void OpenMaEditorTask::open() {
if (stateInfo.hasError() || (maObject.isNull() && documentsToLoad.isEmpty())) {
return;
}
if (maObject.isNull()) {
Document* doc = documentsToLoad.first();
if(!doc){
stateInfo.setError(tr("Documet removed from project"));
return;
}
if (unloadedReference.isValid()) {
GObject* obj = doc->findGObjectByName(unloadedReference.objName);
if (obj!=NULL && obj->getGObjectType() == type) {
maObject = qobject_cast<MultipleAlignmentObject*>(obj);
}
} else {
QList<GObject*> objects = doc->findGObjectByType(type, UOF_LoadedAndUnloaded);
maObject = objects.isEmpty() ? NULL : qobject_cast<MultipleAlignmentObject*>(objects.first());
}
if (maObject.isNull()) {
stateInfo.setError(tr("Multiple alignment object not found"));
return;
}
}
viewName = GObjectViewUtils::genUniqueViewName(maObject->getDocument(), maObject);
uiLog.details(tr("Opening MSA editor for object: %1").arg(maObject->getGObjectName()));
MaEditor* v = getEditor(viewName, maObject);
GObjectViewWindow* w = new GObjectViewWindow(v, viewName, false);
MWMDIManager* mdiManager = AppContext::getMainWindow()->getMDIManager();
mdiManager->addMDIWindow(w);
}
QList<Task*> DefaultConvertFileTask::onSubTaskFinished(Task *subTask) {
QList<Task*> result;
CHECK(!subTask->hasError() && !subTask->isCanceled(), result);
CHECK(!hasError() && !isCanceled(), result);
if (saveTask == subTask) {
return result;
}
SAFE_POINT_EXT(loadTask == subTask, setError("Unknown subtask"), result);
bool mainThread = false;
Document *srcDoc = loadTask->getDocument(mainThread);
SAFE_POINT_EXT(NULL != srcDoc, setError("NULL document"), result);
DocumentFormatRegistry *dfr = AppContext::getDocumentFormatRegistry();
DocumentFormat *df = dfr->getFormatById(targetFormat);
SAFE_POINT_EXT(NULL != df, setError("NULL document format"), result);
QSet<GObjectType> selectedFormatObjectsTypes = df->getSupportedObjectTypes();
QSet<GObjectType> inputFormatObjectTypes;
QListIterator<GObject*> objectsIterator(srcDoc->getObjects());
while (objectsIterator.hasNext()) {
GObject *obj = objectsIterator.next();
inputFormatObjectTypes << obj->getGObjectType();
}
inputFormatObjectTypes.intersect(selectedFormatObjectsTypes);
if (inputFormatObjectTypes.empty()) {
setError(tr("The formats are not compatible: %1 and %2").arg(srcDoc->getDocumentFormatId()).arg(targetFormat));
return result;
}
QString ext = targetFormat;
if (!df->getSupportedDocumentFileExtensions().isEmpty()) {
ext = df->getSupportedDocumentFileExtensions().first();
}
if (targetUrl.isEmpty()) {
QString fileName = srcDoc->getName() + "." + ext;
targetUrl = GUrlUtils::rollFileName(workingDir + fileName, QSet<QString>());
} else {
if (QFileInfo(targetFormat).suffix() != ext) {
targetUrl += "." + ext;
}
targetUrl = GUrlUtils::rollFileName(targetUrl, QSet<QString>());
}
IOAdapterFactory *iof = AppContext::getIOAdapterRegistry()->getIOAdapterFactoryById(IOAdapterUtils::url2io(srcDoc->getURL()));
Document *dstDoc = srcDoc->getSimpleCopy(df, iof, srcDoc->getURL());
saveTask = new SaveDocumentTask(dstDoc, iof, targetUrl);
result << saveTask;
return result;
}
Task::ReportResult GTest_CompareTreesInTwoObjects::report() {
Document* doc = getContext<Document>(this, docContextName);
if (doc == NULL) {
stateInfo.setError(QString("document not found %1").arg(docContextName));
return ReportResult_Finished;
}
Document* doc2 = getContext<Document>(this, secondDocContextName);
if (doc2 == NULL) {
stateInfo.setError(QString("document not found %1").arg(secondDocContextName));
return ReportResult_Finished;
}
const QList<GObject*>& objs = doc->getObjects();
const QList<GObject*>& objs2 = doc2->getObjects();
for (int i = 0; i < objs.size() && i < objs2.size(); ++i){
GObject *obj = objs.at(i), *obj2 = objs2.at(i);
PhyTreeObject *treeObj = NULL, *treeObj2 = NULL;
if (obj->getGObjectType() == GObjectTypes::PHYLOGENETIC_TREE){
treeObj = qobject_cast<PhyTreeObject*>(obj);
}
if (obj2->getGObjectType() == GObjectTypes::PHYLOGENETIC_TREE){
treeObj2 = qobject_cast<PhyTreeObject*>(obj2);
}
if (treeObj == NULL){
stateInfo.setError(QString("can't cast to tree from: %1 in position %2").arg(obj->getGObjectName()).arg(i));
return ReportResult_Finished;
}
if (treeObj2 == NULL){
stateInfo.setError(QString("can't cast to tree from: %1 in position %2").arg(obj2->getGObjectName()).arg(i));
return ReportResult_Finished;
}
if (!PhyTreeObject::treesAreAlike(treeObj->getTree(), treeObj2->getTree())) {
stateInfo.setError(QString("trees in position %1 are different").arg(i));
return ReportResult_Finished;
}
}
return ReportResult_Finished;
}
