| 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.Annotation | |
| contains(Annotation other) | umms.core.annotation.Annotation | |
| copy() | umms.core.annotation.Annotation | |
| disect(Annotation a) | umms.core.annotation.Annotation | |
| disect(List<?extends Annotation > disectors) | umms.core.annotation.Annotation | |
| 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 | |
| fullyContains(Annotation other) | umms.core.annotation.AbstractAnnotation | |
| getBlocks() | umms.core.annotation.Annotation | |
| getBlocks(boolean oriented) | umms.core.annotation.Annotation | |
| getChr() | umms.core.annotation.AbstractAnnotation | |
| getDistanceTo(Annotation other) | umms.core.annotation.AbstractAnnotation | |
| getEnd() | umms.core.annotation.Annotation | |
| getFullInfoString() | umms.core.annotation.AbstractAnnotation | |
| getLengthOnReference() | umms.core.annotation.AbstractAnnotation | |
| getMidpoint() | umms.core.annotation.AbstractAnnotation | |
| getName() | umms.core.annotation.Annotation | |
| getOrientation() | umms.core.annotation.Annotation | |
| getOrientedEnd() | umms.core.annotation.AbstractAnnotation | |
| getOrientedStart() | umms.core.annotation.AbstractAnnotation | |
| getOverlap(Annotation other) | umms.core.annotation.Annotation | |
| getPositionAtReferenceCoordinate(int referenceCoordinate) | umms.core.annotation.AbstractAnnotation | |
| umms::core::annotation::Annotation.getPositionAtReferenceCoordinate(int referenceCoordinate, boolean ignoreOrientation) | umms.core.annotation.Annotation | |
| getReferenceCoordinateAtPosition(int positionInAnnotation) | umms.core.annotation.AbstractAnnotation | |
| umms::core::annotation::Annotation.getReferenceCoordinateAtPosition(int positionInAnnotation, boolean ignoreOrientation) | umms.core.annotation.Annotation | |
| getReferenceName() | umms.core.annotation.Annotation | |
| getSAMEnd() | umms.core.annotation.AbstractAnnotation | |
| getSAMStart() | umms.core.annotation.AbstractAnnotation | |
| getScore() | umms.core.annotation.Annotation | |
| getSize() | umms.core.annotation.AbstractAnnotation | |
| getSpliceConnections() | umms.core.annotation.Annotation | |
| getStart() | umms.core.annotation.Annotation | |
| 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(List<?extends Annotation > others) | umms.core.annotation.AbstractAnnotation | |
| umms::core::annotation::Annotation.intersect(Annotation other) | umms.core.annotation.Annotation | |
| isNegativeStrand() | umms.core.annotation.AbstractAnnotation | |
| isUnoriented() | umms.core.annotation.Annotation | |
| length() | umms.core.annotation.Annotation | |
| MAX_DISTANCE | umms.core.annotation.AbstractAnnotation | static |
| minus(Annotation other) | umms.core.annotation.Annotation | |
| minus(Collection<?extends Annotation > others) | umms.core.annotation.Annotation | |
| moveToCoordinate(int coordinateInReference) | umms.core.annotation.Annotation | |
| numBlocks() | umms.core.annotation.Annotation | |
| overlaps(Annotation other) | umms.core.annotation.AbstractAnnotation | |
| overlaps(Annotation other, int buffer) | umms.core.annotation.AbstractAnnotation | |
| overlaps(Annotation other, boolean considerOrientation) | umms.core.annotation.AbstractAnnotation | |
| overlaps(Collection<?extends Annotation > others) | umms.core.annotation.AbstractAnnotation | |
| overlaps(Collection<?extends Annotation > others, int buffer) | umms.core.annotation.AbstractAnnotation | |
| umms::core::annotation::Annotation.overlaps(Annotation other, int buffer, boolean considerOrientation) | umms.core.annotation.Annotation | |
| overlapsStranded(Annotation other) | umms.core.annotation.AbstractAnnotation | |
| setEnd(int end) | umms.core.annotation.Annotation | |
| setName(String name) | umms.core.annotation.Annotation | |
| setOrientation(char orientation) | umms.core.annotation.AbstractAnnotation | |
| umms::core::annotation::Annotation.setOrientation(Strand orientation) | umms.core.annotation.Annotation | |
| setOrientedEnd(int orientedEnd) | umms.core.annotation.Annotation | |
| setOrientedStart(int orientedStart) | umms.core.annotation.Annotation | |
| setReferenceName(String refName) | umms.core.annotation.Annotation | |
| setScore(double score) | umms.core.annotation.Annotation | |
| setStart(int start) | umms.core.annotation.Annotation | |
| shift(int delta) | umms.core.annotation.Annotation | |
| size() | umms.core.annotation.AbstractAnnotation | |
| stitchTo(Annotation next) | umms.core.annotation.Annotation | |
| 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 | |
| toUCSC() | umms.core.annotation.AbstractAnnotation | |
| trim(int deltaStart, int deltaEnd) | umms.core.annotation.AbstractAnnotation | |
| union(Annotation other) | umms.core.annotation.Annotation | |
1.8.7
