void SequenceInfo::updateCommonStatisticsLayout() {
ADVSequenceWidget *wgt = annotatedDnaView->getSequenceWidgetInFocus();
CHECK(wgt != NULL, );
ADVSequenceObjectContext *ctx = wgt->getActiveSequenceContext();
SAFE_POINT(ctx != NULL, tr("Sequence context is NULL"), );
SAFE_POINT(ctx->getAlphabet() != NULL, tr("Sequence alphbet is NULL"), );
int availableSpace = getAvailableSpace(ctx->getAlphabet()->getType());
QString statsInfo = QString("<table cellspacing=%1>").arg(COMMON_STATISTICS_TABLE_CELLSPACING);
statsInfo += formTableRow(CAPTION_SEQ_REGION_LENGTH, getFormattedLongNumber(currentCommonStatistics.length), availableSpace);
if (ctx->getAlphabet()->isNucleic()) {
statsInfo += formTableRow(CAPTION_SEQ_GC_CONTENT, QString::number(currentCommonStatistics.gcContent, 'f', 2) + "%", availableSpace);
statsInfo += formTableRow(CAPTION_SEQ_MOLAR_WEIGHT, QString::number(currentCommonStatistics.molarWeight, 'f', 2) + " Da", availableSpace);
statsInfo += formTableRow(CAPTION_SEQ_MOLAR_EXT_COEF, QString::number(currentCommonStatistics.molarExtCoef) + " I/mol", availableSpace);
statsInfo += formTableRow(CAPTION_SEQ_MELTING_TM, QString::number(currentCommonStatistics.meltingTm, 'f', 2) + " C", availableSpace);
statsInfo += formTableRow(CAPTION_SEQ_NMOLE_OD, QString::number(currentCommonStatistics.nmoleOD260, 'f', 2), availableSpace);
statsInfo += formTableRow(CAPTION_SEQ_MG_OD, QString::number(currentCommonStatistics.mgOD260, 'f', 2), availableSpace);
} else if (ctx->getAlphabet()->isAmino()) {
statsInfo += formTableRow(CAPTION_SEQ_MOLECULAR_WEIGHT, QString::number(currentCommonStatistics.molecularWeight, 'f', 2), availableSpace);
statsInfo += formTableRow(CAPTION_SEQ_ISOELECTIC_POINT, QString::number(currentCommonStatistics.isoelectricPoint, 'f', 2), availableSpace);
}
statsInfo += "</table>";
statisticLabel->setText(statsInfo);
}
void SecStructPredictViewAction::sl_execute() {
QAction *a = dynamic_cast<QAction*>(sender());
GObjectViewAction *viewAction = dynamic_cast<GObjectViewAction*>(a);
SAFE_POINT(NULL != viewAction, "NULL action",);
AnnotatedDNAView *av = qobject_cast<AnnotatedDNAView*>(viewAction->getObjectView());
SAFE_POINT(NULL != av, "NULL dna view",);
SecStructPredictAlgRegistry *sspar = AppContext::getSecStructPredictAlgRegistry();
SAFE_POINT(NULL != sspar, "NULL SecStructPredictAlgRegistry",);
if (sspar->getAlgNameList().isEmpty()) {
QMessageBox::information(av->getWidget(),
tr("Secondary Structure Prediction"),
tr("No algorithms for secondary structure prediction are available.\nPlease, load the corresponding plugins."));
return;
}
ADVSequenceObjectContext *seqCtx = av->getSequenceInFocus();
SAFE_POINT(NULL != seqCtx, "NULL sequence context",);
SAFE_POINT(NULL != seqCtx->getAlphabet(), "NULL alphabet",);
SAFE_POINT(seqCtx->getAlphabet()->isAmino(), "Wrong alphabet",);
QObjectScopedPointer<SecStructDialog> secStructDialog = new SecStructDialog(seqCtx, av->getWidget());
secStructDialog->exec();
}
void EnzymesADVContext::sl_search() {
GObjectViewAction* action = qobject_cast<GObjectViewAction*>(sender());
assert(action!=NULL);
AnnotatedDNAView* av = qobject_cast<AnnotatedDNAView*>(action->getObjectView());
assert(av!=NULL);
ADVSequenceObjectContext* seqCtx = av->getSequenceInFocus();
assert(seqCtx->getAlphabet()->isNucleic());
QObjectScopedPointer<FindEnzymesDialog> d = new FindEnzymesDialog(seqCtx);
d->exec();
}
void SequenceInfo::updateDinuclLayout()
{
ADVSequenceObjectContext* activeSequenceContext = annotatedDnaView->getSequenceInFocus();
SAFE_POINT(0 != activeSequenceContext, "A sequence context is NULL!",);
const DNAAlphabet* activeSequenceAlphabet = activeSequenceContext->getAlphabet();
SAFE_POINT(0 != activeSequenceAlphabet, "An active sequence alphabet is NULL!",);
QString alphabetId = activeSequenceAlphabet->getId();
if ((alphabetId == BaseDNAAlphabetIds::NUCL_DNA_DEFAULT()) ||
(alphabetId == BaseDNAAlphabetIds::NUCL_RNA_DEFAULT()))
{
dinuclWidget->show();
}
else
{
dinuclWidget->hide();
}
}
void SequenceInfo::updateCharOccurLayout()
{
ADVSequenceObjectContext* activeSequenceContext = annotatedDnaView->getSequenceInFocus();
if (0 != activeSequenceContext)
{
const DNAAlphabet* activeSequenceAlphabet = activeSequenceContext->getAlphabet();
SAFE_POINT(0 != activeSequenceAlphabet, "An active sequence alphabet is NULL!",);
if ((activeSequenceAlphabet->isNucleic()) ||
(activeSequenceAlphabet->isAmino()))
{
charOccurWidget->show();
}
else
{
// Do not show the characters occurrence for raw alphabet
charOccurWidget->hide();
}
}
}