| addBlocks(Annotation block) | umms.core.annotation.BasicAnnotation | |
| addBlocks(Collection<?extends Annotation > blocks) | umms.core.annotation.BasicAnnotation | |
| 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(Annotation a) | umms.core.annotation.AbstractAnnotation | |
| equals(Annotation a, boolean useOrientation) | umms.core.annotation.AbstractAnnotation | |
| expand(int deltaStart, int deltaEnd) | umms.core.annotation.AbstractAnnotation | |
| fromFullInfoString(String fullInfoString) | umms.core.annotation.BasicAnnotation | static |
| fullyContains(Annotation other) | umms.core.annotation.AbstractAnnotation | |
| getBlocks() | umms.core.annotation.BasicAnnotation | |
| getBlocks(boolean oriented) | umms.core.annotation.BasicAnnotation | |
| getChr() | umms.core.annotation.AbstractAnnotation | |
| getDistanceTo(Annotation other) | umms.core.annotation.AbstractAnnotation | |
| getEnd() | umms.core.annotation.BasicAnnotation | |
| getFlankingBlocks(Annotation spliceJunction) | umms.core.annotation.BasicAnnotation | |
| getFullInfoString() | umms.core.annotation.AbstractAnnotation | |
| getLengthOnReference() | umms.core.annotation.AbstractAnnotation | |
| getMatch() | umms.core.annotation.PSLRecord | |
| getMidpoint() | umms.core.annotation.BasicAnnotation | |
| getName() | umms.core.annotation.BasicAnnotation | |
| getOrientation() | umms.core.annotation.BasicAnnotation | |
| getOrientedEnd() | umms.core.annotation.AbstractAnnotation | |
| getOrientedStart() | umms.core.annotation.AbstractAnnotation | |
| getOverlap(Annotation other) | umms.core.annotation.BasicAnnotation | |
| getPercentIdentity() | umms.core.annotation.PSLRecord | |
| getPositionAtReferenceCoordinate(int referenceCoordinate, boolean ignoreOrientation) | umms.core.annotation.BasicAnnotation | |
| umms::core::annotation::AbstractAnnotation.getPositionAtReferenceCoordinate(int referenceCoordinate) | umms.core.annotation.AbstractAnnotation | |
| 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 | |
| getSize() | umms.core.annotation.AbstractAnnotation | |
| getSpliceConnections() | umms.core.annotation.BasicAnnotation | |
| getStart() | umms.core.annotation.BasicAnnotation | |
| getStrand() | umms.core.annotation.AbstractAnnotation | |
| getStrand(String orientation) | umms.core.annotation.AbstractAnnotation | static |
| getStrand(char orientation) | umms.core.annotation.AbstractAnnotation | static |
| 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 | |
| isNegativeStrand() | umms.core.annotation.AbstractAnnotation | |
| isUnoriented() | umms.core.annotation.BasicAnnotation | |
| length() | umms.core.annotation.BasicAnnotation | |
| main(String[] args) | umms.core.annotation.BasicAnnotation | static |
| match | umms.core.annotation.PSLRecord | protected |
| 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 coordinateInReference) | umms.core.annotation.BasicAnnotation | |
| 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 | |
| PSLRecord(BasicAnnotation annotation) | umms.core.annotation.PSLRecord | |
| queryStarts | umms.core.annotation.PSLRecord | protected |
| setEnd(int end) | umms.core.annotation.BasicAnnotation | |
| setMatch(int m) | umms.core.annotation.PSLRecord | |
| setMismatch(int m) | umms.core.annotation.PSLRecord | |
| setName(String n) | umms.core.annotation.BasicAnnotation | |
| setNcount(int c) | umms.core.annotation.PSLRecord | |
| 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 | |
| setQueryEnd(int x) | umms.core.annotation.PSLRecord | |
| setQueryGap(int x) | umms.core.annotation.PSLRecord | |
| setQueryGapBases(int x) | umms.core.annotation.PSLRecord | |
| setQuerySize(int x) | umms.core.annotation.PSLRecord | |
| setQueryStart(int x) | umms.core.annotation.PSLRecord | |
| setReferenceName(String refName) | umms.core.annotation.BasicAnnotation | |
| setRepMatch(int m) | umms.core.annotation.PSLRecord | |
| setScore(double s) | umms.core.annotation.BasicAnnotation | |
| setStart(int start) | umms.core.annotation.BasicAnnotation | |
| setTargetGap(int x) | umms.core.annotation.PSLRecord | |
| setTargetGapBases(int x) | umms.core.annotation.PSLRecord | |
| setTargetSize(int x) | umms.core.annotation.PSLRecord | |
| shift(int delta) | umms.core.annotation.BasicAnnotation | |
| 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 | |
| toShortBED() | umms.core.annotation.AbstractAnnotation | |
| toString() | umms.core.annotation.BasicAnnotation | |
| toUCSC() | umms.core.annotation.AbstractAnnotation | |
| trim(int deltaStart, int deltaEnd) | umms.core.annotation.AbstractAnnotation | |
| union(Annotation other) | umms.core.annotation.BasicAnnotation | |
1.8.7
