setDisabled(false);
denovographgroupbox->setDisabled(false);
+ databasesearchgroupbox->setDisabled(true);
+ searchedsequence->setDisabled(false);
+
+ updateSettingsWhenPeptideTypeChanged(peptidetype->currentIndex());
+ break;
+ case singlecomparison:
+ peptidetype->setDisabled(false);
+ precursormass->setDisabled(true);
+ precursorcharge->setDisabled(false);
+ precursormasserrortolerance->setDisabled(true);
+ brickdatabaseline->setDisabled(false);
+ brickdatabasebutton->setDisabled(false);
+ maximumbricksincombinationbegin->setDisabled(true);
+ maximumbricksincombinationmiddle->setDisabled(true);
+ maximumbricksincombinationend->setDisabled(true);
+ maximumcumulativemass->setDisabled(true);
+ generatebrickspermutations->setDisabled(true);
+ maximumnumberofthreads->setDisabled(true);
+ scoretype->setDisabled(true);
+ hitsreported->setDisabled(true);
+ sequencetag->setDisabled(true);
+ fragmentiontypes->setDisabled(false);
+ clearhitswithoutparent->setDisabled(false);
+ denovographgroupbox->setDisabled(true);
+ databasesearchgroupbox->setDisabled(true);
+ searchedsequence->setDisabled(false);
+
+ updateSettingsWhenPeptideTypeChanged(peptidetype->currentIndex());
+ break;
+ case databasesearch:
+ peptidetype->setDisabled(false);
+ precursormass->setDisabled(false);
+ precursorcharge->setDisabled(false);
+ precursormasserrortolerance->setDisabled(false);
+ brickdatabaseline->setDisabled(false);
+ brickdatabasebutton->setDisabled(false);
+ maximumbricksincombinationbegin->setDisabled(true);
+ maximumbricksincombinationmiddle->setDisabled(true);
+ maximumbricksincombinationend->setDisabled(true);
+ maximumcumulativemass->setDisabled(true);
+ generatebrickspermutations->setDisabled(true);
+ maximumnumberofthreads->setDisabled(false);
+ scoretype->setDisabled(false);
+ hitsreported->setDisabled(false);
+ sequencetag->setDisabled(false);
+ fragmentiontypes->setDisabled(false);
+ clearhitswithoutparent->setDisabled(false);
+ denovographgroupbox->setDisabled(true);
+ databasesearchgroupbox->setDisabled(false);
+ searchedsequence->setDisabled(false);
+
+ updateSettingsWhenPeptideTypeChanged(peptidetype->currentIndex());
break;
- case 1:
+ case dereplication:
+ peptidetype->setDisabled(true);
precursormass->setDisabled(true);
+ precursorcharge->setDisabled(false);
precursormasserrortolerance->setDisabled(true);
+ brickdatabaseline->setDisabled(true);
+ brickdatabasebutton->setDisabled(true);
maximumbricksincombinationbegin->setDisabled(true);
maximumbricksincombinationmiddle->setDisabled(true);
maximumbricksincombinationend->setDisabled(true);
@@ -979,7 +1130,21 @@ void cParametersWidget::updateSettingsWhenModeChanged(int index) {
scoretype->setDisabled(true);
hitsreported->setDisabled(true);
sequencetag->setDisabled(true);
+ fragmentiontypes->setDisabled(false);
+ clearhitswithoutparent->setDisabled(true);
denovographgroupbox->setDisabled(true);
+ databasesearchgroupbox->setDisabled(false);
+ searchedsequence->setDisabled(true);
+
+ resetFragmentIonTypes();
+
+ modificationsgroupbox->setDisabled(true);
+ searchedsequenceNtermmodif->setDisabled(true);
+ searchedsequenceCtermmodif->setDisabled(true);
+ searchedsequenceTmodif->setDisabled(true);
+ cyclicnterminus->setDisabled(true);
+ cycliccterminus->setDisabled(true);
+ enablescrambling->setDisabled(true);
break;
default:
break;
@@ -992,26 +1157,34 @@ void cParametersWidget::resetFragmentIonTypes() {
fragmentiontypes->getList()->clear();
fragmentIonType start, end;
- switch ((peptideType)peptidetype->currentIndex()) {
- case linear:
- case branched:
- start = b_ion;
- end = y_ion_water_and_ammonia_loss;
- break;
- case cyclic:
- start = b_ion;
- end = a_ion_water_and_ammonia_loss;
- break;
- case lasso:
- start = b_ion;
- end = y_ion_water_and_ammonia_loss;
- break;
- case linearpolysaccharide:
- start = ms_nterminal_ion_hplus;
- end = ms_cterminal_ion_kplus;
- break;
- default:
- break;
+
+ if ((modeType)mode->currentIndex() == dereplication) {
+ start = ms_hplus;
+ end = ms_MFe4H;
+ }
+ else {
+ switch ((peptideType)peptidetype->currentIndex()) {
+ case linear:
+ case branched:
+ start = b_ion;
+ end = y_ion_water_and_ammonia_loss;
+ break;
+ case cyclic:
+ start = b_ion;
+ end = a_ion_water_and_ammonia_loss;
+ break;
+ case lasso:
+ start = b_ion;
+ end = y_ion_water_and_ammonia_loss;
+ break;
+ case linearpolysaccharide:
+ start = ms_nterminal_ion_hplus;
+ end = ms_cterminal_ion_kplus;
+ break;
+ case other:
+ default:
+ break;
+ }
}
for (int i = start; i <= end; i++) {
diff --git a/CycloBranch/gui/cParametersWidget.h b/CycloBranch/gui/cParametersWidget.h
index c2ece92..b5661da 100644
--- a/CycloBranch/gui/cParametersWidget.h
+++ b/CycloBranch/gui/cParametersWidget.h
@@ -35,6 +35,7 @@ class QGroupBox;
class QCheckBox;
class QTableWidget;
class QListWidget;
+class QMessageBox;
/**
@@ -148,6 +149,13 @@ class cParametersWidget : public QWidget
QFormLayout* denovographformlayout;
QComboBox* blindedges;
+ QGroupBox* databasesearchgroupbox;
+ QFormLayout* databasesearchformlayout;
+ QLineEdit* sequencedatabaseline;
+ QPushButton* sequencedatabasebutton;
+ QHBoxLayout* sequencedatabaselayout;
+ string sequencedatabasefilename;
+
QGroupBox* searchedsequencegroupbox;
QFormLayout* searchedsequenceformlayout;
QLineEdit* searchedsequence;
@@ -159,6 +167,7 @@ class cParametersWidget : public QWidget
QString lastdirsavesettings;
QString lastdirselectpeaklist;
QString lastdirselectbricksdatabase;
+ QString lastdirselectsequencedatabase;
void deleteRow(int number);
@@ -181,11 +190,13 @@ private slots:
void brickDatabaseButtonReleased();
+ void sequenceDatabaseButtonReleased();
+
void modificationsInsertButtonReleased();
void modificationsRemoveButtonReleased();
- void updateParameters();
+ bool updateParameters();
void updateParametersAndHide();
diff --git a/CycloBranch/gui/cSequenceDatabaseWidget.cpp b/CycloBranch/gui/cSequenceDatabaseWidget.cpp
new file mode 100644
index 0000000..819b1ea
--- /dev/null
+++ b/CycloBranch/gui/cSequenceDatabaseWidget.cpp
@@ -0,0 +1,534 @@
+#include "gui/cSequenceDatabaseWidget.h"
+#include "gui/cMainThread.h"
+
+#include
+#include
+#include
+#include
+#include
+#include
+#include
+#include
+#include
+#include
+#include
+#include
+
+
+cSequenceDatabaseWidget::cSequenceDatabaseWidget(QWidget* parent) {
+ this->parent = parent;
+
+ setWindowTitle("Sequence Database Editor");
+
+ insertrow = new QPushButton(tr("Add Row"));
+ insertrow->setToolTip("Add a new row.");
+ removechecked = new QPushButton(tr(" Remove Rows "));
+ removechecked->setToolTip("Remove selected rows.");
+
+ close = new QPushButton(tr("Close"));
+ close->setToolTip("Close the window.");
+ load = new QPushButton(tr("Load"));
+ load->setToolTip("Load the database of sequences.");
+ save = new QPushButton(QString("Save"));
+ save->setToolTip("Save the database of sequences in the current file. When a file has not been loaded yet, the \"Save As ...\" file dialog is opened.");
+ saveas = new QPushButton(tr("Save As..."));
+ saveas->setToolTip("Save the database of sequences into a file.");
+
+ buttons = new QHBoxLayout();
+ buttons->addWidget(close);
+ buttons->addStretch(1);
+ buttons->addWidget(insertrow);
+ buttons->addWidget(removechecked);
+ buttons->addStretch(10);
+ buttons->addWidget(load);
+ buttons->addWidget(save);
+ buttons->addWidget(saveas);
+
+ database = new QTableWidget(0, 0, this);
+ database->setColumnCount(11);
+ database->setHorizontalHeaderItem(0, new QTableWidgetItem(""));
+ database->setHorizontalHeaderItem(1, new QTableWidgetItem("Type"));
+ database->setHorizontalHeaderItem(2, new QTableWidgetItem("Name"));
+ database->setHorizontalHeaderItem(3, new QTableWidgetItem("Summary Formula"));
+ database->setHorizontalHeaderItem(4, new QTableWidgetItem("Monoisotopic Mass"));
+ database->setHorizontalHeaderItem(5, new QTableWidgetItem("Sequence"));
+ database->setHorizontalHeaderItem(6, new QTableWidgetItem("N-terminal Modification"));
+ database->setHorizontalHeaderItem(7, new QTableWidgetItem("C-terminal Modification"));
+ database->setHorizontalHeaderItem(8, new QTableWidgetItem("Branch Modification"));
+ database->setHorizontalHeaderItem(9, new QTableWidgetItem("Reference"));
+ database->setHorizontalHeaderItem(10, new QTableWidgetItem("Preview"));
+ database->horizontalHeader()->setStretchLastSection(true);
+ for (int i = 0; i < database->columnCount(); i++) {
+ database->resizeColumnToContents(i);
+ }
+
+ headersort.resize(database->columnCount());
+ for (int i = 0; i < database->columnCount(); i++) {
+ headersort[i] = -1;
+ }
+
+ mainlayout = new QVBoxLayout();
+ mainlayout->addWidget(database);
+ mainlayout->addLayout(buttons);
+
+ progress = new QProgressDialog(this);
+ progress->setCancelButton(0);
+ progress->setMinimumDuration(1000);
+ progress->setWindowModality(Qt::WindowModal);
+
+ connect(database->horizontalHeader(), SIGNAL(sectionDoubleClicked(int)), this, SLOT(headerItemDoubleClicked(int)));
+ connect(database, SIGNAL(itemChanged(QTableWidgetItem *)), this, SLOT(itemChanged(QTableWidgetItem *)));
+ connect(insertrow, SIGNAL(released()), this, SLOT(addRow()));
+ connect(removechecked, SIGNAL(released()), this, SLOT(removeEmptyRows()));
+ connect(close, SIGNAL(released()), this, SLOT(closeWindow()));
+ connect(load, SIGNAL(released()), this, SLOT(loadDatabase()));
+ connect(save, SIGNAL(released()), this, SLOT(saveDatabase()));
+ connect(saveas, SIGNAL(released()), this, SLOT(saveDatabaseAs()));
+
+ setLayout(mainlayout);
+
+ resize(1280, 700);
+
+ databasefile = "";
+ lastdir = "./SequenceDatabases/";
+ sequences.clear();
+}
+
+
+cSequenceDatabaseWidget::~cSequenceDatabaseWidget() {
+ deleteTable(false);
+
+ for (int i = 0; i < database->columnCount(); i++) {
+ delete database->horizontalHeaderItem(i);
+ }
+
+ database->setColumnCount(0);
+
+ delete insertrow;
+ delete removechecked;
+ delete close;
+ delete load;
+ delete save;
+ delete saveas;
+ delete database;
+ delete buttons;
+ delete mainlayout;
+ delete progress;
+}
+
+
+void cSequenceDatabaseWidget::closeEvent(QCloseEvent *event) {
+ closeWindow();
+}
+
+
+void cSequenceDatabaseWidget::deleteTable(bool enableprogress) {
+ if (enableprogress) {
+ progress->setLabelText("Clearing the table...");
+ progress->setMinimum(0);
+ progress->setValue(1);
+ progress->setMaximum(database->rowCount());
+ progress->show();
+ }
+
+ for (int i = 0; i < database->rowCount(); i++) {
+ for (int j = 0; j < database->columnCount(); j++) {
+ if ((j == 0) || (j == 1) || (j == 10)) {
+ delete database->cellWidget(i, j);
+ }
+ else {
+ delete database->item(i, j);
+ }
+ }
+
+ if (enableprogress && ((i == 0) || ((i - 1)/100 != i/100))) {
+ progress->setValue(i);
+ }
+ }
+
+ if (enableprogress) {
+ progress->setValue(database->rowCount());
+ progress->hide();
+ }
+ database->setRowCount(0);
+}
+
+
+void cSequenceDatabaseWidget::removeRow(int row) {
+ for (int i = 0; i < database->columnCount(); i++) {
+ if ((i == 0) || (i == 1) || (i == 10)) {
+ delete database->cellWidget(row, i);
+ }
+ else {
+ delete database->item(row, i);
+ }
+ }
+ database->removeRow(row);
+}
+
+
+bool cSequenceDatabaseWidget::checkTable() {
+
+ // check summary formulas
+ for (int i = 0; i < database->rowCount(); i++) {
+ if (!checkFormula(i, database->item(i, 3)->text().toStdString())) {
+ return false;
+ }
+ }
+
+ // check sequences
+ for (int i = 0; i < database->rowCount(); i++) {
+ if (!checkSequence(i)) {
+ return false;
+ }
+ }
+
+ return true;
+}
+
+
+bool cSequenceDatabaseWidget::checkFormula(int row, string& summary) {
+ cSummaryFormula formula;
+ string errmsg;
+ formula.setFormula(summary);
+ if (!formula.isValid(errmsg)) {
+ QMessageBox msgBox;
+ QString errstr = "Syntax error in the row no. ";
+ errstr += to_string(row + 1).c_str();
+ errstr += ": ";
+ errstr += errmsg.c_str();
+ msgBox.setText(errstr);
+ msgBox.exec();
+ return false;
+ }
+ if (database->item(row, 4)) {
+ database->item(row, 4)->setData(Qt::DisplayRole, formula.getMass());
+ }
+ return true;
+}
+
+
+bool cSequenceDatabaseWidget::checkSequence(int row) {
+ regex rx;
+ // [^\\[\\]]+ is used instead of .+ to prevent from a too complex regex error
+ switch ((peptideType)((QComboBox *)database->cellWidget(row, 1))->currentIndex())
+ {
+ case linear:
+ case cyclic:
+ case linearpolysaccharide:
+ rx = "^\\[[^\\[\\]]+\\](-\\[[^\\[\\]]+\\])*$";
+ break;
+ case branched:
+ rx = "^\\[[^\\[\\]]+\\](-\\[[^\\[\\]]+\\])*\\\\\\(\\[[^\\[\\]]+\\](-\\[[^\\[\\]]+\\])*\\\\\\)\\[[^\\[\\]]+\\](-\\[[^\\[\\]]+\\])*$";
+ break;
+ case lasso:
+ rx = "(^(\\[[^\\[\\]]+\\](-\\[[^\\[\\]]+\\])*)?\\\\\\(\\[[^\\[\\]]+\\](-\\[[^\\[\\]]+\\])*\\\\\\)\\[[^\\[\\]]+\\](-\\[[^\\[\\]]+\\])*$|^\\[[^\\[\\]]+\\](-\\[[^\\[\\]]+\\])*\\\\\\(\\[[^\\[\\]]+\\](-\\[[^\\[\\]]+\\])*\\\\\\)(\\[[^\\[\\]]+\\](-\\[[^\\[\\]]+\\])*)?$)";
+ break;
+ case other:
+ default:
+ rx = ".*";
+ break;
+ }
+
+ try {
+ if (!(regex_search(database->item(row, 5)->text().toStdString(), rx))) {
+ QMessageBox msgBox;
+ QString errstr = "Row no. ";
+ errstr += to_string(row + 1).c_str();
+ errstr += ". The format of sequence '";
+ errstr += database->item(row, 5)->text().toStdString().c_str();
+ errstr += "' does not correspond to the sequence type '";
+ errstr += getStringFromPeptideType((peptideType)((QComboBox *)database->cellWidget(row, 1))->currentIndex()).c_str();
+ errstr += "'.";
+ msgBox.setText(errstr);
+ msgBox.exec();
+ return false;
+ }
+ }
+ catch (std::regex_error& e) {
+ QMessageBox msgBox;
+ QString errstr = "Row no. ";
+ errstr += to_string(row + 1).c_str();
+ errstr += ". cSequenceDatabaseWidget::checkSequence: regex_search failed, error no. ";
+ errstr += to_string(e.code()).c_str();
+ errstr += ". Please, check the sequence: '";
+ errstr += database->item(row, 5)->text().toStdString().c_str();
+ errstr += "'.";
+ msgBox.setText(errstr);
+ msgBox.exec();
+ return false;
+ }
+
+ return true;
+}
+
+
+void cSequenceDatabaseWidget::closeWindow() {
+ hide();
+}
+
+
+void cSequenceDatabaseWidget::loadDatabase() {
+ QString filename = QFileDialog::getOpenFileName(this, tr("Load the Database of Sequences"), lastdir, tr("Database of Sequences (*.txt)"));
+ lastdir = filename;
+
+ if (filename.toStdString().compare("") != 0) {
+
+ databasefile = filename;
+ save->setText(QString(" Save '") + QString(databasefile.toStdString().substr(databasefile.toStdString().rfind('/') + 1, databasefile.toStdString().size()).c_str()) + QString("' "));
+
+ inputstream.open(filename.toStdString().c_str());
+
+ if (!inputstream.good()) {
+ QMessageBox msgBox;
+ msgBox.setText("Cannot open the file '" + databasefile + "'.");
+ msgBox.exec();
+ }
+ else {
+
+ deleteTable(true);
+
+ sequences.clear();
+ sequences.loadFromPlainTextStream(inputstream);
+
+ progress->setLabelText("Loading the Sequence Databatase...");
+ progress->setMinimum(0);
+ progress->setValue(1);
+ progress->setMaximum(sequences.size());
+ progress->show();
+
+ cSummaryFormula formula;
+ database->setRowCount(sequences.size());
+ for (int i = 0; i < sequences.size(); i++) {
+ QCheckBox* checkbox = new QCheckBox();
+ database->setCellWidget(i, 0, checkbox);
+
+ QComboBox* combo = new QComboBox();
+ for (int j = 0; j <= (int)other; j++) {
+ combo->addItem(QString(getStringFromPeptideType((peptideType)j).c_str()));
+ }
+ combo->setCurrentIndex((int)sequences[i].getPeptideType());
+ database->setCellWidget(i, 1, combo);
+
+ database->setItem(i, 2, new QTableWidgetItem(sequences[i].getName().c_str()));
+ database->setItem(i, 3, new QTableWidgetItem(sequences[i].getSummaryFormula().c_str()));
+ formula.setFormula(sequences[i].getSummaryFormula());
+ database->setItem(i, 4, new QTableWidgetItem());
+ database->item(i, 4)->setData(Qt::DisplayRole, formula.getMass());
+ database->setItem(i, 5, new QTableWidgetItem(sequences[i].getSequence().c_str()));
+ database->setItem(i, 6, new QTableWidgetItem(sequences[i].getNTterminalModification().c_str()));
+ database->setItem(i, 7, new QTableWidgetItem(sequences[i].getCTterminalModification().c_str()));
+ database->setItem(i, 8, new QTableWidgetItem(sequences[i].getBranchModification().c_str()));
+ database->setItem(i, 9, new QTableWidgetItem(sequences[i].getReference().c_str()));
+
+ database->setCellWidget(i, 10, new QLabel(sequences[i].getNameWithReferenceAsHTMLString().c_str()));
+ ((QLabel *)database->cellWidget(i, 10))->setTextFormat(Qt::RichText);
+ ((QLabel *)database->cellWidget(i, 10))->setTextInteractionFlags(Qt::TextBrowserInteraction);
+ ((QLabel *)database->cellWidget(i, 10))->setOpenExternalLinks(true);
+
+ if ((i == 0) || ((i - 1)/100 != i/100)) {
+ progress->setValue(i);
+ }
+ }
+
+ for (int i = 0; i < database->columnCount(); i++) {
+ database->resizeColumnToContents(i);
+ }
+
+ progress->setValue(sequences.size());
+ progress->hide();
+
+ }
+
+ inputstream.close();
+
+ }
+}
+
+
+void cSequenceDatabaseWidget::saveDatabase() {
+
+ if (!checkTable()) {
+ return;
+ }
+
+ if (databasefile.compare("") == 0) {
+ saveDatabaseAs();
+ return;
+ }
+
+ outputstream.open(databasefile.toStdString().c_str());
+ if (!outputstream.good()) {
+ QMessageBox msgBox;
+ msgBox.setText("Cannot open the file '" + databasefile + "'.");
+ msgBox.exec();
+ }
+ else {
+
+ progress->setLabelText("Saving the Sequence Databatase...");
+ progress->setMinimum(0);
+ progress->setMaximum(100);
+ progress->setValue(1);
+ progress->show();
+
+ cSequence seq;
+ sequences.clear();
+
+ removeEmptyRows();
+
+ progress->setMaximum(database->rowCount());
+
+ for (int i = 0; i < database->rowCount(); i++) {
+ seq.clear();
+ for (int j = 0; j < database->columnCount(); j++) {
+ switch (j)
+ {
+ case 0:
+ // nothing to do
+ break;
+ case 1:
+ seq.setPeptideType((peptideType)(((QComboBox *)database->cellWidget(i,j))->currentIndex()));
+ break;
+ case 2:
+ seq.setName(database->item(i,j)->text().toStdString());
+ break;
+ case 3:
+ seq.setSummaryFormula(database->item(i,j)->text().toStdString());
+ break;
+ case 4:
+ // nothing to do
+ break;
+ case 5:
+ seq.setSequence(database->item(i,j)->text().toStdString());
+ break;
+ case 6:
+ seq.setNTterminalModification(database->item(i,j)->text().toStdString());
+ break;
+ case 7:
+ seq.setCTterminalModification(database->item(i,j)->text().toStdString());
+ break;
+ case 8:
+ seq.setBranchModification(database->item(i,j)->text().toStdString());
+ break;
+ case 9:
+ seq.setReference(database->item(i,j)->text().toStdString());
+ break;
+ default:
+ break;
+ }
+ }
+ sequences.push_back(seq);
+
+ if ((i == 0) || ((i - 1)/100 != i/100)) {
+ progress->setValue(i);
+ }
+ }
+
+ sequences.storeToPlainTextStream(outputstream);
+
+ progress->setValue(database->rowCount());
+ progress->hide();
+
+ }
+ outputstream.close();
+}
+
+
+void cSequenceDatabaseWidget::saveDatabaseAs() {
+
+ if (!checkTable()) {
+ return;
+ }
+
+ QString filename = QFileDialog::getSaveFileName(this, tr("Save Settings As..."), lastdir, tr("Database of Sequences (*.txt)"));
+ lastdir = filename;
+
+ if (filename.toStdString().compare("") != 0) {
+ databasefile = filename;
+ save->setText(QString(" Save '") + QString(databasefile.toStdString().substr(databasefile.toStdString().rfind('/') + 1, databasefile.toStdString().size()).c_str()) + QString("' "));
+ saveDatabase();
+ }
+}
+
+
+void cSequenceDatabaseWidget::addRow() {
+ int row = database->rowCount();
+ database->insertRow(row);
+
+ QCheckBox* checkbox = new QCheckBox();
+ database->setCellWidget(row, 0, checkbox);
+
+ QComboBox* combo = new QComboBox();
+ for (int i = 0; i <= (int)other; i++) {
+ combo->addItem(QString(getStringFromPeptideType((peptideType)i).c_str()));
+ }
+ combo->setCurrentIndex((int)other);
+ database->setCellWidget(row, 1, combo);
+
+ database->setItem(row, 2, new QTableWidgetItem());
+ database->setItem(row, 3, new QTableWidgetItem());
+ database->setItem(row, 4, new QTableWidgetItem());
+ database->setItem(row, 5, new QTableWidgetItem());
+ database->setItem(row, 6, new QTableWidgetItem());
+ database->setItem(row, 7, new QTableWidgetItem());
+ database->setItem(row, 8, new QTableWidgetItem());
+ database->setItem(row, 9, new QTableWidgetItem());
+
+ database->setCellWidget(row, 10, new QLabel());
+ ((QLabel *)database->cellWidget(row, 10))->setTextFormat(Qt::RichText);
+ ((QLabel *)database->cellWidget(row, 10))->setTextInteractionFlags(Qt::TextBrowserInteraction);
+ ((QLabel *)database->cellWidget(row, 10))->setOpenExternalLinks(true);
+}
+
+
+void cSequenceDatabaseWidget::removeEmptyRows() {
+ int i = 0;
+ while (i < database->rowCount()) {
+ if (((QCheckBox *)(database->cellWidget(i, 0)))->isChecked()) {
+ removeRow(i);
+ }
+ else {
+ i++;
+ }
+ }
+}
+
+
+void cSequenceDatabaseWidget::itemChanged(QTableWidgetItem* item) {
+ // recalculate mass when formula is changed
+ if (item->column() == 3) {
+ checkFormula(item->row(), item->text().toStdString());
+ }
+
+ // check sequence
+ if (item->column() == 5) {
+ checkSequence(item->row());
+ }
+
+ // update references preview
+ if (((item->column() == 2) || (item->column() == 9)) && database->cellWidget(item->row(), 10)) {
+ cSequence seq;
+ seq.setName(database->item(item->row(), 2)->text().toStdString());
+ seq.setReference(database->item(item->row(), 9)->text().toStdString());
+ ((QLabel *)database->cellWidget(item->row(), 10))->setText(seq.getNameWithReferenceAsHTMLString().c_str());
+ }
+}
+
+
+void cSequenceDatabaseWidget::headerItemDoubleClicked(int index) {
+ if (headersort[index] == -1) {
+ database->sortByColumn(index, Qt::AscendingOrder);
+ headersort[index] = 1;
+ return;
+ }
+
+ if (headersort[index] == 0) {
+ database->sortByColumn(index, Qt::AscendingOrder);
+ headersort[index] = 1;
+ }
+ else {
+ database->sortByColumn(index, Qt::DescendingOrder);
+ headersort[index] = 0;
+ }
+}
+
diff --git a/CycloBranch/gui/cSequenceDatabaseWidget.h b/CycloBranch/gui/cSequenceDatabaseWidget.h
new file mode 100644
index 0000000..d568f39
--- /dev/null
+++ b/CycloBranch/gui/cSequenceDatabaseWidget.h
@@ -0,0 +1,110 @@
+/**
+ \file cSequenceDatabaseWidget.h
+ \brief Visualization of the database of sequences.
+*/
+
+
+#ifndef _CSEQUENCEDATABASEWIDGET_H
+#define _CSEQUENCEDATABASEWIDGET_H
+
+#include
+#include
+#include "core/cSequenceDatabase.h"
+
+using namespace std;
+
+
+// forward declaration
+class QHBoxLayout;
+class QVBoxLayout;
+class QTableWidget;
+class QTableWidgetItem;
+class QDialogButtonBox;
+class QPushButton;
+class QLabel;
+class QComboBox;
+class QProgressDialog;
+
+
+/**
+ \brief The widget representing the dialog 'About'.
+*/
+class cSequenceDatabaseWidget : public QWidget
+{
+ Q_OBJECT
+
+public:
+
+
+ /**
+ \brief The constructor.
+ \param parent pointer to a parent widget
+ */
+ cSequenceDatabaseWidget(QWidget* parent = (QWidget *)0);
+
+
+ /**
+ \brief The destructor.
+ */
+ ~cSequenceDatabaseWidget();
+
+
+ /**
+ \brief Handle the window close event.
+ \param event pointer to QCloseEvent
+ */
+ void closeEvent(QCloseEvent *event);
+
+
+private:
+ QWidget* parent;
+ QPushButton* insertrow;
+ QPushButton* removechecked;
+ QPushButton* close;
+ QPushButton* load;
+ QPushButton* save;
+ QPushButton* saveas;
+ QTableWidget* database;
+ QHBoxLayout* buttons;
+ QVBoxLayout* mainlayout;
+ QProgressDialog* progress;
+
+ QString databasefile;
+ QString lastdir;
+ ifstream inputstream;
+ ofstream outputstream;
+ cSequenceDatabase sequences;
+
+ vector headersort;
+
+ void deleteTable(bool enableprogress);
+
+ void removeRow(int row);
+
+ bool checkTable();
+
+ bool checkFormula(int row, string& summary);
+
+ bool checkSequence(int row);
+
+private slots:
+
+ void closeWindow();
+
+ void loadDatabase();
+
+ void saveDatabase();
+
+ void saveDatabaseAs();
+
+ void addRow();
+
+ void removeEmptyRows();
+
+ void itemChanged(QTableWidgetItem* item);
+
+ void headerItemDoubleClicked(int index);
+
+};
+
+#endif
\ No newline at end of file
diff --git a/CycloBranch/gui/cSpectrumDetailWidget.cpp b/CycloBranch/gui/cSpectrumDetailWidget.cpp
index bd8881b..a3b82b3 100644
--- a/CycloBranch/gui/cSpectrumDetailWidget.cpp
+++ b/CycloBranch/gui/cSpectrumDetailWidget.cpp
@@ -59,19 +59,24 @@ string cSpectrumDetailWidget::getDetailsAsHTMLString() {
string s = "";
if (theoreticalspectrum) {
- s += "Acronym Peptide Name:
";
- s += theoreticalspectrum->getAcronymPeptideNameWithHTMLReferences();
- s += "
";
- s += "Full Peptide Name:
";
- s += theoreticalspectrum->getRealPeptideName() + "
";
- if ((int)theoreticalspectrum->getPath().size() > 0) {
+ if (parameters && ((parameters->mode == denovoengine) || (parameters->mode == singlecomparison) || (parameters->mode == databasesearch))) {
+
+ s += "Acronym Peptide Name:
";
+ s += theoreticalspectrum->getAcronymPeptideNameWithHTMLReferences();
+ s += "
";
+ s += "Full Peptide Name:
";
+ s += theoreticalspectrum->getRealPeptideName() + "
";
+
+ if ((int)theoreticalspectrum->getPath().size() > 0) {
+ s += "
";
+ s += "Path in the De Novo Graph:
";
+ s += theoreticalspectrum->getPath();
+ }
+
s += "
";
- s += "Path in the De Novo Graph:
";
- s += theoreticalspectrum->getPath();
+
}
-
- s += "
";
s += "Unmatched Measured Peaks:
" + theoreticalspectrum->getUnmatchedPeaks() + "
";
s += "Theoretical Peaks:
" + theoreticalspectrum->getTheoreticalPeaks()->print(true);
@@ -90,7 +95,10 @@ cSpectrumDetailWidget::~cSpectrumDetailWidget() {
delete graphicalspectrum;
delete graphicalspectrumscroll;
- delete textedit;
+ if (parameters && ((parameters->mode == denovoengine) || (parameters->mode == singlecomparison) || (parameters->mode == databasesearch))) {
+ delete textedit;
+ }
+
delete textbrowser;
delete zoomin;
@@ -118,7 +126,8 @@ cSpectrumDetailWidget::~cSpectrumDetailWidget() {
delete formlayout;
delete formwidget;
- if (parameters) {
+ if (parameters && ((parameters->mode == denovoengine) || (parameters->mode == singlecomparison) || (parameters->mode == databasesearch))) {
+
switch (parameters->peptidetype)
{
case linear:
@@ -135,9 +144,12 @@ cSpectrumDetailWidget::~cSpectrumDetailWidget() {
break;
case linearpolysaccharide:
break;
+ case other:
+ break;
default:
break;
}
+
}
delete vsplitter1;
@@ -168,24 +180,28 @@ void cSpectrumDetailWidget::prepareToShow(peptideType peptidetype) {
vsplitter2 = new QSplitter();
vsplitter2->setOrientation(Qt::Vertical);
- switch (peptidetype)
- {
- case linear:
- linearwidget = new cLinearWidget();
- break;
- case cyclic:
- cyclicwidget = new cCyclicWidget();
- break;
- case branched:
- branchedwidget = new cBranchedWidget();
- break;
- case lasso:
- lassowidget = new cLassoWidget();
- break;
- case linearpolysaccharide:
- break;
- default:
- break;
+ if (parameters && ((parameters->mode == denovoengine) || (parameters->mode == singlecomparison) || (parameters->mode == databasesearch))) {
+ switch (peptidetype)
+ {
+ case linear:
+ linearwidget = new cLinearWidget();
+ break;
+ case cyclic:
+ cyclicwidget = new cCyclicWidget();
+ break;
+ case branched:
+ branchedwidget = new cBranchedWidget();
+ break;
+ case lasso:
+ lassowidget = new cLassoWidget();
+ break;
+ case linearpolysaccharide:
+ break;
+ case other:
+ break;
+ default:
+ break;
+ }
}
graphicalspectrumscroll = new QScrollArea();
@@ -193,10 +209,12 @@ void cSpectrumDetailWidget::prepareToShow(peptideType peptidetype) {
graphicalspectrumscroll->setWidget(graphicalspectrum);
//graphicalspectrumscroll->setWidgetResizable(true);
- textedit = new QTextEdit();
- textedit->setReadOnly(true);
- textedit->setFont(QFont("Courier", 9));
- textedit->setLineWrapMode(QTextEdit::NoWrap);
+ if (parameters && ((parameters->mode == denovoengine) || (parameters->mode == singlecomparison) || (parameters->mode == databasesearch))) {
+ textedit = new QTextEdit();
+ textedit->setReadOnly(true);
+ textedit->setFont(QFont("Courier", 9));
+ textedit->setLineWrapMode(QTextEdit::NoWrap);
+ }
textbrowser = new QTextBrowser();
textbrowser->setReadOnly(true);
@@ -260,77 +278,81 @@ void cSpectrumDetailWidget::prepareToShow(peptideType peptidetype) {
formlayout->addRow(tr("Hide matched peaks: "), hidematched);
formlayout->addRow(tr("Hide unmatched peaks: "), hideunmatched);
- // cyclic
- if (parameters && theoreticalspectrum && (parameters->peptidetype == cyclic)) {
- int r = (int)theoreticalspectrum->getAcronyms().size();
- int hint = (int)theoreticalspectrum->getVisualCoverage().size()/(2*r);
+ if (parameters && ((parameters->mode == denovoengine) || (parameters->mode == singlecomparison) || (parameters->mode == databasesearch))) {
- rotation = new QComboBox();
- rotation->addItem(tr("all"));
+ // cyclic
+ if (parameters && theoreticalspectrum && (parameters->peptidetype == cyclic)) {
+ int r = (int)theoreticalspectrum->getAcronyms().size();
+ int hint = (int)theoreticalspectrum->getVisualCoverage().size()/(2*r);
- string s;
- if (theoreticalspectrum->getVisualCoverage().size() > 0) {
- for (int i = 0; i < 2*r; i++) {
- s = theoreticalspectrum->getVisualCoverage()[i*hint].name.substr(0, theoreticalspectrum->getVisualCoverage()[i*hint].name.rfind('_'));
- rotation->addItem(tr(s.c_str()));
+ rotation = new QComboBox();
+ rotation->addItem(tr("all"));
+
+ string s;
+ if (theoreticalspectrum->getVisualCoverage().size() > 0) {
+ for (int i = 0; i < 2*r; i++) {
+ s = theoreticalspectrum->getVisualCoverage()[i*hint].name.substr(0, theoreticalspectrum->getVisualCoverage()[i*hint].name.rfind('_'));
+ rotation->addItem(tr(s.c_str()));
+ }
}
- }
- connect(rotation, SIGNAL(currentIndexChanged(int)), graphicalspectrum, SLOT(rotationChanged(int)));
- connect(rotation, SIGNAL(currentIndexChanged(QString)), graphicalspectrum, SLOT(rotationChanged(QString)));
- connect(rotation, SIGNAL(currentIndexChanged(int)), cyclicwidget, SLOT(rotationChanged(int)));
- formlayout->addRow(tr("Ring break up point: "), rotation);
- }
+ connect(rotation, SIGNAL(currentIndexChanged(int)), graphicalspectrum, SLOT(rotationChanged(int)));
+ connect(rotation, SIGNAL(currentIndexChanged(QString)), graphicalspectrum, SLOT(rotationChanged(QString)));
+ connect(rotation, SIGNAL(currentIndexChanged(int)), cyclicwidget, SLOT(rotationChanged(int)));
+ formlayout->addRow(tr("Ring break up point: "), rotation);
+ }
- // branched
- if (parameters && (parameters->peptidetype == branched)) {
- trotation = new QComboBox();
- trotation->addItem(tr("all"));
- trotation->addItem(tr("1 (left-to-right)"));
- trotation->addItem(tr("2 (top-to-right)"));
- trotation->addItem(tr("3 (right-to-left)"));
- trotation->addItem(tr("4 (left-to-top)"));
- trotation->addItem(tr("5 (top-to-left)"));
- trotation->addItem(tr("6 (right-to-top)"));
-
- connect(trotation, SIGNAL(currentIndexChanged(int)), graphicalspectrum, SLOT(trotationChanged(int)));
- connect(trotation, SIGNAL(currentIndexChanged(int)), branchedwidget, SLOT(trotationChanged(int)));
- formlayout->addRow(tr("Linearized sequence: "), trotation);
- }
+ // branched
+ if (parameters && (parameters->peptidetype == branched)) {
+ trotation = new QComboBox();
+ trotation->addItem(tr("all"));
+ trotation->addItem(tr("1 (left-to-right)"));
+ trotation->addItem(tr("2 (top-to-right)"));
+ trotation->addItem(tr("3 (right-to-left)"));
+ trotation->addItem(tr("4 (left-to-top)"));
+ trotation->addItem(tr("5 (top-to-left)"));
+ trotation->addItem(tr("6 (right-to-top)"));
+
+ connect(trotation, SIGNAL(currentIndexChanged(int)), graphicalspectrum, SLOT(trotationChanged(int)));
+ connect(trotation, SIGNAL(currentIndexChanged(int)), branchedwidget, SLOT(trotationChanged(int)));
+ formlayout->addRow(tr("Linearized sequence: "), trotation);
+ }
- // lasso
- if (parameters && theoreticalspectrum && (parameters->peptidetype == lasso)) {
- int r = (int)theoreticalspectrum->getAcronyms().size() - (int)theoreticalspectrum->getCandidate().getBranchSize();
- int hint = (int)theoreticalspectrum->getVisualCoverage().size()/(2*r);
+ // lasso
+ if (parameters && theoreticalspectrum && (parameters->peptidetype == lasso)) {
+ int r = (int)theoreticalspectrum->getAcronyms().size() - (int)theoreticalspectrum->getCandidate().getBranchSize();
+ int hint = (int)theoreticalspectrum->getVisualCoverage().size()/(2*r);
- rotation = new QComboBox();
- rotation->addItem(tr("all"));
+ rotation = new QComboBox();
+ rotation->addItem(tr("all"));
- string s;
- if (theoreticalspectrum->getVisualCoverage().size() > 0) {
- for (int i = 0; i < 2*r; i++) {
- s = theoreticalspectrum->getVisualCoverage()[i*hint].name.substr(0, theoreticalspectrum->getVisualCoverage()[i*hint].name.find('_'));
- rotation->addItem(tr(s.c_str()));
+ string s;
+ if (theoreticalspectrum->getVisualCoverage().size() > 0) {
+ for (int i = 0; i < 2*r; i++) {
+ s = theoreticalspectrum->getVisualCoverage()[i*hint].name.substr(0, theoreticalspectrum->getVisualCoverage()[i*hint].name.find('_'));
+ rotation->addItem(tr(s.c_str()));
+ }
}
+
+ connect(rotation, SIGNAL(currentIndexChanged(int)), graphicalspectrum, SLOT(rotationChanged(int)));
+ connect(rotation, SIGNAL(currentIndexChanged(QString)), graphicalspectrum, SLOT(rotationChanged(QString)));
+ connect(rotation, SIGNAL(currentIndexChanged(int)), lassowidget, SLOT(rotationChanged(int)));
+ formlayout->addRow(tr("Ring break up point: "), rotation);
+
+ trotation = new QComboBox();
+ trotation->addItem(tr("all"));
+ trotation->addItem(tr("1 (left-to-right)"));
+ trotation->addItem(tr("2 (top-to-right)"));
+ trotation->addItem(tr("3 (right-to-left)"));
+ trotation->addItem(tr("4 (left-to-top)"));
+ trotation->addItem(tr("5 (top-to-left)"));
+ trotation->addItem(tr("6 (right-to-top)"));
+
+ connect(trotation, SIGNAL(currentIndexChanged(int)), graphicalspectrum, SLOT(trotationChanged(int)));
+ connect(trotation, SIGNAL(currentIndexChanged(int)), lassowidget, SLOT(trotationChanged(int)));
+ formlayout->addRow(tr("Linearized sequence: "), trotation);
}
- connect(rotation, SIGNAL(currentIndexChanged(int)), graphicalspectrum, SLOT(rotationChanged(int)));
- connect(rotation, SIGNAL(currentIndexChanged(QString)), graphicalspectrum, SLOT(rotationChanged(QString)));
- connect(rotation, SIGNAL(currentIndexChanged(int)), lassowidget, SLOT(rotationChanged(int)));
- formlayout->addRow(tr("Ring break up point: "), rotation);
-
- trotation = new QComboBox();
- trotation->addItem(tr("all"));
- trotation->addItem(tr("1 (left-to-right)"));
- trotation->addItem(tr("2 (top-to-right)"));
- trotation->addItem(tr("3 (right-to-left)"));
- trotation->addItem(tr("4 (left-to-top)"));
- trotation->addItem(tr("5 (top-to-left)"));
- trotation->addItem(tr("6 (right-to-top)"));
-
- connect(trotation, SIGNAL(currentIndexChanged(int)), graphicalspectrum, SLOT(trotationChanged(int)));
- connect(trotation, SIGNAL(currentIndexChanged(int)), lassowidget, SLOT(trotationChanged(int)));
- formlayout->addRow(tr("Linearized sequence: "), trotation);
}
formwidget = new QWidget();
@@ -341,86 +363,102 @@ void cSpectrumDetailWidget::prepareToShow(peptideType peptidetype) {
vsplitter1->setStretchFactor(0, 7);
vsplitter1->setStretchFactor(1, 3);
- switch (peptidetype)
- {
- case linear:
- vsplitter2->addWidget(formwidget);
- vsplitter2->addWidget(linearwidget);
- vsplitter2->addWidget(textedit);
- vsplitter2->setStretchFactor(0, 2);
- vsplitter2->setStretchFactor(1, 3);
- vsplitter2->setStretchFactor(2, 5);
- break;
- case cyclic:
- vsplitter2->addWidget(formwidget);
- vsplitter2->addWidget(cyclicwidget);
- vsplitter2->addWidget(textedit);
- vsplitter2->setStretchFactor(0, 2);
- vsplitter2->setStretchFactor(1, 3);
- vsplitter2->setStretchFactor(2, 5);
- break;
- case branched:
- vsplitter2->addWidget(formwidget);
- vsplitter2->addWidget(branchedwidget);
- vsplitter2->addWidget(textedit);
- vsplitter2->setStretchFactor(0, 2);
- vsplitter2->setStretchFactor(1, 3);
- vsplitter2->setStretchFactor(2, 5);
- break;
- case lasso:
- vsplitter2->addWidget(formwidget);
- vsplitter2->addWidget(lassowidget);
- vsplitter2->addWidget(textedit);
- vsplitter2->setStretchFactor(0, 2);
- vsplitter2->setStretchFactor(1, 3);
- vsplitter2->setStretchFactor(2, 5);
- break;
- case linearpolysaccharide:
- vsplitter2->addWidget(formwidget);
- vsplitter2->addWidget(textedit);
- vsplitter2->setStretchFactor(0, 2);
- vsplitter2->setStretchFactor(1, 8);
- break;
- default:
- break;
- }
-
- hsplitter->addWidget(vsplitter1);
- hsplitter->addWidget(vsplitter2);
- hsplitter->setStretchFactor(0, 6);
- hsplitter->setStretchFactor(1, 4);
-
- mainbox = new QHBoxLayout();
- mainbox->addWidget(hsplitter);
- setLayout(mainbox);
-
- resize(1280, 700);
-
- if (parameters && theoreticalspectrum) {
+ if (parameters && ((parameters->mode == denovoengine) || (parameters->mode == singlecomparison) || (parameters->mode == databasesearch))) {
switch (peptidetype)
{
case linear:
- linearwidget->initialize(parameters, theoreticalspectrum);
+ vsplitter2->addWidget(formwidget);
+ vsplitter2->addWidget(linearwidget);
+ vsplitter2->addWidget(textedit);
+ vsplitter2->setStretchFactor(0, 2);
+ vsplitter2->setStretchFactor(1, 3);
+ vsplitter2->setStretchFactor(2, 5);
break;
case cyclic:
- cyclicwidget->initialize(parameters, theoreticalspectrum);
+ vsplitter2->addWidget(formwidget);
+ vsplitter2->addWidget(cyclicwidget);
+ vsplitter2->addWidget(textedit);
+ vsplitter2->setStretchFactor(0, 2);
+ vsplitter2->setStretchFactor(1, 3);
+ vsplitter2->setStretchFactor(2, 5);
break;
case branched:
- branchedwidget->initialize(parameters, theoreticalspectrum);
+ vsplitter2->addWidget(formwidget);
+ vsplitter2->addWidget(branchedwidget);
+ vsplitter2->addWidget(textedit);
+ vsplitter2->setStretchFactor(0, 2);
+ vsplitter2->setStretchFactor(1, 3);
+ vsplitter2->setStretchFactor(2, 5);
break;
case lasso:
- lassowidget->initialize(parameters, theoreticalspectrum);
+ vsplitter2->addWidget(formwidget);
+ vsplitter2->addWidget(lassowidget);
+ vsplitter2->addWidget(textedit);
+ vsplitter2->setStretchFactor(0, 2);
+ vsplitter2->setStretchFactor(1, 3);
+ vsplitter2->setStretchFactor(2, 5);
break;
case linearpolysaccharide:
+ vsplitter2->addWidget(formwidget);
+ vsplitter2->addWidget(textedit);
+ vsplitter2->setStretchFactor(0, 2);
+ vsplitter2->setStretchFactor(1, 8);
+ break;
+ case other:
break;
default:
break;
}
+
+ }
+
+ if (parameters && (parameters->mode == dereplication)) {
+ vsplitter2->addWidget(formwidget);
+ }
+
+ hsplitter->addWidget(vsplitter1);
+ hsplitter->addWidget(vsplitter2);
+ hsplitter->setStretchFactor(0, 6);
+ hsplitter->setStretchFactor(1, 4);
+
+ mainbox = new QHBoxLayout();
+ mainbox->addWidget(hsplitter);
+ setLayout(mainbox);
+
+ resize(1280, 700);
+
+ if (parameters && theoreticalspectrum) {
+
+ if ((parameters->mode == denovoengine) || (parameters->mode == singlecomparison) || (parameters->mode == databasesearch)) {
+
+ switch (peptidetype)
+ {
+ case linear:
+ linearwidget->initialize(parameters, theoreticalspectrum);
+ break;
+ case cyclic:
+ cyclicwidget->initialize(parameters, theoreticalspectrum);
+ break;
+ case branched:
+ branchedwidget->initialize(parameters, theoreticalspectrum);
+ break;
+ case lasso:
+ lassowidget->initialize(parameters, theoreticalspectrum);
+ break;
+ case linearpolysaccharide:
+ break;
+ case other:
+ break;
+ default:
+ break;
+ }
- graphicalspectrum->initialize(parameters, theoreticalspectrum);
+ textedit->setHtml(theoreticalspectrum->getCoverageBySeries().c_str());
+
+ }
- textedit->setHtml(theoreticalspectrum->getCoverageBySeries().c_str());
+ graphicalspectrum->initialize(parameters, theoreticalspectrum);
textbrowser->setHtml(getDetailsAsHTMLString().c_str());
}
diff --git a/CycloBranch/parallel/cGraphReaderThread.cpp b/CycloBranch/parallel/cGraphReaderThread.cpp
index 6697502..17f4316 100644
--- a/CycloBranch/parallel/cGraphReaderThread.cpp
+++ b/CycloBranch/parallel/cGraphReaderThread.cpp
@@ -3,7 +3,7 @@
#include "gui/cMainThread.h"
-int cGraphReaderThread::getTheoreticalSpectraIter(bool cterminalstartingnode, cCandidateSet* candidates, int nodeid, vector& composition, double precursormass, long long &count, int startmodifID, int endmodifID, int middlemodifID, int middlepos, vector& perspectivepath, double cummass, bool* terminatecomputation) {
+int cGraphReaderThread::getTheoreticalSpectraIter(bool cterminalstartingnode, cCandidateSet* candidates, int nodeid, vector& composition, double precursormass, int startmodifID, int endmodifID, int middlemodifID, int middlepos, vector& perspectivepath, double cummass, bool* terminatecomputation) {
nodeEdge ne;
int tmpmiddlemodifID = 0;
int finish;
@@ -52,7 +52,7 @@ int cGraphReaderThread::getTheoreticalSpectraIter(bool cterminalstartingnode, cC
}
composition.push_back((*graph)[nodeid][i].composition);
- finish = getTheoreticalSpectraIter(cterminalstartingnode, candidates, (*graph)[nodeid][i].targetnode, composition, precursormass, count, startmodifID, (*graph)[nodeid][i].endmodifID, tmpmiddlemodifID, middlepos, perspectivepath, cummass + (*graph)[nodeid][i].massdifference, terminatecomputation);
+ finish = getTheoreticalSpectraIter(cterminalstartingnode, candidates, (*graph)[nodeid][i].targetnode, composition, precursormass, startmodifID, (*graph)[nodeid][i].endmodifID, tmpmiddlemodifID, middlepos, perspectivepath, cummass + (*graph)[nodeid][i].massdifference, terminatecomputation);
composition.pop_back();
perspectivepath.pop_back();
@@ -78,34 +78,48 @@ int cGraphReaderThread::getTheoreticalSpectraIter(bool cterminalstartingnode, cC
if ((parameters->peptidetype == branched) || (parameters->peptidetype == lasso)) {
result.getSet().clear();
candidate.prepareBranchedCandidate(result, parameters->peptidetype, terminatecomputation);
- candidates->lock();
- for (auto i = result.getSet().begin(); i != result.getSet().end(); ++i) {
- candidates->getSet().insert(*i);
+ if (scanmode == 0) {
+ candidates->lock();
+ for (auto i = result.getSet().begin(); i != result.getSet().end(); ++i) {
+ candidates->getSet().insert(*i);
+ }
+ candidates->unlock();
+ }
+ else {
+ *count += (long long unsigned)result.getSet().size();
+ if (*count > maximumcandidates) {
+ return -1;
+ }
}
- candidates->unlock();
}
else {
- candidates->lock();
- candidates->getSet().insert(candidate);
- candidates->unlock();
- }
-
- count++;
-
- candidates->lock();
- size = candidates->size();
- candidates->unlock();
-
- while (size >= parameters->maximumnumberofcandidates) {
- usleep(1000);
-
- if (*terminatecomputation) {
- return -1;
+ if (scanmode == 0) {
+ candidates->lock();
+ candidates->getSet().insert(candidate);
+ candidates->unlock();
+ }
+ else {
+ *count += 1;
+ if (*count > maximumcandidates) {
+ return -1;
+ }
}
+ }
+ if (scanmode == 0) {
candidates->lock();
size = candidates->size();
candidates->unlock();
+ while (size >= parameters->maximumnumberofcandidates) {
+ usleep(1000);
+
+ if (*terminatecomputation) {
+ return -1;
+ }
+ candidates->lock();
+ size = candidates->size();
+ candidates->unlock();
+ }
}
}
@@ -118,11 +132,11 @@ int cGraphReaderThread::getTheoreticalSpectraIter(bool cterminalstartingnode, cC
}
-int cGraphReaderThread::reverseCTerminalCandidates(int nodeid, cCandidateSet* candidates, double precursormass, long long &count, int startmodifID, bool* terminatecomputation) {
+int cGraphReaderThread::reverseCTerminalCandidates(int nodeid, cCandidateSet* candidates, double precursormass, int startmodifID, bool* terminatecomputation) {
vector composition;
vector perspectivepath;
- if (getTheoreticalSpectraIter((*graph)[nodeid].checkIonAnnotation(y_ion), candidates, nodeid, composition, precursormass, count, startmodifID, 0, 0, -1, perspectivepath, (*graph)[nodeid].getMZRatio(), terminatecomputation) == -1) {
+ if (getTheoreticalSpectraIter((*graph)[nodeid].checkIonAnnotation(y_ion), candidates, nodeid, composition, precursormass, startmodifID, 0, 0, -1, perspectivepath, (*graph)[nodeid].getMZRatio(), terminatecomputation) == -1) {
return -1;
}
@@ -137,22 +151,24 @@ cGraphReaderThread::cGraphReaderThread() {
parameters = 0;
os = 0;
lastsystemnode = 0;
- mode = 0;
+ scanmode = 0;
terminatecomputation = 0;
+ count = 0;
// delete thread when run is finished
connect(this, SIGNAL(finished()), this, SLOT(deleteLater()));
}
-void cGraphReaderThread::initialize(vector& graph, cBricksDatabase& bricksdatabasewithcombinations, cCandidateSet& candidates, cParameters* parameters, cMainThread* os, int lastsystemnode, bool& terminatecomputation) {
+void cGraphReaderThread::initialize(vector& graph, cBricksDatabase& bricksdatabasewithcombinations, cCandidateSet& candidates, cParameters* parameters, cMainThread* os, int lastsystemnode, long long unsigned& count, int scanmode, bool& terminatecomputation) {
this->graph = &graph;
this->bricksdatabasewithcombinations = &bricksdatabasewithcombinations;
this->candidates = &candidates;
this->parameters = parameters;
this->os = os;
this->lastsystemnode = lastsystemnode;
- this->mode = mode;
+ this->count = &count;
+ this->scanmode = scanmode;
this->terminatecomputation = &terminatecomputation;
}
@@ -160,15 +176,14 @@ void cGraphReaderThread::initialize(vector& graph, cBricksData
void cGraphReaderThread::run() {
vector composition;
vector perspectivepath;
- long long count = 0;
int startmodifID = 0;
double unchargedprecursormass = uncharge(parameters->precursormass, parameters->precursorcharge);
switch (parameters->peptidetype)
{
case cyclic:
- if (getTheoreticalSpectraIter(false, candidates, 0, composition, unchargedprecursormass, count, 0, 0, 0, -1, perspectivepath, (*graph)[0].getMZRatio(), terminatecomputation) == -1) {
- // terminated by user
+ if (getTheoreticalSpectraIter(false, candidates, 0, composition, unchargedprecursormass, 0, 0, 0, -1, perspectivepath, (*graph)[0].getMZRatio(), terminatecomputation) == -1) {
+ // terminated
return;
}
break;
@@ -178,8 +193,8 @@ void cGraphReaderThread::run() {
if (i - 2 > 0) {
startmodifID = i - 2;
}
- if (reverseCTerminalCandidates(i, candidates, unchargedprecursormass, count, startmodifID, terminatecomputation) == -1) {
- // terminated by user
+ if (reverseCTerminalCandidates(i, candidates, unchargedprecursormass, startmodifID, terminatecomputation) == -1) {
+ // terminated
return;
}
}
@@ -189,8 +204,8 @@ void cGraphReaderThread::run() {
if (i - 1/*2*/ > 0) {
startmodifID = i - 1/*2*/;
}
- if (reverseCTerminalCandidates(i, candidates, unchargedprecursormass, count, startmodifID, terminatecomputation) == -1) {
- // terminated by user
+ if (reverseCTerminalCandidates(i, candidates, unchargedprecursormass, startmodifID, terminatecomputation) == -1) {
+ // terminated
return;
}
}
@@ -200,12 +215,14 @@ void cGraphReaderThread::run() {
if (i - 1 > 0) {
startmodifID = i - 1;
}
- if (reverseCTerminalCandidates(i, candidates, unchargedprecursormass, count, startmodifID, terminatecomputation) == -1) {
- // terminated by user
+ if (reverseCTerminalCandidates(i, candidates, unchargedprecursormass, startmodifID, terminatecomputation) == -1) {
+ // terminated
return;
}
}
break;
+ case other:
+ break;
default:
break;
}
diff --git a/CycloBranch/parallel/cGraphReaderThread.h b/CycloBranch/parallel/cGraphReaderThread.h
index 4084b04..fbaa489 100644
--- a/CycloBranch/parallel/cGraphReaderThread.h
+++ b/CycloBranch/parallel/cGraphReaderThread.h
@@ -40,12 +40,13 @@ class cGraphReaderThread : public QThread {
cParameters* parameters;
cMainThread* os;
int lastsystemnode;
- int mode;
+ long long unsigned* count;
+ int scanmode;
bool* terminatecomputation;
- int getTheoreticalSpectraIter(bool cterminalstartingnode, cCandidateSet* candidates, int nodeid, vector& composition, double precursormass, long long &count, int startmodifID, int endmodifID, int middlemodifID, int middlepos, vector& perspectivepath, double cummass, bool* terminatecomputation);
+ int getTheoreticalSpectraIter(bool cterminalstartingnode, cCandidateSet* candidates, int nodeid, vector& composition, double precursormass, int startmodifID, int endmodifID, int middlemodifID, int middlepos, vector& perspectivepath, double cummass, bool* terminatecomputation);
- int reverseCTerminalCandidates(int nodeid, cCandidateSet* candidates, double precursormass, long long& count, int startmodifID, bool* terminatecomputation);
+ int reverseCTerminalCandidates(int nodeid, cCandidateSet* candidates, double precursormass, int startmodifID, bool* terminatecomputation);
public:
@@ -64,9 +65,11 @@ class cGraphReaderThread : public QThread {
\param parameters pointer to program parameters
\param os pointer to the main thread of the application
\param lastsystemnode position of the last system node in the de novo graph
+ \param count an output number of peptide sequence candidates
+ \param scanmode 0 = get candidates; 1 = calculate the number of peptide sequence candidates
\param terminatecomputation reference to a variable determining that the thread must be stopped
*/
- void initialize(vector& graph, cBricksDatabase& bricksdatabasewithcombinations, cCandidateSet& candidates, cParameters* parameters, cMainThread* os, int lastsystemnode, bool& terminatecomputation);
+ void initialize(vector& graph, cBricksDatabase& bricksdatabasewithcombinations, cCandidateSet& candidates, cParameters* parameters, cMainThread* os, int lastsystemnode, long long unsigned& count, int scanmode, bool& terminatecomputation);
protected:
diff --git a/CycloBranch/parallel/cSpectrumComparatorThread.cpp b/CycloBranch/parallel/cSpectrumComparatorThread.cpp
index 1ea74cd..f519934 100644
--- a/CycloBranch/parallel/cSpectrumComparatorThread.cpp
+++ b/CycloBranch/parallel/cSpectrumComparatorThread.cpp
@@ -106,7 +106,7 @@ void cSpectrumComparatorThread::run() {
double score;
permutations.getSet().clear();
- if ((parameters->mode == 0) && (parameters->generatebrickspermutations)) {
+ if ((parameters->mode == denovoengine) && (parameters->generatebrickspermutations)) {
candidate.getPermutations(permutations, terminatecomputation);
}
else {
@@ -145,6 +145,8 @@ void cSpectrumComparatorThread::run() {
case linearpolysaccharide:
theoreticalpeaksrealsize = tsp.compareLinearPolysaccharide(peaklist, *bricksdatabasewithcombinations, false, *rxsequencetag, *rxsearchedsequence);
break;
+ case other:
+ break;
default:
break;
}
diff --git a/CycloBranch/parallel/cSpectrumComparatorThread.h b/CycloBranch/parallel/cSpectrumComparatorThread.h
index b716ec4..5431536 100644
--- a/CycloBranch/parallel/cSpectrumComparatorThread.h
+++ b/CycloBranch/parallel/cSpectrumComparatorThread.h
@@ -26,7 +26,7 @@ bool compareBandAllIonsDesc(cTheoreticalSpectrum& a, cTheoreticalSpectrum& b);
/**
- \brief Compare scores of two theoretical spectra (number of b-ions + water loss b-ions and all ions as a secondary score).
+ \brief Compare scores of two theoretical spectra (number of b-ions + dehydrated b-ions and all ions as a secondary score).
\param a first theoretical spectrum
\param b second theoretical spectrum
\retval bool true if the score of \a a is greater than the score of \a b
@@ -35,7 +35,7 @@ bool compareBBwaterLossAndAllIonsDesc(cTheoreticalSpectrum& a, cTheoreticalSpect
/**
- \brief Compare scores of two theoretical spectra (number of b-ions + ammonia loss b-ions and all ions as a secondary score).
+ \brief Compare scores of two theoretical spectra (number of b-ions + deamidated b-ions and all ions as a secondary score).
\param a first theoretical spectrum
\param b second theoretical spectrum
\retval bool true if the score of \a a is greater than the score of \a b