QString GraphicsItemNode::getNodeText()
{
QString nodeText;
if (g_settings->displayNodeCustomLabels && m_deBruijnNode->m_customLabel.length() > 0)
nodeText += m_deBruijnNode->m_customLabel + "\n";
if (g_settings->displayNodeNumbers)
nodeText += m_deBruijnNode->getNodeNumberText(true) + "\n";
if (g_settings->displayNodeLengths)
nodeText += formatIntForDisplay(m_deBruijnNode->m_length) + " bp\n";
if (g_settings->displayNodeCoverages)
nodeText += formatDoubleForDisplay(m_deBruijnNode->m_coverage, 1) + "x\n";
//Remove last newline before returning
return nodeText.left(nodeText.size()-1);
}
QueryPathsDialog::QueryPathsDialog(QWidget * parent, BlastQuery * query) :
QDialog(parent),
ui(new Ui::QueryPathsDialog)
{
ui->setupUi(this);
setWindowFlags(windowFlags() | Qt::WindowStaysOnTopHint);
connect(this, SIGNAL(rejected()), this, SLOT(hidden()));
connect(ui->tableWidget, SIGNAL(itemSelectionChanged()), this, SLOT(tableSelectionChanged()));
g_memory->queryPathDialogIsVisible = true;
g_memory->queryPaths.clear();
ui->tableWidget->setHorizontalHeaderLabels(QStringList() << "Path" << "Length\n(bp)" << "Query\ncovered\nby path" <<
"Query\ncovered\nby hits" << "Mean hit\nidentity" << "Total\nhit mis-\nmatches" <<
"Total\nhit gap\nopens" << "Length\ndiscre-\npancy" << "E-value\nproduct");
QString queryDescription = "Query name: " + query->getName();
queryDescription += " type: " + query->getTypeString();
queryDescription += " length: " + formatIntForDisplay(query->getLength());
if (query->getSequenceType() == PROTEIN)
queryDescription += " (" + formatIntForDisplay(3 * query->getLength()) + " bp)";
else
queryDescription += " bp";
ui->queryLabel->setText(queryDescription);
ui->tableWidget->clearContents();
ui->tableWidget->setSortingEnabled(false);
int pathCount = query->getPathCount();
ui->tableWidget->setRowCount(pathCount);
if (pathCount == 0)
return;
QList<BlastQueryPath> paths = query->getPaths();
for (int i = 0; i < pathCount; ++i)
{
BlastQueryPath * queryPath = &paths[i];
QTableWidgetItem * pathString = new QTableWidgetItem(queryPath->getPath().getString(true));
pathString->setFlags(Qt::ItemIsEnabled | Qt::ItemIsSelectable);
int length = queryPath->getPath().getLength();
TableWidgetItemInt * pathLength = new TableWidgetItemInt(formatIntForDisplay(length), length);
pathLength->setFlags(Qt::ItemIsEnabled | Qt::ItemIsSelectable);
double queryCoveragePath = queryPath->getPathQueryCoverage();
TableWidgetItemDouble * pathQueryCoveragePath = new TableWidgetItemDouble(formatDoubleForDisplay(100.0 * queryCoveragePath, 2) + "%", queryCoveragePath);
pathQueryCoveragePath->setFlags(Qt::ItemIsEnabled | Qt::ItemIsSelectable);
pathLength->setFlags(Qt::ItemIsEnabled | Qt::ItemIsSelectable);
double queryCoverageHits = queryPath->getHitsQueryCoverage();
TableWidgetItemDouble * pathQueryCoverageHits = new TableWidgetItemDouble(formatDoubleForDisplay(100.0 * queryCoverageHits, 2) + "%", queryCoverageHits);
pathQueryCoverageHits->setFlags(Qt::ItemIsEnabled | Qt::ItemIsSelectable);
double percIdentity = queryPath->getMeanHitPercIdentity();
TableWidgetItemDouble * pathPercIdentity = new TableWidgetItemDouble(formatDoubleForDisplay(percIdentity, 2) + "%", percIdentity);
pathPercIdentity->setFlags(Qt::ItemIsEnabled | Qt::ItemIsSelectable);
int mismatches = queryPath->getTotalHitMismatches();
TableWidgetItemInt * pathMismatches = new TableWidgetItemInt(formatIntForDisplay(mismatches), mismatches);
pathMismatches->setFlags(Qt::ItemIsEnabled | Qt::ItemIsSelectable);
int gapOpens = queryPath->getTotalHitGapOpens();
TableWidgetItemInt * pathGapOpens = new TableWidgetItemInt(formatIntForDisplay(gapOpens), gapOpens);
pathGapOpens->setFlags(Qt::ItemIsEnabled | Qt::ItemIsSelectable);
double lengthDisc = queryPath->getRelativeLengthDiscrepancy();
QString lengthDiscSign = "";
if (lengthDisc > 0.0)
lengthDiscSign = "+";
TableWidgetItemDouble * pathLengthDisc = new TableWidgetItemDouble(lengthDiscSign + formatDoubleForDisplay(100.0 * lengthDisc, 2) + "%", lengthDisc);
pathLengthDisc->setFlags(Qt::ItemIsEnabled | Qt::ItemIsSelectable);
double evalueProduct = queryPath->getEvalueProduct();
TableWidgetItemDouble * pathEvalueProduct = new TableWidgetItemDouble(QString::number(evalueProduct), evalueProduct);
pathEvalueProduct->setFlags(Qt::ItemIsEnabled | Qt::ItemIsSelectable);
ui->tableWidget->setItem(i, 0, pathString);
ui->tableWidget->setItem(i, 1, pathLength);
ui->tableWidget->setItem(i, 2, pathQueryCoveragePath);
ui->tableWidget->setItem(i, 3, pathQueryCoverageHits);
ui->tableWidget->setItem(i, 4, pathPercIdentity);
ui->tableWidget->setItem(i, 5, pathMismatches);
ui->tableWidget->setItem(i, 6, pathGapOpens);
ui->tableWidget->setItem(i, 7, pathLengthDisc);
ui->tableWidget->setItem(i, 8, pathEvalueProduct);
}
ui->tableWidget->resizeColumns();
ui->tableWidget->setSortingEnabled(true);
ui->queryPathsInfoText->setInfoText("This table shows information about the possible paths through the graph which "
"represent the query. These paths can be either simple (residing within a single "
"node) or complex (spanning multiple nodes). The columns in the table are as "
"follows:"
"<br><br>"
"<b>Path</b>: This is the query path through the graph, as written in Bandage's "
"path notation. The nodes in the path are separated by commas. The start position "
"in the first node is shown in parentheses at the beginning of the path. The end "
"position in the last node is shown in parentheses at the end of the path."
"<br><br>"
"<b>Length</b>: This is the path length. It is shown in base pairs, whether the "
"query is a nucleotide query or a protein query."
"<br><br>"
"<b>Query covered by path</b>: This is the fraction of the query which is covered "
"by the path. It is calculated by taking 100% and subtracting the fraction of the "
"query which is not captured by the start and the fraction of the query which is "
"not captured by the end."
"<br><br>"
"<b>Query covered by hits</b>: This is the fraction of the query which is covered "
"by the BLAST hits in this path. Since a path may contain nodes or parts of nodes which "
"are not covered by BLAST hits, this value will be less than or equal to the 'Query "
"covered by path' value."
"<br><br>"
"<b>Mean hit identity</b>: This is the mean of the percent identity for the BLAST "
"hits in this path, weighted by the hits' lengths."
"<br><br>"
"<b>Total hit mismatches</b>: This is the sum of the mismatches for the BLAST hits "
"in this path."
"<br><br>"
"<b>Total hit gap opens</b>: This is the sum of the gap opens for the BLAST hits "
"in this path."
"<br><br>"
"<b>Length discrepancy</b>: This is the percent difference in the path length and "
"the appropriate length for the relecant fraction of the query. A positive value "
"indicates that the path is too long; a negative value indicates that the path is "
"too short."
"<br><br>"
"<b>E-value product</b>: This is the product of the e-values for the BLAST hits "
"in this path.");
}
void SettingsDialog::loadOrSaveSettingsToOrFromWidgets(bool setWidgets, Settings * settings)
{
void (*doubleFunctionPointer)(double *, QDoubleSpinBox *, bool);
void (*intFunctionPointer)(int *, QSpinBox *);
void (*colourFunctionPointer)(QColor *, ColourButton *);
void (*sciNotFunctionPointer)(SciNot *, QDoubleSpinBox *, QSpinBox *);
void (*checkBoxFunctionPointer)(bool *, QCheckBox *);
if (setWidgets)
{
doubleFunctionPointer = setOneWidgetFromSetting;
intFunctionPointer = setOneWidgetFromSetting;
colourFunctionPointer = setOneWidgetFromSetting;
sciNotFunctionPointer = setOneWidgetFromSetting;
checkBoxFunctionPointer = setOneWidgetFromSetting;
}
else
{
doubleFunctionPointer = setOneSettingFromWidget;
intFunctionPointer = setOneSettingFromWidget;
colourFunctionPointer = setOneSettingFromWidget;
sciNotFunctionPointer = setOneSettingFromWidget;
checkBoxFunctionPointer = setOneSettingFromWidget;
}
intFunctionPointer(&settings->manualBasePairsPerSegment, ui->basePairsPerSegmentSpinBox);
doubleFunctionPointer(&settings->readDepthEffectOnWidth, ui->readDepthEffectOnWidthSpinBox, true);
doubleFunctionPointer(&settings->readDepthPower, ui->readDepthPowerSpinBox, false);
doubleFunctionPointer(&settings->edgeWidth, ui->edgeWidthSpinBox, false);
doubleFunctionPointer(&settings->outlineThickness, ui->outlineThicknessSpinBox, false);
doubleFunctionPointer(&settings->textOutlineThickness, ui->textOutlineThicknessSpinBox, false);
colourFunctionPointer(&settings->edgeColour, ui->edgeColourButton);
colourFunctionPointer(&settings->outlineColour, ui->outlineColourButton);
colourFunctionPointer(&settings->selectionColour, ui->selectionColourButton);
colourFunctionPointer(&settings->textColour, ui->textColourButton);
colourFunctionPointer(&settings->textOutlineColour, ui->textOutlineColourButton);
intFunctionPointer(&settings->randomColourPositiveSaturation, ui->randomColourPositiveSaturationSpinBox);
intFunctionPointer(&settings->randomColourNegativeSaturation, ui->randomColourNegativeSaturationSpinBox);
intFunctionPointer(&settings->randomColourPositiveLightness, ui->randomColourPositiveLightnessSpinBox);
intFunctionPointer(&settings->randomColourNegativeLightness, ui->randomColourNegativeLightnessSpinBox);
intFunctionPointer(&settings->randomColourPositiveOpacity, ui->randomColourPositiveOpacitySpinBox);
intFunctionPointer(&settings->randomColourNegativeOpacity, ui->randomColourNegativeOpacitySpinBox);
colourFunctionPointer(&settings->uniformPositiveNodeColour, ui->uniformPositiveNodeColourButton);
colourFunctionPointer(&settings->uniformNegativeNodeColour, ui->uniformNegativeNodeColourButton);
colourFunctionPointer(&settings->uniformNodeSpecialColour, ui->uniformNodeSpecialColourButton);
colourFunctionPointer(&settings->lowReadDepthColour, ui->lowReadDepthColourButton);
colourFunctionPointer(&settings->highReadDepthColour, ui->highReadDepthColourButton);
doubleFunctionPointer(&settings->lowReadDepthValue, ui->lowReadDepthValueSpinBox, false);
doubleFunctionPointer(&settings->highReadDepthValue, ui->highReadDepthValueSpinBox, false);
colourFunctionPointer(&settings->noBlastHitsColour, ui->noBlastHitsColourButton);
intFunctionPointer(&settings->contiguitySearchSteps, ui->contiguitySearchDepthSpinBox);
colourFunctionPointer(&settings->contiguousStrandSpecificColour, ui->contiguousStrandSpecificColourButton);
colourFunctionPointer(&settings->contiguousEitherStrandColour, ui->contiguousEitherStrandColourButton);
colourFunctionPointer(&settings->maybeContiguousColour, ui->maybeContiguousColourButton);
colourFunctionPointer(&settings->notContiguousColour, ui->notContiguousColourButton);
colourFunctionPointer(&settings->contiguityStartingColour, ui->contiguityStartingColourButton);
intFunctionPointer(&settings->maxQueryPathNodes, ui->maxPathNodesSpinBox);
doubleFunctionPointer(&settings->minQueryCoveredByPath, ui->minQueryCoveredByPathSpinBox, true);
checkBoxFunctionPointer(&settings->minQueryCoveredByHitsOn, ui->minQueryCoveredByHitsCheckBox);
doubleFunctionPointer(&settings->minQueryCoveredByHits, ui->minQueryCoveredByHitsSpinBox, true);
checkBoxFunctionPointer(&settings->minMeanHitIdentityOn, ui->minMeanHitIdentityCheckBox);
doubleFunctionPointer(&settings->minMeanHitIdentity, ui->minMeanHitIdentitySpinBox, true);
checkBoxFunctionPointer(&settings->maxEValueProductOn, ui->maxEValueProductCheckBox);
sciNotFunctionPointer(&settings->maxEValueProduct, ui->maxEValueCoefficientSpinBox, ui->maxEValueExponentSpinBox);
checkBoxFunctionPointer(&settings->minLengthPercentageOn, ui->minLengthPercentageCheckBox);
doubleFunctionPointer(&settings->minLengthPercentage, ui->minLengthPercentageSpinBox, true);
checkBoxFunctionPointer(&settings->maxLengthPercentageOn, ui->maxLengthPercentageCheckBox);
doubleFunctionPointer(&settings->maxLengthPercentage, ui->maxLengthPercentageSpinBox, true);
checkBoxFunctionPointer(&settings->minLengthBaseDiscrepancyOn, ui->minLengthBaseDiscrepancyCheckBox);
intFunctionPointer(&settings->minLengthBaseDiscrepancy, ui->minLengthBaseDiscrepancySpinBox);
checkBoxFunctionPointer(&settings->maxLengthBaseDiscrepancyOn, ui->maxLengthBaseDiscrepancyCheckBox);
intFunctionPointer(&settings->maxLengthBaseDiscrepancy, ui->maxLengthBaseDiscrepancySpinBox);
//A couple of settings are not in a spin box, check box or colour button, so
//they have to be done manually, not with those function pointers.
if (setWidgets)
{
ui->graphLayoutQualitySlider->setValue(settings->graphLayoutQuality);
ui->antialiasingOnRadioButton->setChecked(settings->antialiasing);
ui->antialiasingOffRadioButton->setChecked(!settings->antialiasing);
ui->readDepthValueAutoRadioButton->setChecked(settings->autoReadDepthValue);
ui->readDepthValueManualRadioButton->setChecked(!settings->autoReadDepthValue);
basePairsPerSegmentManualChanged();
ui->basePairsPerSegmentAutoLabel->setText(formatIntForDisplay(settings->autoBasePairsPerSegment));
ui->lowReadDepthAutoValueLabel2->setText(formatDoubleForDisplay(g_assemblyGraph->m_firstQuartileReadDepth, 2));
ui->highReadDepthAutoValueLabel2->setText(formatDoubleForDisplay(g_assemblyGraph->m_thirdQuartileReadDepth, 2));
ui->basePairsPerSegmentAutoRadioButton->setChecked(settings->nodeLengthMode == AUTO_NODE_LENGTH);
ui->basePairsPerSegmentManualRadioButton->setChecked(settings->nodeLengthMode != AUTO_NODE_LENGTH);
ui->positionVisibleRadioButton->setChecked(!settings->positionTextNodeCentre);
ui->positionCentreRadioButton->setChecked(settings->positionTextNodeCentre);
}
else
{
settings->graphLayoutQuality = ui->graphLayoutQualitySlider->value();
settings->antialiasing = ui->antialiasingOnRadioButton->isChecked();
settings->autoReadDepthValue = ui->readDepthValueAutoRadioButton->isChecked();
if (ui->basePairsPerSegmentAutoRadioButton->isChecked())
settings->nodeLengthMode = AUTO_NODE_LENGTH;
else
settings->nodeLengthMode = MANUAL_NODE_LENGTH;
settings->positionTextNodeCentre = ui->positionCentreRadioButton->isChecked();
}
}
