| AbstractPairedEndAlignment(BasicAnnotation b) | umms.core.alignment.AbstractPairedEndAlignment | |
| addBlocks(Annotation block) | umms.core.annotation.BasicAnnotation | |
| addBlocks(Collection<?extends Annotation > blocks) | umms.core.annotation.BasicAnnotation | |
| asAnnotation(SingleEndAlignment firstMate, SingleEndAlignment secondMate, boolean fullFragment) | umms.core.alignment.AbstractPairedEndAlignment | protectedstatic |
| BasicAnnotation() | umms.core.annotation.BasicAnnotation | |
| BasicAnnotation(SAMRecord samRecord) | umms.core.annotation.BasicAnnotation | |
| BasicAnnotation(String ucsc) | umms.core.annotation.BasicAnnotation | |
| BasicAnnotation(String referenceName, int start, int end, Strand orientation, String name) | umms.core.annotation.BasicAnnotation | |
| BasicAnnotation(String referenceName, Strand orientation, String name, Collection<?extends Annotation > blocks) | umms.core.annotation.BasicAnnotation | |
| BasicAnnotation(String referenceName, int start, int end) | umms.core.annotation.BasicAnnotation | |
| BasicAnnotation(String referenceName, int start, int end, Strand orientation) | umms.core.annotation.BasicAnnotation | |
| BasicAnnotation(String referenceName, int start, int end, String orientation) | umms.core.annotation.BasicAnnotation | |
| BasicAnnotation(BasicAnnotation other) | umms.core.annotation.BasicAnnotation | |
| BasicAnnotation(Annotation other) | umms.core.annotation.BasicAnnotation | |
| BasicAnnotation(Collection<?extends Annotation > blocks) | umms.core.annotation.BasicAnnotation | |
| BasicAnnotation(Collection<?extends Annotation > blocks, Strand orientation, String name) | umms.core.annotation.BasicAnnotation | |
| BasicAnnotation(Collection<?extends Annotation > blocks, String name) | umms.core.annotation.BasicAnnotation | |
| BasicAnnotation(String referenceName, CompoundInterval blocks, Strand orientation, String name) | umms.core.annotation.BasicAnnotation | |
| BasicAnnotation(String referenceName, CompoundInterval blocks, Strand orientation) | umms.core.annotation.BasicAnnotation | |
| BasicAnnotation(String referenceName, CompoundInterval blocks) | umms.core.annotation.BasicAnnotation | |
| blocks | umms.core.annotation.BasicAnnotation | protected |
| compareTo(Annotation other) | umms.core.annotation.AbstractAnnotation | |
| compareToAnnotation(Annotation b) | umms.core.annotation.AbstractAnnotation | |
| compareToAnnotation(Annotation b, boolean useOrientation) | umms.core.annotation.AbstractAnnotation | |
| complement() | umms.core.annotation.BasicAnnotation | |
| contains(Annotation other) | umms.core.annotation.BasicAnnotation | |
| copy() | umms.core.annotation.BasicAnnotation | |
| createFromUCSC(String ucsc) | umms.core.annotation.BasicAnnotation | static |
| disect(Annotation a) | umms.core.annotation.BasicAnnotation | |
| disect(List<?extends Annotation > disectors) | umms.core.annotation.BasicAnnotation | |
| equals(Object o) | umms.core.alignment.FragmentAlignment | |
| umms::core::alignment::AbstractPairedEndAlignment.equals(Annotation a) | umms.core.annotation.AbstractAnnotation | |
| umms::core::alignment::AbstractPairedEndAlignment.equals(Annotation a, boolean useOrientation) | umms.core.annotation.AbstractAnnotation | |
| expand(int deltaStart, int deltaEnd) | umms.core.annotation.AbstractAnnotation | |
| FragmentAlignment(SingleEndAlignment read1, SingleEndAlignment read2) | umms.core.alignment.FragmentAlignment | |
| FragmentAlignment(SingleEndAlignment read1, SingleEndAlignment read2, TranscriptionRead transcriptionRead) | umms.core.alignment.FragmentAlignment | |
| fromFullInfoString(String fullInfoString) | umms.core.annotation.BasicAnnotation | static |
| fullyContains(Annotation other) | umms.core.annotation.AbstractAnnotation | |
| getAlignmentEnd() | umms.core.alignment.AbstractPairedEndAlignment | |
| getAlignmentStart() | umms.core.alignment.AbstractPairedEndAlignment | |
| getAttribute(String attribute) | umms.core.alignment.AbstractPairedEndAlignment | |
| getBlocks() | umms.core.annotation.BasicAnnotation | |
| getBlocks(boolean oriented) | umms.core.annotation.BasicAnnotation | |
| getChr() | umms.core.alignment.AbstractPairedEndAlignment | |
| getChromosome() | umms.core.alignment.AbstractPairedEndAlignment | |
| getDistanceTo(Annotation other) | umms.core.annotation.AbstractAnnotation | |
| getEnd() | umms.core.alignment.AbstractPairedEndAlignment | |
| getFirstFragmentPositionStranded() | umms.core.alignment.AbstractPairedEndAlignment | |
| getFirstMate() | umms.core.alignment.AbstractPairedEndAlignment | |
| getFlankingBlocks(Annotation spliceJunction) | umms.core.annotation.BasicAnnotation | |
| getFragment(CoordinateSpace C) | umms.core.alignment.AbstractPairedEndAlignment | |
| getFragmentEnd() | umms.core.alignment.AbstractPairedEndAlignment | |
| getFragmentMidpoint(Annotation annot) | umms.core.alignment.AbstractPairedEndAlignment | |
| getFragmentSize(CoordinateSpace C) | umms.core.alignment.AbstractPairedEndAlignment | |
| getFragmentStart() | umms.core.alignment.AbstractPairedEndAlignment | |
| getFragmentStrand() | umms.core.alignment.AbstractPairedEndAlignment | |
| getFullInfoString() | umms.core.annotation.AbstractAnnotation | |
| getHeader() | umms.core.alignment.AbstractPairedEndAlignment | |
| getIntervalBetweenReads() | umms.core.alignment.AbstractPairedEndAlignment | |
| getLastFragmentPositionStranded() | umms.core.alignment.AbstractPairedEndAlignment | |
| getLengthOnReference() | umms.core.annotation.AbstractAnnotation | |
| getMappingQuality() | umms.core.alignment.AbstractPairedEndAlignment | |
| getMidpoint() | umms.core.annotation.BasicAnnotation | |
| getName() | umms.core.annotation.BasicAnnotation | |
| getOrientation() | umms.core.alignment.AbstractPairedEndAlignment | |
| getOrientedEnd() | umms.core.annotation.AbstractAnnotation | |
| getOrientedStart() | umms.core.annotation.AbstractAnnotation | |
| getOverlap(Annotation other) | umms.core.annotation.BasicAnnotation | |
| getPositionAtReferenceCoordinate(int referenceCoordinate, boolean ignoreOrientation) | umms.core.annotation.BasicAnnotation | |
| umms::core::annotation::AbstractAnnotation.getPositionAtReferenceCoordinate(int referenceCoordinate) | umms.core.annotation.AbstractAnnotation | |
| getReadAlignmentBlocks(CoordinateSpace C) | umms.core.alignment.AbstractPairedEndAlignment | |
| getReadAlignments(CoordinateSpace space) | umms.core.alignment.AbstractPairedEndAlignment | |
| getReadMates() | umms.core.alignment.AbstractPairedEndAlignment | |
| getReadName() | umms.core.alignment.AbstractPairedEndAlignment | |
| getReadSequence() | umms.core.alignment.AbstractPairedEndAlignment | |
| getReferenceCoordinateAtPosition(int positionInAnnotation, boolean ignoreOrientation) | umms.core.annotation.BasicAnnotation | |
| umms::core::annotation::AbstractAnnotation.getReferenceCoordinateAtPosition(int positionInAnnotation) | umms.core.annotation.AbstractAnnotation | |
| getReferenceName() | umms.core.annotation.BasicAnnotation | |
| getSAMEnd() | umms.core.annotation.AbstractAnnotation | |
| getSAMStart() | umms.core.annotation.AbstractAnnotation | |
| getScore() | umms.core.annotation.BasicAnnotation | |
| getSecondMate() | umms.core.alignment.AbstractPairedEndAlignment | |
| getSize() | umms.core.annotation.AbstractAnnotation | |
| umms::core::annotation::BasicAnnotation.getSpliceConnections() | umms.core.annotation.BasicAnnotation | |
| umms::core::alignment::Alignment.getSpliceConnections() | umms.core.alignment.Alignment | |
| getStart() | umms.core.alignment.AbstractPairedEndAlignment | |
| getStrand() | umms.core.annotation.AbstractAnnotation | |
| getStrand(String orientation) | umms.core.annotation.AbstractAnnotation | static |
| getStrand(char orientation) | umms.core.annotation.AbstractAnnotation | static |
| getWeight() | umms.core.alignment.AbstractPairedEndAlignment | |
| hashCode() | umms.core.alignment.FragmentAlignment | |
| hasIndel() | umms.core.alignment.AbstractPairedEndAlignment | |
| hasOrientation() | umms.core.annotation.AbstractAnnotation | |
| intersect(Annotation other) | umms.core.annotation.BasicAnnotation | |
| umms::core::annotation::AbstractAnnotation.intersect(List<?extends Annotation > others) | umms.core.annotation.AbstractAnnotation | |
| isChimera() | umms.core.alignment.AbstractPairedEndAlignment | |
| isDuplicate() | umms.core.alignment.AbstractPairedEndAlignment | |
| isMapped() | umms.core.alignment.AbstractPairedEndAlignment | |
| isNegativeStrand() | umms.core.alignment.AbstractPairedEndAlignment | |
| isPaired() | umms.core.alignment.AbstractPairedEndAlignment | |
| isProperPair() | umms.core.alignment.AbstractPairedEndAlignment | |
| isUnoriented() | umms.core.annotation.BasicAnnotation | |
| length() | umms.core.annotation.BasicAnnotation | |
| main(String[] args) | umms.core.annotation.BasicAnnotation | static |
| MAX_DISTANCE | umms.core.annotation.AbstractAnnotation | static |
| minus(Annotation other) | umms.core.annotation.BasicAnnotation | |
| minus(Collection<?extends Annotation > others) | umms.core.annotation.BasicAnnotation | |
| moveToCoordinate(int coord) | umms.core.alignment.AbstractPairedEndAlignment | |
| numBlocks() | umms.core.annotation.BasicAnnotation | |
| overlaps(Annotation other, int buffer, boolean considerOrientation) | umms.core.annotation.BasicAnnotation | |
| overlaps(List<?extends Annotation > otherBlocks, int buffer) | umms.core.annotation.BasicAnnotation | |
| umms::core::annotation::AbstractAnnotation.overlaps(Annotation other) | umms.core.annotation.AbstractAnnotation | |
| umms::core::annotation::AbstractAnnotation.overlaps(Annotation other, int buffer) | umms.core.annotation.AbstractAnnotation | |
| umms::core::annotation::AbstractAnnotation.overlaps(Annotation other, boolean considerOrientation) | umms.core.annotation.AbstractAnnotation | |
| umms::core::annotation::AbstractAnnotation.overlaps(Collection<?extends Annotation > others) | umms.core.annotation.AbstractAnnotation | |
| umms::core::annotation::AbstractAnnotation.overlaps(Collection<?extends Annotation > others, int buffer) | umms.core.annotation.AbstractAnnotation | |
| overlapsStranded(Annotation other) | umms.core.annotation.AbstractAnnotation | |
| refreshAttributeMap() | umms.core.alignment.AbstractPairedEndAlignment | |
| setAttribute(String attribute, String value) | umms.core.alignment.AbstractPairedEndAlignment | |
| setDuplicateFlag(boolean duplicateFlag) | umms.core.alignment.AbstractPairedEndAlignment | |
| setEnd(int end) | umms.core.annotation.BasicAnnotation | |
| setFragmentStrand(TranscriptionRead transcriptionRead) | umms.core.alignment.AbstractPairedEndAlignment | |
| setHeader(SAMFileHeader header) | umms.core.alignment.AbstractPairedEndAlignment | |
| setName(String n) | umms.core.annotation.BasicAnnotation | |
| setOrientation(Strand orientation) | umms.core.annotation.BasicAnnotation | |
| umms::core::annotation::AbstractAnnotation.setOrientation(char orientation) | umms.core.annotation.AbstractAnnotation | |
| setOrientedEnd(int orientedEnd) | umms.core.annotation.BasicAnnotation | |
| setOrientedStart(int orientedStart) | umms.core.annotation.BasicAnnotation | |
| setProperPairFlag(boolean properPairFlag) | umms.core.alignment.AbstractPairedEndAlignment | |
| setReferenceName(String refName) | umms.core.annotation.BasicAnnotation | |
| setScore(double s) | umms.core.annotation.BasicAnnotation | |
| setStart(int start) | umms.core.annotation.BasicAnnotation | |
| shift(int delta) | umms.core.alignment.AbstractPairedEndAlignment | |
| size() | umms.core.annotation.AbstractAnnotation | |
| stitchTo(Annotation next) | umms.core.annotation.BasicAnnotation | |
| toBED() | umms.core.annotation.AbstractAnnotation | |
| toBED(int r, int g, int b) | umms.core.annotation.AbstractAnnotation | |
| toBEDGraph() | umms.core.annotation.AbstractAnnotation | |
| toCigar() | umms.core.annotation.AbstractAnnotation | |
| toSAMRecord() | umms.core.alignment.AbstractPairedEndAlignment | |
| toShortBED() | umms.core.annotation.AbstractAnnotation | |
| toString() | umms.core.alignment.AbstractPairedEndAlignment | |
| toUCSC() | umms.core.annotation.AbstractAnnotation | |
| trim(int deltaStart, int deltaEnd) | umms.core.annotation.AbstractAnnotation | |
| union(Annotation other) | umms.core.annotation.BasicAnnotation | |
1.8.7
