chadoToGFF(Feature, String, Hashtable, Hashtable, Hashtable, List, Hashtable, Hashtable, Hashtable, Hashtable, GmodDAO, FeatureLoc, ByteBuffer, boolean) |  | 0% |  | 0% | 56 | 56 | 149 | 149 | 1 | 1 |
commit(Vector, boolean) |  | 0% |  | 0% | 39 | 39 | 99 | 99 | 1 | 1 |
appendControlledVocabulary(ByteBuffer, GmodDAO, FeatureCvTerm, List, List, List, boolean) |  | 0% |  | 0% | 27 | 27 | 80 | 80 | 1 | 1 |
getGeneFeature(String, List, GmodDAO, boolean) |  | 0% |  | 0% | 18 | 18 | 69 | 69 | 1 | 1 |
getInputStream() |  | 0% |  | 0% | 13 | 13 | 59 | 59 | 1 | 1 |
constructCvTermString(ByteBuffer, GmodDAO, FeatureCvTerm, List, List, DbXRef, boolean, boolean) |  | 0% |  | 0% | 28 | 28 | 68 | 68 | 1 | 1 |
getGff(GmodDAO, Feature) |  | 0% |  | 0% | 12 | 12 | 66 | 66 | 1 | 1 |
getFeaturesInRange(Feature, Range, GmodDAO) |  | 0% |  | 0% | 6 | 6 | 39 | 39 | 1 | 1 |
main(String[]) |  | 0% |  | 0% | 3 | 3 | 36 | 36 | 1 | 1 |
commitChadoTransaction(ChadoTransaction, GmodDAO, Timestamp) |  | 0% |  | 0% | 21 | 21 | 46 | 46 | 1 | 1 |
getUpdateResiduesColumnTransactions(ChadoTransaction) |  | 0% |  | 0% | 10 | 10 | 33 | 33 | 1 | 1 |
buildGffLineFromId(GmodDAO, int, Hashtable, String, int, ByteBuffer, Feature) |  | 0% |  | 0% | 3 | 3 | 25 | 25 | 1 | 1 |
checkFeatureTimestamp(String, String, GmodDAO, String, Hashtable, ChadoTransaction) |  | 0% |  | 0% | 9 | 9 | 24 | 24 | 1 | 1 |
getOrganismsContainingSrcFeatures() |  | 0% | | n/a | 1 | 1 | 27 | 27 | 1 | 1 |
constructExceptionMessage(RuntimeException, Vector, int) |  | 0% |  | 0% | 10 | 10 | 18 | 18 | 1 | 1 |
adjustChildCoordinates(FeatureLoc, GmodDAO) |  | 0% |  | 0% | 6 | 6 | 22 | 22 | 1 | 1 |
getPolypeptideFeatures(String) |  | 0% |  | 0% | 7 | 7 | 23 | 23 | 1 | 1 |
getSynonymTypeNames(String, GFFStreamFeature) |  | 0% |  | 0% | 5 | 5 | 20 | 20 | 1 | 1 |
getGffDocuments(String, String, String) |  | 0% |  | 0% | 5 | 5 | 13 | 13 | 1 | 1 |
getCdsFeatureLocsByTranscriptName(String) |  | 0% |  | 0% | 6 | 6 | 18 | 18 | 1 | 1 |
reset(String, String) |  | 0% |  | 0% | 4 | 4 | 14 | 14 | 1 | 1 |
checkPubDbXRef(List, int, Pub, FeatureCvTerm) |  | 0% |  | 0% | 5 | 5 | 13 | 13 | 1 | 1 |
getGraphData(int, String) |  | 0% |  | 0% | 3 | 3 | 23 | 23 | 1 | 1 |
DatabaseDocument(String, JPasswordField, String, String, boolean, InputStreamProgressListener) |  | 0% |  | 0% | 3 | 3 | 21 | 21 | 1 | 1 |
DatabaseDocument(String, JPasswordField) |  | 0% |  | 0% | 4 | 4 | 18 | 18 | 1 | 1 |
DatabaseDocument(String, JPasswordField, String, String, ByteBuffer, String) |  | 0% |  | 0% | 3 | 3 | 20 | 20 | 1 | 1 |
getFeatureCvTermDbXRef(GmodDAO, List) |  | 0% |  | 0% | 5 | 5 | 15 | 15 | 1 | 1 |
getFeatureCvTermPub(GmodDAO, List) |  | 0% |  | 0% | 5 | 5 | 15 | 15 | 1 | 1 |
DatabaseDocument(String, JPasswordField, String, String, boolean) |  | 0% |  | 0% | 3 | 3 | 19 | 19 | 1 | 1 |
DatabaseDocument(String, JPasswordField, String, String) |  | 0% |  | 0% | 3 | 3 | 18 | 18 | 1 | 1 |
getCvterms(String, String, boolean) |  | 0% |  | 0% | 6 | 6 | 13 | 13 | 1 | 1 |
getDAOOnly() |  | 0% | | n/a | 1 | 1 | 13 | 13 | 1 | 1 |
getCdsFeatureLocsByPeptideName(String) |  | 0% |  | 0% | 4 | 4 | 14 | 14 | 1 | 1 |
getAllFeatureSynonyms(List) |  | 0% |  | 0% | 3 | 3 | 10 | 10 | 1 | 1 |
getFeaturePubs(GmodDAO, List) |  | 0% |  | 0% | 3 | 3 | 10 | 10 | 1 | 1 |
getFeatureCvTermsByFeature(GmodDAO, List) |  | 0% |  | 0% | 3 | 3 | 10 | 10 | 1 | 1 |
getCvtermFromGoId(String) |  | 0% |  | 0% | 6 | 6 | 11 | 11 | 1 | 1 |
getCvTermByCvTermId(int, Feature) |  | 0% |  | 0% | 4 | 4 | 16 | 16 | 1 | 1 |
getCvterms(GmodDAO) |  | 0% |  | 0% | 2 | 2 | 13 | 13 | 1 | 1 |
getPartOfFeatures(String) |  | 0% |  | 0% | 4 | 4 | 12 | 12 | 1 | 1 |
getChadoGeneByAnyCurrentName(String) |  | 0% |  | 0% | 4 | 4 | 12 | 12 | 1 | 1 |
getCvControledCurationNames() |  | 0% |  | 0% | 5 | 5 | 12 | 12 | 1 | 1 |
getOrganismNames() |  | 0% |  | 0% | 4 | 4 | 11 | 11 | 1 | 1 |
getDAO() |  | 0% |  | 0% | 4 | 4 | 8 | 8 | 1 | 1 |
getChadoSequence(String) |  | 0% | | n/a | 1 | 1 | 7 | 7 | 1 | 1 |
getOutputStream() |  | 0% |  | 0% | 2 | 2 | 7 | 7 | 1 | 1 |
getUniqueNames(ChadoTransaction) |  | 0% |  | 0% | 5 | 5 | 7 | 7 | 1 | 1 |
getName() |  | 0% |  | 0% | 2 | 2 | 6 | 6 | 1 | 1 |
getDatabaseNames() |  | 0% |  | 0% | 2 | 2 | 9 | 9 | 1 | 1 |
getCvTermByCvAndCvTerm(String, String) |  | 0% |  | 0% | 4 | 4 | 8 | 8 | 1 | 1 |
getCvTermByCvPartAndCvTerm(String, String) |  | 0% |  | 0% | 4 | 4 | 8 | 8 | 1 | 1 |
indexOfIgnoreCase(String, String, int) |  | 0% |  | 0% | 3 | 3 | 6 | 6 | 1 | 1 |
insertCvTerm(CvTerm) |  | 0% | | n/a | 1 | 1 | 5 | 5 | 1 | 1 |
getCvtermID(String) |  | 0% |  | 0% | 3 | 3 | 7 | 7 | 1 | 1 |
getFeatureLoc(List, int) |  | 0% |  | 0% | 3 | 3 | 5 | 5 | 1 | 1 |
getChars(byte[]) |  | 0% |  | 0% | 2 | 2 | 4 | 4 | 1 | 1 |
getGraphs() |  | 0% |  | 0% | 3 | 3 | 5 | 5 | 1 | 1 |
DatabaseDocument(DatabaseDocument, String, Feature, Range, InputStreamProgressListener) |  | 0% | | n/a | 1 | 1 | 6 | 6 | 1 | 1 |
getCvTermByCvTermName(String) |  | 0% |  | 0% | 3 | 3 | 7 | 7 | 1 | 1 |
reset() |  | 0% |  | 0% | 3 | 3 | 8 | 8 | 1 | 1 |
getCvTerm(int, GmodDAO, boolean) |  | 0% |  | 0% | 3 | 3 | 5 | 5 | 1 | 1 |
initMDC(DatabaseDocument) |  | 0% | | n/a | 1 | 1 | 8 | 8 | 1 | 1 |
getSimilarityMatches(List) |  | 0% |  | 0% | 2 | 2 | 4 | 4 | 1 | 1 |
append(String) |  | 0% | | n/a | 1 | 1 | 1 | 1 | 1 | 1 |
getChadoSequence(Feature, ByteBuffer) |  | 0% | | n/a | 1 | 1 | 5 | 5 | 1 | 1 |
showCvTermLookUp() |  | 0% | | n/a | 1 | 1 | 7 | 7 | 1 | 1 |
DatabaseDocument(DatabaseDocument, String, String, boolean, InputStreamProgressListener) |  | 0% | | n/a | 1 | 1 | 4 | 4 | 1 | 1 |
getCvTermsByCvName(String) |  | 0% |  | 0% | 2 | 2 | 4 | 4 | 1 | 1 |
createDatabaseDocument() |  | 0% | | n/a | 1 | 1 | 1 | 1 | 1 | 1 |
getCvtermName(int, GmodDAO, boolean) |  | 0% |  | 0% | 2 | 2 | 3 | 3 | 1 | 1 |
getChadoSequence(GmodDAO, ByteBuffer) |  | 0% | | n/a | 1 | 1 | 3 | 3 | 1 | 1 |
loadCvTerms() |  | 0% | | n/a | 1 | 1 | 4 | 4 | 1 | 1 |
getUserName() |  | 0% | | n/a | 1 | 1 | 3 | 3 | 1 | 1 |
isCvThreadAlive() |  | 0% |  | 0% | 3 | 3 | 5 | 5 | 1 | 1 |
getFeatureByUniquename(String) |  | 0% | | n/a | 1 | 1 | 2 | 2 | 1 | 1 |
getOrganismByCommonName(String) |  | 0% | | n/a | 1 | 1 | 2 | 2 | 1 | 1 |
getClustersByFeatureIds(List) |  | 0% | | n/a | 1 | 1 | 2 | 2 | 1 | 1 |
getParentFeaturesByChildFeatureIds(List) |  | 0% | | n/a | 1 | 1 | 2 | 2 | 1 | 1 |
getFeatureDbXRefsByFeatureId(List) |  | 0% | | n/a | 1 | 1 | 2 | 2 | 1 | 1 |
getFeaturesByListOfIds(List) |  | 0% | | n/a | 1 | 1 | 2 | 2 | 1 | 1 |
getFeaturePropByFeatureIds(List) |  | 0% | | n/a | 1 | 1 | 2 | 2 | 1 | 1 |
getFeatureLocsByListOfIds(List) |  | 0% | | n/a | 1 | 1 | 2 | 2 | 1 | 1 |
ping() | | 0% | | n/a | 1 | 1 | 2 | 2 | 1 | 1 |
getResidueFeatures(Integer) | | 0% | | n/a | 1 | 1 | 1 | 1 | 1 | 1 |
setReadChildren(boolean) | | 0% | | n/a | 1 | 1 | 2 | 2 | 1 | 1 |
setName(String) | | 0% | | n/a | 1 | 1 | 2 | 2 | 1 | 1 |
setRange(Range) | | 0% | | n/a | 1 | 1 | 2 | 2 | 1 | 1 |
setLazyFeatureLoad(boolean) | | 0% | | n/a | 1 | 1 | 2 | 2 | 1 | 1 |
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getPfield() | | 0% | | n/a | 1 | 1 | 1 | 1 | 1 | 1 |
isSingleSchema() | | 0% | | n/a | 1 | 1 | 1 | 1 | 1 | 1 |
getIdFeatureStore() | | 0% | | n/a | 1 | 1 | 1 | 1 | 1 | 1 |
isLazyFeatureLoad() | | 0% | | n/a | 1 | 1 | 1 | 1 | 1 | 1 |
setTYPES(String[][][]) | | 0% | | n/a | 1 | 1 | 2 | 2 | 1 | 1 |
readable() | | 0% | | n/a | 1 | 1 | 1 | 1 | 1 | 1 |
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getParent() | | 0% | | n/a | 1 | 1 | 1 | 1 | 1 | 1 |
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static {...} |  | 100% | | n/a | 0 | 1 | 0 | 10 | 0 | 1 |