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Searched refs:CHECK_EXT (Results 1 – 25 of 257) sorted by relevance

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/dports/biology/ugene/ugene-40.1/src/corelibs/U2Formats/src/ace/
H A DAceImportUtils.cpp212 CHECK_EXT(*len != 0, os->setError(DocumentFormatUtils::tr("Unexpected end of file")), ); in skipBreaks()
213 CHECK_EXT(lineOk || io->isEof(), os->setError(DocumentFormatUtils::tr("Line is too long")), ); in skipBreaks()
243 CHECK_EXT(ok, os->setError(DocumentFormatUtils::tr("Parameter is not a digit")), -1); in getSubString()
270 CHECK_EXT(len > 0, os->setError(DocumentFormatUtils::tr("No consensus")), ); in parseConsensus()
304 CHECK_EXT(!name.isEmpty(), os->setError(DocumentFormatUtils::tr("An empty sequence name")), ""); in getName()
386 CHECK_EXT(!line.contains(space), os->setError(DocumentFormatUtils::tr("Bad AF note")), 0); in readsPos()
390 CHECK_EXT(ok, os->setError(DocumentFormatUtils::tr("Bad AF note")), 0); in readsPos()
434 CHECK_EXT(ok, os->setError(DocumentFormatUtils::tr("Bad AF note")), 0); in paddedStartCons()
464 CHECK_EXT(len > 0, os->setError(DocumentFormatUtils::tr("Unexpected end of file")), ); in parseRdAndQaTag()
490 CHECK_EXT(clearRangeStart <= clearRangeEnd && in parseRdAndQaTag()
[all …]
H A DAceFormat.cpp212 CHECK_EXT(!io->hasError(), ti.setError(io->errorString()), ); in skipBreaks()
214 CHECK_EXT(lineOk, ti.setError(ACEFormat::tr("Line is too long")), ); in skipBreaks()
231 CHECK_EXT(!io->hasError(), ti.setError(io->errorString()), ); in parseConsensus()
232 CHECK_EXT(len > 0, ti.setError(ACEFormat::tr("No consensus")), ); in parseConsensus()
241 CHECK_EXT(!io->hasError(), ti.setError(io->errorString()), ); in parseConsensus()
316 CHECK_EXT(!io->hasError(), ti.setError(io->errorString()), ); in parseRDandQATag()
317 CHECK_EXT(len > 0, ti.setError(ACEFormat::tr("No sequence")), ); in parseRDandQATag()
326 CHECK_EXT(!io->hasError(), ti.setError(io->errorString()), ); in parseRDandQATag()
347 CHECK_EXT(checkSeq(sequence), ti.setError(ACEFormat::tr("Bad sequence data")), ); in parseRDandQATag()
398 CHECK_EXT(!io->hasError(), os.setError(io->errorString()), ); in load()
[all …]
/dports/biology/ugene/ugene-40.1/src/plugins/CoreTests/src/
H A DDnaStatisticsTests.cpp67 CHECK_EXT(!regionsString.isEmpty(), emptyValue(REGIONS_ATTR), ); in init()
150 CHECK_EXT(expectedStats.length == result.length, in report()
157 CHECK_EXT(qFuzzyCompare(expectedStats.gcContent + 1, result.gcContent + 1), in report()
164 CHECK_EXT(qFuzzyCompare(expectedStats.meltingTemp + 1, result.meltingTemp + 1), in report()
171 CHECK_EXT(qFuzzyCompare(expectedStats.ssMolecularWeight + 1, result.ssMolecularWeight + 1), in report()
178 CHECK_EXT(expectedStats.ssExtinctionCoefficient == result.ssExtinctionCoefficient, in report()
192 CHECK_EXT(qFuzzyCompare(expectedStats.ssOd260Mass + 1, result.ssOd260Mass + 1), in report()
199 CHECK_EXT(qFuzzyCompare(expectedStats.dsMolecularWeight + 1, result.dsMolecularWeight + 1), in report()
206 CHECK_EXT(expectedStats.dsExtinctionCoefficient == result.dsExtinctionCoefficient, in report()
220 CHECK_EXT(qFuzzyCompare(expectedStats.dsOd260Mass + 1, result.dsOd260Mass + 1), in report()
[all …]
H A DMcaObjectTests.cpp53 …CHECK_EXT(nullptr != doc1, setError(QString("document not found: %1").arg(docContextName)), Report… in report()
55 …CHECK_EXT(1 == objs1.size(), setError(QString("document '%1' contains several objects: the compari… in report()
57 …CHECK_EXT(nullptr != mca1, setError(QString("document '%1' contains an incorrect object: expected … in report()
60 …CHECK_EXT(nullptr != doc2, setError(QString("document not found: %1").arg(secondDocContextName)), … in report()
62 …CHECK_EXT(1 == objs2.size(), setError(QString("document '%1' contains several objects: the compari… in report()
64 …CHECK_EXT(nullptr != mca2, setError(QString("document '%1' contains an incorrect object: expected … in report()
68 …CHECK_EXT((nullptr == reference1 && nullptr == reference2) || (nullptr != reference1 && nullptr !=… in report()
72 CHECK_EXT(rowsNumber1 == rowsNumber2, in report()
86 …CHECK_EXT(areEqual, setError(QString("The rows with number %1 differ from each other").arg(i)), Re… in report()
90 CHECK_EXT(areReferencesEqual, setError("References are not equal"), ReportResult_Finished); in report()
H A DMsaObjectTests.cpp53 …CHECK_EXT(nullptr != doc1, setError(QString("document not found: %1").arg(docContextName)), Report… in report()
56 …CHECK_EXT(1 == objs1.size(), setError(QString("document '%1' contains several objects: the compari… in report()
59 …CHECK_EXT(nullptr != msa1, setError(QString("document '%1' contains an incorrect object: expected … in report()
62 …CHECK_EXT(nullptr != doc2, setError(QString("document not found: %1").arg(secondDocContextName)), … in report()
65 …CHECK_EXT(1 == objs2.size(), setError(QString("document '%1' contains several objects: the compari… in report()
68 …CHECK_EXT(nullptr != msa2, setError(QString("document '%1' contains an incorrect object: expected … in report()
72 CHECK_EXT(rowsNumber1 == rowsNumber2, in report()
86 …CHECK_EXT(areEqual, setError(QString("The rows with number %1 differ from each other").arg(i)), Re… in report()
/dports/biology/ugene/ugene-40.1/src/corelibs/U2Formats/src/
H A DPhylipFormat.cpp53 CHECK_EXT(d != nullptr, os.setError(L10N::badArgument("doc")), ); in storeDocument()
54 CHECK_EXT(io != nullptr && io->isOpen(), os.setError(L10N::badArgument("IO adapter")), ); in storeDocument()
57 … CHECK_EXT(d->getObjects().size() == 1, os.setError("Incorrect number of objects in document"), ); in storeDocument()
65 CHECK_EXT(!os.isCoR(), os.setError(L10N::errorWritingFile(d->getURL())), ); in storeDocument()
138 CHECK_EXT(len == header.length(), os.setError(L10N::errorTitle()), ); in storeEntry()
214 CHECK_EXT(!io->hasError(), os.setError(io->errorString()), MultipleSequenceAlignment()); in parse()
222 CHECK_EXT(!io->hasError(), os.setError(io->errorString()), MultipleSequenceAlignment()); in parse()
259 CHECK_EXT(len == header.length(), os.setError(L10N::errorTitle()), ); in storeEntry()
336 CHECK_EXT(!io->hasError(), os.setError(io->errorString()), MultipleSequenceAlignment()); in parse()
350 CHECK_EXT(!io->hasError(), os.setError(io->errorString()), MultipleSequenceAlignment()); in parse()
[all …]
H A DFastqFormat.cpp143 CHECK_EXT(!io->hasError(), os.setError(io->errorString()), QString()); in readSequenceName()
146 CHECK_EXT(!io->hasError(), os.setError(io->errorString()), QString()); in readSequenceName()
173 CHECK_EXT(!io->hasError(), os.setError(io->errorString()), ); in readSequence()
205 CHECK_EXT(!io->hasError(), os.setError(io->errorString()), ); in readQuality()
400 CHECK_EXT(!emptyObjects || merge, os.setError(Document::tr("Document is empty.")), ); in load()
470 CHECK_EXT(io != nullptr, os.setError("can't write sequence"), ); in writeSequence()
487 CHECK_EXT((writtenCount == len) && (writtenEoln > 0), os.setError(errorMessage), ); in writeSequence()
497 CHECK_EXT(writtenCount == block.length(), os.setError(errorMessage), ); in writeEntry()
507 CHECK_EXT(writtenCount == block.length(), os.setError(errorMessage), ); in writeEntry()
514 CHECK_EXT(wholeSeq.length() == quality.length(), os.setError(errorMessage), ); in writeEntry()
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/dports/biology/ugene/ugene-40.1/src/plugins/external_tool_support/src/peak2gene/
H A DPeak2GeneFormatLoader.cpp38 CHECK_EXT(nullptr != ioAdapter, os.setError(L10N::nullPointerError("IO adapter")), ); in Peak2GeneFormatLoader()
39 CHECK_EXT(ioAdapter->isOpen(), os.setError(L10N::errorReadingFile(ioAdapter->getURL())), ); in Peak2GeneFormatLoader()
96 …CHECK_EXT(!lineValues[ChromName].isEmpty(), skipLine = true; os.addWarning(QString("Chrom name is … in getChromName()
105 CHECK_EXT(ok, skipLine = true; os.addWarning(tr("Incorrect start position at line %1: '%2'") in getRegion()
111 CHECK_EXT(ok, skipLine = true; os.addWarning(tr("Incorrect end position at line %1: '%2'") in getRegion()
120 …CHECK_EXT(!lineValues[PeakName].isEmpty(), skipLine = true; os.addWarning(QString("Peak name is em… in getPeakName()
129 CHECK_EXT(ok, skipLine = true; os.addWarning(tr("Incorrect peak score at line %1: '%2'") in getPeakScore()
139 CHECK_EXT(ok, skipLine = true; os.addWarning(tr("Incorrect NA value at line %1: '%2'") in getNa()
147 …CHECK_EXT(!lineValues[Genes].isEmpty(), skipLine = true; os.addWarning(QString("Genes list is empt… in getGenes()
154 …CHECK_EXT(!lineValues[Strand].isEmpty(), skipLine = true; os.addWarning(QString("Strand is empty a… in getStrand()
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H A DGene2PeakFormatLoader.cpp38 CHECK_EXT(nullptr != ioAdapter, os.setError(L10N::nullPointerError("IO adapter")), ); in Gene2PeakFormatLoader()
39 CHECK_EXT(ioAdapter->isOpen(), os.setError(L10N::errorReadingFile(ioAdapter->getURL())), ); in Gene2PeakFormatLoader()
62 …CHECK_EXT(lineValues.size() == COLUMNS_COUNT, skipLine = true; os.addWarning(QString("Incorrect co… in parseLine()
93 …CHECK_EXT(!lineValues[ChromName].isEmpty(), skipLine = true; os.addWarning(QString("Chrom name is … in getChromName()
102 CHECK_EXT(ok, skipLine = true; os.addWarning(tr("Incorrect start position at line %1: '%2'") in getRegion()
108 CHECK_EXT(ok, skipLine = true; os.addWarning(tr("Incorrect end position at line %1: '%2'") in getRegion()
117 …CHECK_EXT(!lineValues[Gene].isEmpty(), skipLine = true; os.addWarning(QString("Genes list is empty… in getGene()
126 CHECK_EXT(ok, skipLine = true; os.addWarning(tr("Incorrect NA value at line %1: '%2'") in getNa()
134 …CHECK_EXT(!lineValues[Strand].isEmpty(), skipLine = true; os.addWarning(QString("Strand is empty a… in getStrand()
141 …CHECK_EXT(!lineValues[PeakName].isEmpty(), skipLine = true; os.addWarning(QString("Peak name is em… in getPeakName()
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/dports/biology/ugene/ugene-40.1/src/plugins/clark_support/src/
H A DClarkTests.cpp52 CHECK_EXT(!database1.isEmpty(), setError("Database 1 URL is empty"), ); in init()
61 CHECK_EXT(!database2.isEmpty(), setError("Database 2 URL is empty"), ); in init()
87 …CHECK_EXT(QFileInfo::exists(database1), setError(QString("Database 1 doesn't exist: '%1'").arg(dat… in report()
88 …CHECK_EXT(QFileInfo(database1).isDir(), setError(QString("Database 1 is not a directory: '%1'").ar… in report()
90 …CHECK_EXT(QFileInfo::exists(database2), setError(QString("Database 2 doesn't exist: '%1'").arg(dat… in report()
91 …CHECK_EXT(QFileInfo(database2).isDir(), setError(QString("Database 2 is not a directory: '%1'").ar… in report()
97 …CHECK_EXT(opened, setError(QString("Can't open metafile '%1' for reading").arg(metafile1.fileName(… in report()
103 …CHECK_EXT(opened, setError(QString("Can't open metafile '%1' for reading").arg(metafile2.fileName(… in report()
118 CHECK_EXT(metafile1Line == metafile2Line, in report()
128 CHECK_EXT(metafileStream1.atEnd() && metafileStream2.atEnd(), in report()
/dports/biology/ugene/ugene-40.1/src/plugins/api_tests/src/core/dbi/sequence/
H A DSequenceDbiUnitTests.cpp154 CHECK_EXT(expectedSeq == actualSeq, t->SetError("incorrect updated sequence"), ); in checkUpdateSequence()
165 CHECK_EXT(region.startPos == 0, t->SetError("region start position should be 0"), ); in replaceRegion()
208 CHECK_EXT(os.hasError(), SetError("error should be thrown"), ); in Test()
209 CHECK_EXT(seq.id.isEmpty(), SetError("sequence id shuld be empty"), ); in Test()
220 CHECK_EXT(id == seq.id, SetError("incorrect expected sequence id"), ); in Test()
237 CHECK_EXT(!seq.id.isEmpty(), SetError("sequence id should not be empty"), ); in Test()
259 CHECK_EXT(expected == actual, SetError("incorrect expected sequence data"), ); in Test()
279 CHECK_EXT(expected == actual, SetError("incorrect expected sequence data"), ); in Test()
292 CHECK_EXT(res.isEmpty(), SetError("sequence data should be empty"), ); in Test()
343 CHECK_EXT(!seq.id.isEmpty(), SetError("sequence id should not be empty"), ); in Test()
[all …]
/dports/biology/ugene/ugene-40.1/src/plugins/GUITestBase/src/runnables/ugene/plugins/workflow_designer/
H A DCreateElementWithCommandLineToolFiller.cpp159 CHECK_EXT(nullptr != nameEdit, errorMessage = "leName not found", false); in processFirstPage()
171 CHECK_EXT(nullptr != leToolPath, errorMessage = "leName not found", false); in processFirstPage()
194 CHECK_EXT(false, errorMessage = "Unexpected tool type", false); in processFirstPage()
206 CHECK_EXT(nullptr != pbAddInput, errorMessage = "pbAddInput not found", false); in processSecondPage()
209 CHECK_EXT(nullptr != tvInput, errorMessage = "tvInput not found", false); in processSecondPage()
221 CHECK_EXT(nullptr != pbAdd, errorMessage = "pbAdd not found", false); in processThirdPage()
235 CHECK_EXT(nullptr != pbAddOutput, errorMessage = "pbAddOutput not found", false); in processFourthPage()
238 CHECK_EXT(nullptr != tvOutput, errorMessage = "tvOutput not found", false); in processFourthPage()
250 CHECK_EXT(nullptr != teCommand, errorMessage = "teCommand not found", false); in processFifthPage()
266 CHECK_EXT(nullptr != teDescription, errorMessage = "teCommand not found", false); in processSixthPage()
[all …]
/dports/biology/ugene/ugene-40.1/src/plugins/diamond_support/src/
H A DGenomesPreparationTask.cpp37 CHECK_EXT(genomesUrls.count() > 0, setError(tr("Genomes URLs are not set")), ); in GenomesPreparationTask()
38 …CHECK_EXT(!preparedGenomesFileUrl.isEmpty(), setError(tr("File URL to write prepared genomes is em… in GenomesPreparationTask()
53 CHECK_EXT(readerInited, setError(reader.getErrorMessage()), ); in run()
57 CHECK_EXT(writerInited, setError(L10N::errorOpeningFileWrite(preparedGenomesFileUrl)), ); in run()
62 CHECK_EXT(nullptr != sequence, setError(reader.getErrorMessage()), ); in run()
64 CHECK_EXT(written, setError(L10N::errorWritingFile(preparedGenomesFileUrl)), ); in run()
/dports/biology/ugene/ugene-40.1/src/plugins/api_tests/src/core/util/
H A DDatatypeSerializeUtilsUnitTest.cpp37 CHECK_EXT(chr1.seqLength == chr2.seqLength, os.setError("seqLength"), ); in checkEqual()
38 CHECK_EXT(chr1.baseCalls == chr2.baseCalls, os.setError("baseCalls"), ); in checkEqual()
39 CHECK_EXT(chr1.A == chr2.A, os.setError("A"), ); in checkEqual()
40 CHECK_EXT(chr1.C == chr2.C, os.setError("C"), ); in checkEqual()
41 CHECK_EXT(chr1.G == chr2.G, os.setError("G"), ); in checkEqual()
42 CHECK_EXT(chr1.T == chr2.T, os.setError("T"), ); in checkEqual()
43 CHECK_EXT(chr1.prob_A == chr2.prob_A, os.setError("prob_A"), ); in checkEqual()
44 CHECK_EXT(chr1.prob_C == chr2.prob_C, os.setError("prob_C"), ); in checkEqual()
45 CHECK_EXT(chr1.prob_G == chr2.prob_G, os.setError("prob_G"), ); in checkEqual()
46 CHECK_EXT(chr1.prob_T == chr2.prob_T, os.setError("prob_T"), ); in checkEqual()
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/dports/biology/ugene/ugene-40.1/src/plugins/external_tool_support/src/custom_tools/
H A DCustomToolConfigParser.cpp58 …CHECK_EXT(file.open(QIODevice::ReadOnly), os.setError(tr("Invalid config file format: file %1 cann… in parse()
67 …CHECK_EXT(!nodesList.isEmpty(), os.setError(tr("Invalid config file format: custom tool descriptio… in parse()
68 …CHECK_EXT(1 == nodesList.count(), os.setError(tr("Invalid config file format: there are too many e… in parse()
71 CHECK_EXT(!configElement.isNull(), os.setError(tr("Can't parse the config file")), nullptr); in parse()
74 …CHECK_EXT(HARDCODED_EXPECTED_VERSION == version, os.setError(tr("Can't parse config with version %… in parse()
160 …CHECK_EXT(!tool->getId().isEmpty(), os.setError(tr("The tool id is not specified in the config fil… in validate()
161 …CHECK_EXT(!tool->getId().contains(QRegularExpression("[^A-Za-z0-9_\\-]")), os.setError(tr("The too… in validate()
162 …CHECK_EXT(!tool->getId().startsWith("USUPP_"), os.setError(tr("The custom tool's ID shouldn't star… in validate()
163 …CHECK_EXT(!tool->getId().startsWith("UCUST_"), os.setError(tr("The custom tool's ID shouldn't star… in validate()
164 …CHECK_EXT(!tool->getName().isEmpty(), os.setError(tr("The tool name is not specified in the config… in validate()
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/dports/biology/ugene/ugene-40.1/src/plugins/wevote_support/src/
H A DPrepareWevoteTaxonomyDataTask.cpp52 CHECK_EXT(taxonomyDataPath->isValid(), setError(tr("Taxonomy data are missed")), ); in PrepareWevoteTaxonomyDataTask()
57 CHECK_EXT(!taxonomyNamesUrl.isEmpty(), in PrepareWevoteTaxonomyDataTask()
59 CHECK_EXT(!taxonomyNodesUrl.isEmpty(), in PrepareWevoteTaxonomyDataTask()
100 CHECK_EXT(isSourceOpened, setError(L10N::errorOpeningFileRead(sourceFile.fileName())), ); in prepareNamesFile()
104 …CHECK_EXT(isDestinationOpened, setError(L10N::errorOpeningFileWrite(destinationFile.fileName())), … in prepareNamesFile()
123 CHECK_EXT(isSourceOpened, setError(L10N::errorOpeningFileRead(sourceFile.fileName())), ); in prepareNodesFile()
127 …CHECK_EXT(isDestinationOpened, setError(L10N::errorOpeningFileWrite(destinationFile.fileName())), … in prepareNodesFile()
H A DWevoteTask.cpp84 …CHECK_EXT(QFileInfo(wevotePrefix + SUFFIX).exists(), setError(tr("Wevote output file not found")),… in run()
110 …CHECK_EXT(!wevoteTaxonomyDir.isEmpty(), setError(tr("Can't find prepared taxonomy for WEVOTE")), a… in getArguments()
124 … CHECK_EXT(success, setError(tr("Can't overwrite the file \"%1\"").arg(settings.outputFileUrl)), ); in moveFile()
134 CHECK_EXT(columns.size() >= 2, setError(tr("Too few columns in the result file.")), ); in parseClassification()
137 CHECK_EXT(ok, setError(tr("Can't parse the taxID: \"%1\"").arg(columns.last())), ); in parseClassification()
/dports/biology/ugene/ugene-40.1/src/corelibs/U2Core/src/datatype/
H A DUdrSchema.cpp73 CHECK_EXT(!contains(desc.getName()), os.setError("Duplicate name"), ); in addField()
75 … CHECK_EXT(NOT_INDEXED == desc.getIndexType(), os.setError("BLOB data can not be indexed"), ); in addField()
77 …CHECK_EXT(UdrSchemaRegistry::isCorrectName(desc.getName()), os.setError("Incorrect field name"), ); in addField()
82 CHECK_EXT(multiIndex.toSet().size() == multiIndex.size(), os.setError("Not unique fields"), ); in addMultiIndex()
86 CHECK_EXT(BLOB != field.getDataType(), os.setError("BLOB data can not be indexed"), ); in addMultiIndex()
88 CHECK_EXT(!multiIndexes.contains(multiIndex), os.setError("Duplicate multi index"), ); in addMultiIndex()
105 …CHECK_EXT(0 <= fieldNum && fieldNum < size(), os.setError("Out of range"), FieldDesc("", INTEGER)); in getField()
/dports/biology/ugene/ugene-40.1/src/plugins/dbi_bam/src/
H A DSamtoolsBasedDbi.cpp226 CHECK_EXT(U2DbiState_Ready == dbi.getState(), in countObjects()
239 CHECK_EXT(U2DbiState_Ready == dbi.getState(), in getObjectNames()
247 CHECK_EXT(U2DbiState_Ready == dbi.getState(), in getObject()
259 CHECK_EXT(U2DbiState_Ready == dbi.getState(), in getObjects()
276 CHECK_EXT(U2DbiState_Ready == dbi.getState(), in getParents()
283 CHECK_EXT(U2DbiState_Ready == dbi.getState(), in getFolders()
290 CHECK_EXT(U2DbiState_Ready == dbi.getState(), in countObjects()
294 CHECK_EXT(U2ObjectDbi::ROOT_FOLDER == folder, in countObjects()
302 CHECK_EXT(U2DbiState_Ready == dbi.getState(), in getObjects()
306 CHECK_EXT(U2ObjectDbi::ROOT_FOLDER == folder, in getObjects()
[all …]
/dports/biology/ugene/ugene-40.1/src/plugins/external_tool_support/src/blast_plus/align_worker_subtasks/
H A DBlastReadsSubTask.cpp138 … CHECK_EXT(!refObject.isNull(), setError(L10N::nullPointerError("Reference sequence")), result); in onSubTaskFinished()
166 …CHECK_EXT(!msaObject.isNull(), setError(L10N::nullPointerError("MSA object for %1").arg(getReadNam… in onSubTaskFinished()
168 …CHECK_EXT(2 == rowCount, setError(L10N::internalError("Wrong rows count: " + QString::number(rowCo… in onSubTaskFinished()
180 CHECK_EXT(nullptr != factory, setError("MSADistanceAlgorithmFactory is NULL"), result); in onSubTaskFinished()
184 CHECK_EXT(nullptr != algo, setError("MSADistanceAlgorithm is NULL"), result); in onSubTaskFinished()
265 CHECK_EXT(!readObject.isNull(), setError(L10N::nullPointerError("U2SequenceObject")), nullptr); in getBlastTask()
326 CHECK_EXT(!readObject.isNull(), setError(L10N::nullPointerError("Read sequence")), U2Region()); in getReferenceRegion()
339 CHECK_EXT(!refObject.isNull(), setError(L10N::nullPointerError("Reference sequence")), ); in createAlignment()
341 CHECK_EXT(!readObject.isNull(), setError(L10N::nullPointerError("Read sequence")), ); in createAlignment()
377 …CHECK_EXT(nullptr != algo, os.setError(BlastAndSwReadTask::tr("The %1 algorithm is not found. Add … in getAbstractAlignmentTaskFactory()
[all …]
/dports/biology/ugene/ugene-40.1/src/plugins/external_tool_support/src/bedtools/
H A DBedtoolsIntersectTask.cpp72 CHECK_EXT(!settings.inputA.isEmpty(), setError(tr("No input A URL")), ); in prepare()
73 CHECK_EXT(!settings.inputB.isEmpty(), setError(tr("No input B URL(s)")), ); in prepare()
74 CHECK_EXT(!settings.out.isEmpty(), setError(tr("Output URL is not set")), ); in prepare()
175 CHECK_EXT(ioFactory != nullptr, setError(tr("Failed to get IOAdapterFactory")), res); in onSubTaskFinished()
182 CHECK_EXT(resultDoc != nullptr, setError(tr("Result document is NULL")), res); in onSubTaskFinished()
184 CHECK_EXT(!result.isEmpty(), setError(tr("No annotation tables resultDoc")), res); in onSubTaskFinished()
195 CHECK_EXT(bed != nullptr, setError(tr("Failed to get BED format")), nullptr); in createAnnotationsDocument()
198 CHECK_EXT(ioFactory != nullptr, setError(tr("Failed to get IOAdapterFactory")), nullptr); in createAnnotationsDocument()
/dports/biology/ugene/ugene-40.1/src/corelibs/U2View/src/ov_text/
H A DSimpleTextObjectViewTasks.cpp42 CHECK_EXT(nullptr != obj, stateInfo.setError(tr("Invalid object detected!")), ); in OpenSimpleTextObjectViewTask()
43 CHECK_EXT(GObjectTypes::TEXT == obj->getGObjectType(), in OpenSimpleTextObjectViewTask()
47 CHECK_EXT(nullptr != doc, stateInfo.setError(tr("Invalid document detected!")), ); in OpenSimpleTextObjectViewTask()
96 CHECK_EXT(doc->isLoaded(), stateInfo.setError(tr("Document is not loaded!")), ); in open()
99 CHECK_EXT(nullptr != obj, stateInfo.setError(tr("Invalid object detected!")), ); in open()
/dports/biology/ugene/ugene-40.1/src/corelibs/U2Lang/src/support/
H A DSimpleWorkflowTask.cpp90 …CHECK_EXT(!schemaPath.isEmpty(), setError(tr("Internal error: cannot find workflow %1").arg(conf.s… in prepare()
171 CHECK_EXT(!msaObjectPointer.isNull(), setError(tr("Object '%1' removed").arg(docName)), ); in prepare()
186 …CHECK_EXT(!msaObjectPointer.isNull(), setError(tr("Object '%1' removed").arg(docName)), ReportResu… in report()
187 …CHECK_EXT(!msaObjectPointer->isStateLocked(), setError(tr("Object '%1' is locked").arg(docName)), … in report()
214 CHECK_EXT(d != nullptr, setError(tr("Result document not found!")), res); in getResult()
215 …CHECK_EXT(d->getObjects().size() == 1, setError(tr("Result document content not matched! %1").arg(… in getResult()
218 …CHECK_EXT(maObj != nullptr, setError(tr("Result document contains no MSA! %1").arg(d->getURLString… in getResult()
/dports/biology/ugene/ugene-40.1/src/corelibs/U2Core/src/tasks/
H A DCloneObjectTask.cpp40 CHECK_EXT(nullptr != srcObj, setError(tr("Invalid source object")), ); in CloneObjectTask()
41 CHECK_EXT(nullptr != dstDoc, setError(tr("Invalid destination document")), ); in CloneObjectTask()
52 CHECK_EXT(dstDbiRef.isValid(), setError(tr("Invalid destination database reference")), ); in CloneObjectTask()
68 CHECK_EXT(!srcObj.isNull(), setError(tr("The object has been removed")), ); in run()
/dports/biology/ugene/ugene-40.1/src/plugins/external_tool_support/src/stringtie/
H A DStringtieGeneAbundanceReportTask.cpp76 …CHECK_EXT(QDir(tmpDir).exists(), setError(tr("The directory \"%1\" did not created").arg(tmpDir)),… in run()
93 …CHECK_EXT(QDir(runDir).exists(), setError(tr("The directory \"%1\" did not created").arg(runDir)),… in run()
135 CHECK_EXT(blockLen <= 0 || terminatorFound, in mergeFpkmToReportUrl()
142 CHECK_EXT(terminatorFound, in mergeFpkmToReportUrl()
147 CHECK_EXT(buf.size() == 3, in mergeFpkmToReportUrl()
228 CHECK_EXT(parsedLines.size() > 0, in sortAndShrinkToTemp()
235 CHECK_EXT(indexFpkm != -1, in sortAndShrinkToTemp()
259 CHECK_EXT(line.size() >= indexFpkm, in sortAndShrinkToTemp()

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