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();
}
}
}
void uHMMPlugin::sl_search() {
//to select a sequence
//1. check that annotated DNA view is active
//2. if not -> check that DNASequence object is selected in project view
U2SequenceObject* obj = NULL;
MWMDIWindow* w = AppContext::getMainWindow()->getMDIManager()->getActiveWindow();
if (w!=NULL) {
GObjectViewWindow* ow = qobject_cast<GObjectViewWindow*>(w);
if (ow!=NULL) {
GObjectView* ov = ow->getObjectView();
AnnotatedDNAView* av = qobject_cast<AnnotatedDNAView*>(ov);
if (av!=NULL) {
ADVSequenceObjectContext* seqCtx = av->getSequenceInFocus();
obj = seqCtx->getSequenceObject();
}
}
}
if (obj == NULL) {
ProjectView* pv = AppContext::getProjectView();
if (pv!=NULL) {
const GObjectSelection* sel = pv->getGObjectSelection();
GObject* o = sel->getSelectedObjects().size() == 1 ? sel->getSelectedObjects().first() : NULL;
obj = qobject_cast<U2SequenceObject*>(o);
}
}
QWidget *p = (QWidget*)AppContext::getMainWindow()->getQMainWindow();
if (obj == NULL) {
QMessageBox::critical(p, tr("Error"), tr("Error! Select sequence in Project view or open sequence view."));
return;
}
U2OpStatusImpl os;
DNASequence sequence = obj->getWholeSequence(os);
CHECK_OP_EXT(os, QMessageBox::critical(QApplication::activeWindow(), L10N::errorTitle(), os.getError()), );
QObjectScopedPointer<HMMSearchDialogController> d = new HMMSearchDialogController(sequence, obj, p);
d->exec();
}
void HMMADVContext::sl_search() {
GObjectViewAction* action = qobject_cast<GObjectViewAction*>(sender());
assert(action!=NULL);
AnnotatedDNAView* av = qobject_cast<AnnotatedDNAView*>(action->getObjectView());
assert(av!=NULL);
QWidget *p;
if (av->getWidget()){
p = av->getWidget();
}else{
p = (QWidget*)AppContext::getMainWindow()->getQMainWindow();
}
ADVSequenceObjectContext* seqCtx = av->getSequenceInFocus();
if(seqCtx == NULL) {
QMessageBox::critical(p, tr("Error"), tr("No sequences found"));
return;
}
U2OpStatusImpl os;
DNASequence sequence = seqCtx->getSequenceObject()->getWholeSequence(os);
CHECK_OP_EXT(os, QMessageBox::critical(QApplication::activeWindow(), L10N::errorTitle(), os.getError()), );
QObjectScopedPointer<HMMSearchDialogController> d = new HMMSearchDialogController(sequence, seqCtx->getSequenceObject(), p);
d->exec();
}
void ADVClipboard::copySequenceSelection(bool complement, bool amino) {
ADVSequenceObjectContext* seqCtx = getSequenceContext();
if (seqCtx == NULL) {
QMessageBox::critical(QApplication::activeWindow(), L10N::errorTitle(), "No sequence selected!");
return;
}
QString res;
QVector<U2Region> regions = seqCtx->getSequenceSelection()->getSelectedRegions();
#ifdef UGENE_X86
int totalLen = 0;
foreach (const U2Region& r, regions) {
totalLen += r.length;
}
if (totalLen > MAX_COPY_SIZE_FOR_X86) {
QMessageBox::critical(QApplication::activeWindow(), L10N::errorTitle(), COPY_FAILED_MESSAGE);
return;
}
#endif
if (!regions.isEmpty()) {
U2SequenceObject* seqObj = seqCtx->getSequenceObject();
DNATranslation* complTT = complement ? seqCtx->getComplementTT() : NULL;
DNATranslation* aminoTT = amino ? seqCtx->getAminoTT() : NULL;
U2OpStatus2Log os;
QList<QByteArray> seqParts = U2SequenceUtils::extractRegions(seqObj->getSequenceRef(), regions, complTT, aminoTT, false, os);
if (os.hasError()) {
QMessageBox::critical(QApplication::activeWindow(), L10N::errorTitle(), tr("An error occurred during getting sequence data: %1").arg(os.getError()));
return;
}
if (seqParts.size() == 1) {
putIntoClipboard(seqParts.first());
return;
}
res = U1SequenceUtils::joinRegions(seqParts);
}
putIntoClipboard(res);
}