Task::ReportResult GTest_DNASequenceQualityScores::report() {
GObject *obj = getContext<GObject>(this, objContextName);
if(obj==NULL){
stateInfo.setError(QString("wrong value: %1").arg(OBJ_ATTR));
return ReportResult_Finished;
}
U2SequenceObject * mySequence = qobject_cast<U2SequenceObject*>(obj);
if(mySequence==NULL){
stateInfo.setError(QString("Can't cast to sequence from: %1").arg(obj->getGObjectName()));
return ReportResult_Finished;
}
const DNAQuality& quality = mySequence->getQuality();
if (quality.isEmpty()) {
stateInfo.setError("Sequence doesn't have quality scores");
return ReportResult_Finished;
}
if (quality.qualCodes != qualityScores) {
stateInfo.setError( QString("Quality scores are not valid! The score is %1, expected %2").arg(quality.qualCodes.constData()).arg(qualityScores.constData()));
return ReportResult_Finished;
}
return ReportResult_Finished;
}
Task::ReportResult GTest_DNAMulSequenceQuality::report() {
GObject *obj = getContext<GObject>(this,objContextName);
if (obj==NULL) {
stateInfo.setError(QString("wrong object name: %1").arg(objContextName));
return ReportResult_Finished;
}
MAlignmentObject* myMSequence= qobject_cast<MAlignmentObject*>(obj);
if(myMSequence==NULL){
stateInfo.setError(QString("Can not cast to alignment from: %1").arg(obj->getGObjectName()));
return ReportResult_Finished;
}
bool ok_flag=false;
foreach(const MAlignmentRow& myItem , myMSequence->getMAlignment().getRows()){
if (myItem.getName() == seqName){
ok_flag = true;
//QByteArray qualityCodes = myItem.getCoreQuality().qualCodes;
//if (qualityCodes != expectedQuality){
// stateInfo.setError(
// QString("Quality scores are not valid! The score is %1, expected %2").arg(qualityCodes.constData()).arg(expectedQuality.constData())
// );
// return ReportResult_Finished;
//}
}
}
if(!ok_flag){
stateInfo.setError(QString("Sequence %1 is not found in the alignment").arg(seqName));
}
return ReportResult_Finished;
}
Task::ReportResult GTest_DNASequencePart::report() {
GObject *obj = getContext<GObject>(this,objContextName);
if (obj==NULL) {
stateInfo.setError(QString("wrong value: %1").arg(OBJ_ATTR));
return ReportResult_Finished;
}
U2SequenceObject * objSequence = qobject_cast<U2SequenceObject*>(obj);
if (objSequence==NULL) {
stateInfo.setError(QString("can't cast to sequence from: %1").arg(obj->getGObjectName()));
return ReportResult_Finished;
}
if (objSequence->getSequenceLength() < startPos + subseq.length()) {
stateInfo.setError(QString("sequence size is less that region end: size=%1, region-end=%2, objectName=%3").arg(objSequence->getSequenceLength()).arg(startPos + subseq.length()).arg(obj->getGObjectName()));
return ReportResult_Finished;
}
QByteArray objSubSeq = objSequence->getSequenceData(U2Region(startPos, subseq.length()));
if (!objSequence->getAlphabet()->isCaseSensitive()) {
subseq = subseq.toUpper();
}
if (objSubSeq != subseq){
stateInfo.setError(QString("region not matched: %1, expected %2").arg(objSubSeq.constData()).arg(subseq.constData()));
return ReportResult_Finished;
}
return ReportResult_Finished;
}
Task::ReportResult GTest_DNASequenceQualityValue::report() {
GObject *obj = getContext<GObject>(this, objContextName);
if(obj==NULL){
stateInfo.setError(QString("wrong value: %1").arg(OBJ_ATTR));
return ReportResult_Finished;
}
U2SequenceObject * mySequence = qobject_cast<U2SequenceObject*>(obj);
if(mySequence==NULL){
stateInfo.setError(QString("Can't cast to sequence from: %1").arg(obj->getGObjectName()));
return ReportResult_Finished;
}
const DNAQuality& quality = mySequence->getQuality();
if ( (pos < 0) || (pos > quality.qualCodes.count() - 1 ) ) {
stateInfo.setError(QString("Quality scores doesn't have position %1").arg(pos));
return ReportResult_Finished;
}
int val = quality.getValue(pos);
if (val != expectedVal) {
stateInfo.setError( QString("Quality score values do not match! The score is %1, expected %2").arg(val).arg(expectedVal));
return ReportResult_Finished;
}
return ReportResult_Finished;
}
Task::ReportResult GTest_DNASequencInMulSequence::report() {
GObject *obj = getContext<GObject>(this, objContextName);
if(obj==NULL){
stateInfo.setError(QString("wrong value: %1").arg(OBJ_ATTR));
return ReportResult_Finished;
}
MAlignmentObject* myMSequence= qobject_cast<MAlignmentObject*>(obj);
if(myMSequence==NULL){
stateInfo.setError(QString("can't cast to sequence from: %1").arg(obj->getGObjectName()));
return ReportResult_Finished;
}
int tempSize=myMSequence->getNumRows();
if (tempSize != seqInMSeq){
stateInfo.setError(QString("numbers of Sequence not match: %1, expected %2 ").arg(tempSize).arg(seqInMSeq));
}
return ReportResult_Finished;
}
Task::ReportResult GTest_DNASequenceSize::report() {
GObject *obj = getContext<GObject>(this, objContextName);
if(obj==NULL){
stateInfo.setError(QString("wrong value: %1").arg(OBJ_ATTR));
return ReportResult_Finished;
}
U2SequenceObject * mySequence = qobject_cast<U2SequenceObject*>(obj);
if(mySequence==NULL){
stateInfo.setError(QString("can't cast to sequence from: %1").arg(obj->getGObjectName()));
return ReportResult_Finished;
}
int tempLength=mySequence->getSequenceLength();
if (tempLength != seqSize){
stateInfo.setError(QString("sequence size not matched: %1, expected %2 ").arg(tempLength).arg(seqSize));
}
return ReportResult_Finished;
}
Task::ReportResult GTest_DNAMulSequenceAlphabetId::report() {
GObject *obj = getContext<GObject>(this, objContextName);
if(obj==NULL){
stateInfo.setError(QString("wrong value: %1").arg(OBJ_ATTR));
return ReportResult_Finished;
}
MAlignmentObject* myMSequence= qobject_cast<MAlignmentObject*>(obj);
if(myMSequence==NULL){
stateInfo.setError(QString("can't cast to sequence from: %1").arg(obj->getGObjectName()));
return ReportResult_Finished;
}
const DNAAlphabet *tempAlphabet = myMSequence->getAlphabet();
if( tempAlphabet->getId() != alpId){
stateInfo.setError(QString("Alphabet id not matched: %1 expected %2").arg(tempAlphabet->getId()).arg(alpId));
}
return ReportResult_Finished;
}
Task::ReportResult GTest_DNATranslation3to1Test::report() {
GObject *obj = getContext<GObject>(this, objContextName);
if (obj==NULL){
stateInfo.setError(QString("wrong value: %1").arg(OBJ_ATTR));
return ReportResult_Finished;
}
U2SequenceObject * mySequence = qobject_cast<U2SequenceObject*>(obj);
if(mySequence==NULL){
stateInfo.setError(QString("error can't cast to sequence from: %1").arg(obj->getGObjectName()));
return ReportResult_Finished;
}
if(!(mySequence->getAlphabet()->isNucleic())){
stateInfo.setError(QString("error Alphabet is not Nucleic: %1").arg(mySequence->getAlphabet()->getId()));
return ReportResult_Finished;
}
DNATranslation* aminoTransl = 0;
DNATranslationRegistry* tr = AppContext::getDNATranslationRegistry();
QList<DNATranslation*> aminoTs = tr->lookupTranslation(mySequence->getAlphabet(), DNATranslationType_NUCL_2_AMINO);
if (!aminoTs.empty()) {
aminoTransl = tr->getStandardGeneticCodeTranslation(mySequence->getAlphabet());
}
int tempValue;
if(strTo == -1){
tempValue=-1;
} else{
tempValue=(strTo-strFrom+1);
}
QByteArray myByteArray = mySequence->getSequenceData(U2Region(strFrom,tempValue));
QByteArray rezult(myByteArray.length() / 3, 0);
int n = aminoTransl->translate(myByteArray, myByteArray.length(), rezult.data(), rezult.length());
assert(n == rezult.length()); Q_UNUSED(n);
if(rezult != stringValue.toLatin1()){
stateInfo.setError(QString("translated sequence not matched: %1, expected %2 ").arg(rezult.data()).arg(stringValue));
return ReportResult_Finished;
}
return ReportResult_Finished;
}
Task::ReportResult GTest_DNAMulSequencePart::report() {
GObject *obj = getContext<GObject>(this,objContextName);
if (obj==NULL) {
stateInfo.setError(QString("wrong value: %1").arg(OBJ_ATTR));
return ReportResult_Finished;
}
MAlignmentObject* myMSequence= qobject_cast<MAlignmentObject*>(obj);
if(myMSequence==NULL){
stateInfo.setError(QString("can't cast to sequence from: %1").arg(obj->getGObjectName()));
return ReportResult_Finished;
}
if (myMSequence->getLength() < startPos + subseq.length()) {
stateInfo.setError(QString("sequence size is less that region end: size=%1, region-end=%").arg(myMSequence->getLength(), startPos + subseq.length()));
return ReportResult_Finished;
}
if (!myMSequence->getAlphabet()->isCaseSensitive()) {
subseq = subseq.toUpper();
}
bool ok_flag=false;
U2OpStatus2Log os;
const MAlignment ma = myMSequence->getMAlignment();
foreach(const MAlignmentRow& myItem , ma.getRows()){
if (myItem.getName() == seqName){
ok_flag=true;
QByteArray objSubSeq = myItem.mid(startPos, subseq.length(), os).toByteArray(subseq.length(), os);
if (objSubSeq != subseq){
stateInfo.setError(QString("region not matched: %1, expected %2").arg(objSubSeq.constData()).arg(subseq.constData()));
return ReportResult_Finished;
}
}
}
if(!ok_flag){
stateInfo.setError(QString("no Sequence name: %1").arg(seqName));
}
return ReportResult_Finished;
}
void GTest_CalculateTreeFromAligment::prepare() {
GObject *obj = getContext<GObject>(this, objContextName);
if(obj==NULL){
stateInfo.setError(QString("wrong value: %1").arg(objContextName));
return;
}
MultipleSequenceAlignmentObject* maObj = qobject_cast<MultipleSequenceAlignmentObject*>(obj);
if(maObj==NULL){
stateInfo.setError(QString("can't cast to multimple alignment object from: %1").arg(obj->getGObjectName()));
return;
}
CreatePhyTreeSettings settings;
settings.algorithmId = algName;
settings.mb_ngen = 1000;
settings.mrBayesSettingsScript = QString("Begin MrBayes;\n"
"lset Nst=2 rates=gamma ngammacat=4;\n"
"mcmc ngen=1000 samplefreq=100 printfreq=1000 nchains=4 temp=0.4 savebrlens=yes "
"startingtree=random seed=10;\n"
"sumt burnin=10;\n"
"End;\n");
task = new PhyTreeGeneratorLauncherTask(maObj->getMultipleAlignment(), settings);
if (task == NULL) {
stateInfo.setError(QString("Algorithm %1 not found").arg(algName));
return;
}
addSubTask(task);
}
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;
}
