public abstract class ConsequenceTypeCalculator extends Object
Modifier and Type | Field and Description |
---|---|
protected static String |
CNV_EXTRA_PADDING |
protected int |
cnvExtraPadding |
protected static String |
COMPLEMENTARY_START_CODON |
protected org.opencb.biodata.models.variant.avro.ConsequenceType |
consequenceType |
protected static String |
DOWN_UP_STREAM_GENE_TAG |
protected org.opencb.biodata.models.core.Gene |
gene |
protected GenomeDBAdaptor |
genomeDBAdaptor |
protected Boolean |
imprecise |
protected static String |
IMPRECISE |
protected org.slf4j.Logger |
logger |
protected static String |
MT |
protected static int |
NO_EXON_OVERLAP |
protected HashSet<String> |
SoNames |
protected static String |
START_CODON |
protected static String |
SV_EXTRA_PADDING |
protected int |
svExtraPadding |
protected org.opencb.biodata.models.core.Transcript |
transcript |
protected org.opencb.biodata.models.variant.Variant |
variant |
Constructor and Description |
---|
ConsequenceTypeCalculator() |
Modifier and Type | Method and Description |
---|---|
protected void |
addNonCodingSOs(boolean isIntronicVariant) |
protected void |
decideStopCodonModificationAnnotation(Set<String> soNames,
String referenceCodon,
String modifiedCodon,
boolean useMitochondrialCode) |
protected int |
getEnd(int extraPadding) |
protected char[] |
getReverseComplementaryCodon(String transcriptSequence,
int modifiedCodonStart) |
protected List<org.opencb.biodata.models.variant.avro.SequenceOntologyTerm> |
getSequenceOntologyTerms(HashSet<String> soNames) |
protected int |
getStart(int extraPadding) |
protected void |
parseQueryParam(org.opencb.commons.datastore.core.QueryOptions queryOptions) |
protected Boolean |
regionsOverlap(Integer region1Start,
Integer region1End,
Integer region2Start,
Integer region2End) |
abstract List<org.opencb.biodata.models.variant.avro.ConsequenceType> |
run(org.opencb.biodata.models.variant.Variant variant,
List<org.opencb.biodata.models.core.Gene> geneList,
boolean[] overlapsRegulatoryRegion,
org.opencb.commons.datastore.core.QueryOptions queryOptions) |
protected int |
setCdsAndProteinPosition(int cdnaVariantPosition,
int firstCdsPhase,
int cdnaCodingStart) |
protected boolean |
setInsertionAlleleAminoacidChange(String referenceCodon,
char[] modifiedCodonArray,
char[] formattedReferenceCodonArray,
char[] formattedModifiedCodonArray,
boolean useMitochondrialCode,
boolean firstCodon) |
protected abstract void |
solveCodingNegativeTranscript() |
protected abstract void |
solveCodingPositiveTranscript() |
protected void |
solveIntergenic(List<org.opencb.biodata.models.variant.avro.ConsequenceType> consequenceTypeList,
boolean isIntergenic) |
protected void |
solveMiRNA(int cdnaVariantStart,
int cdnaVariantEnd,
boolean isIntronicVariant) |
protected void |
solveNegativeTranscript(List<org.opencb.biodata.models.variant.avro.ConsequenceType> consequenceTypeList) |
protected abstract void |
solveNonCodingNegativeTranscript() |
protected abstract void |
solveNonCodingPositiveTranscript() |
protected void |
solvePositiveTranscript(List<org.opencb.biodata.models.variant.avro.ConsequenceType> consequenceTypeList) |
protected void |
solveRegulatoryRegions(boolean[] overlapsRegulatoryRegion,
List<org.opencb.biodata.models.variant.avro.ConsequenceType> consequenceTypeList) |
protected int |
updateNegativeInsertionCodonArrays(String reverseTranscriptSequence,
char[] formattedReferenceCodon1Array,
int reverseTranscriptSequencePosition,
int modifiedCodonPosition,
char[] formattedModifiedCodonArray,
char[] modifiedCodonArray) |
protected int |
updatePositiveInsertionCodonArrays(String transcriptSequence,
char[] modifiedCodonArray,
int transcriptSequencePosition,
int modifiedCodonPosition,
char[] formattedReferenceCodonArray,
char[] formattedModifiedCodonArray) |
protected static final String START_CODON
protected static final String COMPLEMENTARY_START_CODON
protected static final String MT
protected org.slf4j.Logger logger
protected org.opencb.biodata.models.variant.avro.ConsequenceType consequenceType
protected org.opencb.biodata.models.core.Gene gene
protected org.opencb.biodata.models.core.Transcript transcript
protected org.opencb.biodata.models.variant.Variant variant
protected GenomeDBAdaptor genomeDBAdaptor
protected Boolean imprecise
protected int svExtraPadding
protected int cnvExtraPadding
protected static final String IMPRECISE
protected static final String SV_EXTRA_PADDING
protected static final String CNV_EXTRA_PADDING
protected static final String DOWN_UP_STREAM_GENE_TAG
protected static final int NO_EXON_OVERLAP
public abstract List<org.opencb.biodata.models.variant.avro.ConsequenceType> run(org.opencb.biodata.models.variant.Variant variant, List<org.opencb.biodata.models.core.Gene> geneList, boolean[] overlapsRegulatoryRegion, org.opencb.commons.datastore.core.QueryOptions queryOptions)
protected void parseQueryParam(org.opencb.commons.datastore.core.QueryOptions queryOptions)
protected int getStart(int extraPadding)
protected int getEnd(int extraPadding)
protected void solvePositiveTranscript(List<org.opencb.biodata.models.variant.avro.ConsequenceType> consequenceTypeList)
protected void solveNegativeTranscript(List<org.opencb.biodata.models.variant.avro.ConsequenceType> consequenceTypeList)
protected abstract void solveNonCodingNegativeTranscript()
protected abstract void solveCodingNegativeTranscript()
protected char[] getReverseComplementaryCodon(String transcriptSequence, int modifiedCodonStart)
protected abstract void solveNonCodingPositiveTranscript()
protected abstract void solveCodingPositiveTranscript()
protected int setCdsAndProteinPosition(int cdnaVariantPosition, int firstCdsPhase, int cdnaCodingStart)
protected Boolean regionsOverlap(Integer region1Start, Integer region1End, Integer region2Start, Integer region2End)
protected void solveIntergenic(List<org.opencb.biodata.models.variant.avro.ConsequenceType> consequenceTypeList, boolean isIntergenic)
protected void solveRegulatoryRegions(boolean[] overlapsRegulatoryRegion, List<org.opencb.biodata.models.variant.avro.ConsequenceType> consequenceTypeList)
protected void decideStopCodonModificationAnnotation(Set<String> soNames, String referenceCodon, String modifiedCodon, boolean useMitochondrialCode)
protected void solveMiRNA(int cdnaVariantStart, int cdnaVariantEnd, boolean isIntronicVariant)
protected void addNonCodingSOs(boolean isIntronicVariant)
protected List<org.opencb.biodata.models.variant.avro.SequenceOntologyTerm> getSequenceOntologyTerms(HashSet<String> soNames)
protected int updateNegativeInsertionCodonArrays(String reverseTranscriptSequence, char[] formattedReferenceCodon1Array, int reverseTranscriptSequencePosition, int modifiedCodonPosition, char[] formattedModifiedCodonArray, char[] modifiedCodonArray)
protected int updatePositiveInsertionCodonArrays(String transcriptSequence, char[] modifiedCodonArray, int transcriptSequencePosition, int modifiedCodonPosition, char[] formattedReferenceCodonArray, char[] formattedModifiedCodonArray)
protected boolean setInsertionAlleleAminoacidChange(String referenceCodon, char[] modifiedCodonArray, char[] formattedReferenceCodonArray, char[] formattedModifiedCodonArray, boolean useMitochondrialCode, boolean firstCodon)
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