| addBlock(String name, int start, int end) | broad.core.annotation.BasicGenomicAnnotation | |
| addExtraScore(double score) | broad.core.annotation.BasicLightweightAnnotation | |
| addScore(double score) | broad.pda.datastructures.Alignments | |
| Alignments(String ucsc) | broad.pda.datastructures.Alignments | |
| Alignments(String chr, int start, int end) | broad.pda.datastructures.Alignments | |
| Alignments(String chr, int start, int end, Strand strand) | broad.pda.datastructures.Alignments | |
| Alignments(String chr, int start, int end, String strand) | broad.pda.datastructures.Alignments | |
| Alignments(String chr, int start, int end, Strand strand, String name) | broad.pda.datastructures.Alignments | |
| Alignments(String chr, String start, String end) | broad.pda.datastructures.Alignments | |
| Alignments(Annotation a) | broad.pda.datastructures.Alignments | |
| Alignments(String fileName, boolean fromFileName) | broad.pda.datastructures.Alignments | |
| Alignments(LightweightGenomicAnnotation a) | broad.pda.datastructures.Alignments | |
| Alignments(Alignment record) | broad.pda.datastructures.Alignments | |
| Alignments(nextgen.core.alignment.Alignment record) | broad.pda.datastructures.Alignments | |
| almostEqual(LightweightGenomicAnnotation other, int fudge) | broad.core.annotation.BasicLightweightAnnotation | |
| BasicGenomicAnnotation() | broad.core.annotation.BasicGenomicAnnotation | protected |
| BasicGenomicAnnotation(String name) | broad.core.annotation.BasicGenomicAnnotation | |
| BasicGenomicAnnotation(String name, String chr, int start, int end) | broad.core.annotation.BasicGenomicAnnotation | |
| BasicGenomicAnnotation(String name, String chr, int start, int end, Strand strand) | broad.core.annotation.BasicGenomicAnnotation | |
| BasicGenomicAnnotation(LightweightGenomicAnnotation ga) | broad.core.annotation.BasicGenomicAnnotation | |
| BasicGenomicAnnotation(Annotation ga) | broad.core.annotation.BasicGenomicAnnotation | |
| BasicGenomicAnnotation(GenomicAnnotation ga) | broad.core.annotation.BasicGenomicAnnotation | |
| BasicGenomicAnnotation(String[] info) | broad.core.annotation.BasicGenomicAnnotation | |
| BasicLightweightAnnotation() | broad.core.annotation.BasicLightweightAnnotation | |
| BasicLightweightAnnotation(String chr, int start, int end) | broad.core.annotation.BasicLightweightAnnotation | |
| BasicLightweightAnnotation(String chr, int start, int end, String orientation) | broad.core.annotation.BasicLightweightAnnotation | |
| BasicLightweightAnnotation(String chr, int start, int end, Strand orientation, String name) | broad.core.annotation.BasicLightweightAnnotation | |
| BasicLightweightAnnotation(String chr, int start, int end, String orientation, double Scr) | broad.core.annotation.BasicLightweightAnnotation | |
| BasicLightweightAnnotation(String chr, String start, String end) | broad.core.annotation.BasicLightweightAnnotation | |
| BasicLightweightAnnotation(LightweightGenomicAnnotation annotation) | broad.core.annotation.BasicLightweightAnnotation | |
| BasicLightweightAnnotation(Annotation annotation) | broad.core.annotation.BasicLightweightAnnotation | |
| compareTo(GenomicAnnotation arg0) | broad.core.annotation.BasicGenomicAnnotation | |
| broad::core::annotation::BasicLightweightAnnotation.compareTo(LightweightGenomicAnnotation b) | broad.core.annotation.BasicLightweightAnnotation | |
| compareToAnnotation(Annotation b) | umms.core.annotation.Annotation | |
| complement() | umms.core.annotation.Annotation | |
| containedWithin(Alignments align) | broad.pda.datastructures.Alignments | |
| containedWithin(Alignments interval, Alignments gene) | broad.pda.datastructures.Alignments | |
| contains(LightweightGenomicAnnotation other) | broad.core.annotation.BasicLightweightAnnotation | |
| umms::core::annotation::Annotation.contains(Annotation other) | umms.core.annotation.Annotation | |
| copy() | umms.core.annotation.Annotation | |
| createFromUCSC(String ucsc) | broad.core.annotation.BasicLightweightAnnotation | static |
| disect(Annotation a) | broad.core.annotation.BasicGenomicAnnotation | |
| disect(List<?extends Annotation > disectors) | broad.core.annotation.BasicGenomicAnnotation | |
| distanceBetween(Alignments align1, Alignments align2) | broad.pda.datastructures.Alignments | static |
| equals(Annotation other) | umms.core.annotation.Annotation | |
| equals(Annotation other, boolean useOrientation) | umms.core.annotation.Annotation | |
| expand(int deltaStart, int deltaEnd) | umms.core.annotation.Annotation | |
| fullyContains(Annotation annotation) | umms.core.annotation.Annotation | |
| broad::core::annotation::BasicLightweightAnnotation.getBlocks() | umms.core.annotation.Annotation | |
| broad::core::annotation::BasicLightweightAnnotation.getBlocks(boolean oriented) | umms.core.annotation.Annotation | |
| broad::core::annotation::GenomicAnnotation.getBlocks() | broad.core.annotation.GenomicAnnotation | |
| getChr() | umms.core.annotation.Annotation | |
| getChromosome() | broad.core.annotation.BasicLightweightAnnotation | |
| getChromosomeString() | broad.core.annotation.BasicLightweightAnnotation | |
| getCountScore() | broad.pda.datastructures.Alignments | |
| getDistanceTo(LightweightGenomicAnnotation other) | broad.core.annotation.BasicLightweightAnnotation | |
| umms::core::annotation::Annotation.getDistanceTo(Annotation other) | umms.core.annotation.Annotation | |
| getEnd() | broad.core.annotation.LightweightGenomicAnnotation | |
| getExtraScore(int i) | broad.core.annotation.BasicLightweightAnnotation | |
| getExtraScores() | broad.core.annotation.BasicLightweightAnnotation | |
| getFivePrimeBases() | broad.core.annotation.BasicGenomicAnnotation | |
| getFullInfoString() | umms.core.annotation.Annotation | |
| getId() | broad.core.annotation.BasicGenomicAnnotation | |
| getLength() | broad.core.annotation.BasicGenomicAnnotation | |
| getLengthOnReference() | umms.core.annotation.Annotation | |
| broad::core::annotation::BasicLightweightAnnotation.getLocationString() | broad.core.annotation.BasicLightweightAnnotation | |
| broad::core::annotation::GenomicAnnotation.getLocationString() | broad.core.annotation.GenomicAnnotation | |
| getMiddle() | broad.core.annotation.BasicLightweightAnnotation | |
| getMidPoint() | broad.pda.datastructures.Alignments | |
| getMidpoint() | umms.core.annotation.Annotation | |
| broad::core::annotation::BasicLightweightAnnotation.getName() | broad.core.annotation.LightweightGenomicAnnotation | |
| broad::core::annotation::GenomicAnnotation.broad::core::annotation::Feature.getName() | broad.core.annotation.Feature | |
| broad::core::annotation::BasicLightweightAnnotation.getOrientation() | broad.core.annotation.LightweightGenomicAnnotation | |
| broad::core::annotation::GenomicAnnotation.getOrientation() | broad.core.annotation.GenomicAnnotation | |
| getOrientedEnd() | broad.core.annotation.BasicGenomicAnnotation | |
| getOrientedStart() | broad.core.annotation.BasicGenomicAnnotation | |
| getOverlap(LightweightGenomicAnnotation other) | broad.core.annotation.BasicLightweightAnnotation | |
| umms::core::annotation::Annotation.getOverlap(Annotation other) | umms.core.annotation.Annotation | |
| getPositionAtReferenceCoordinate(int referenceCoordinate) | umms.core.annotation.Annotation | |
| getPositionAtReferenceCoordinate(int referenceCoordinate, boolean ignoreOrientation) | umms.core.annotation.Annotation | |
| getReferenceCoordinateAtPosition(int positionInAnnotation) | umms.core.annotation.Annotation | |
| getReferenceCoordinateAtPosition(int positionInAnnotation, boolean ignoreOrientation) | umms.core.annotation.Annotation | |
| getReferenceName() | umms.core.annotation.Annotation | |
| getSAMEnd() | umms.core.annotation.Annotation | |
| getSAMStart() | umms.core.annotation.Annotation | |
| getScore() | broad.pda.datastructures.Alignments | |
| getScores() | broad.pda.datastructures.Alignments | |
| getSequence(Sequence chr, boolean repeatMask) | broad.pda.datastructures.Alignments | |
| getSequence(String genomeDir) | broad.pda.datastructures.Alignments | |
| broad::core::annotation::BasicGenomicAnnotation.getSequence() | broad.core.annotation.BasicGenomicAnnotation | |
| getSize() | umms.core.annotation.Annotation | |
| getSpliceConnections() | umms.core.annotation.Annotation | |
| getStart() | broad.core.annotation.LightweightGenomicAnnotation | |
| getStrand() | umms.core.annotation.Annotation | |
| getThreePrimeBases() | broad.core.annotation.BasicGenomicAnnotation | |
| hashCode() | broad.core.annotation.BasicLightweightAnnotation | |
| hasOrientation() | umms.core.annotation.Annotation | |
| inReversedOrientation() | broad.core.annotation.BasicLightweightAnnotation | |
| intersect(LightweightGenomicAnnotation other) | broad.core.annotation.BasicLightweightAnnotation | |
| intersect(Collection<?extends Annotation > annotations) | broad.core.annotation.BasicLightweightAnnotation | |
| broad::core::annotation::LightweightGenomicAnnotation.intersect(Annotation other) | umms.core.annotation.Annotation | |
| broad::core::annotation::LightweightGenomicAnnotation.intersect(List<?extends Annotation > annotations) | umms.core.annotation.Annotation | |
| isFlankedBy(TwoSubjectAnnotation twoSubjectAnnotation, int buffer) | broad.core.annotation.BasicGenomicAnnotation | |
| isNegativeStrand() | umms.core.annotation.Annotation | |
| isUnoriented() | umms.core.annotation.Annotation | |
| lastIdxWhereListSearchBroke() | broad.core.annotation.BasicGenomicAnnotation | |
| length() | broad.pda.datastructures.Alignments | |
| mayHaveBlocks() | broad.core.annotation.BasicGenomicAnnotation | |
| merge(Alignments a1, Alignments a2) | broad.pda.datastructures.Alignments | |
| merge(Alignments a1) | broad.pda.datastructures.Alignments | |
| mergeAllOverlappers(TreeSet< BasicLightweightAnnotation > regions) | broad.core.annotation.BasicLightweightAnnotation | 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(Collection<?extends Annotation > others, int buffer) | broad.core.annotation.BasicLightweightAnnotation | |
| overlaps(Collection<?extends Annotation > others) | broad.core.annotation.BasicLightweightAnnotation | |
| broad::core::annotation::LightweightGenomicAnnotation.overlaps(Annotation other, int buffer) | umms.core.annotation.Annotation | |
| broad::core::annotation::LightweightGenomicAnnotation.overlaps(Annotation other) | umms.core.annotation.Annotation | |
| broad::core::annotation::LightweightGenomicAnnotation.overlaps(Annotation other, int buffer, boolean considerOrientation) | umms.core.annotation.Annotation | |
| broad::core::annotation::LightweightGenomicAnnotation.overlaps(Annotation other, boolean considerOrientation) | umms.core.annotation.Annotation | |
| overlapsAtAll(Alignments align) | broad.pda.datastructures.Alignments | |
| overlapsAtAll(Set< Alignments > set) | broad.pda.datastructures.Alignments | |
| overlapsCollection(Collection< Alignments > c) | broad.pda.datastructures.Alignments | |
| overlapsStranded(Annotation other) | umms.core.annotation.Annotation | |
| reduceToDifference(GenomicAnnotation other) | broad.core.annotation.BasicGenomicAnnotation | |
| removeExtraScores() | broad.core.annotation.BasicLightweightAnnotation | |
| setBoundariesFromAnnoations(List<?extends GenomicAnnotation > annotations) | broad.core.annotation.BasicLightweightAnnotation | |
| setChromosome(String chr) | broad.core.annotation.BasicLightweightAnnotation | |
| setCountScore(double score) | broad.pda.datastructures.Alignments | |
| setEnd(int end) | broad.core.annotation.LightweightGenomicAnnotation | |
| setFivePrimeBuffer(int bufferSize) | broad.core.annotation.BasicGenomicAnnotation | |
| setId(String id) | broad.core.annotation.BasicGenomicAnnotation | |
| setLine(String line) | broad.pda.datastructures.Alignments | |
| setName(String name) | broad.core.annotation.LightweightGenomicAnnotation | |
| setOrientation(boolean orientation) | broad.core.annotation.BasicGenomicAnnotation | |
| broad::core::annotation::BasicLightweightAnnotation.setOrientation(String orientation) | broad.core.annotation.BasicLightweightAnnotation | |
| broad::core::annotation::BasicLightweightAnnotation.umms::core::annotation::Annotation.setOrientation(char orientation) | umms.core.annotation.Annotation | |
| broad::core::annotation::BasicLightweightAnnotation.umms::core::annotation::Annotation.setOrientation(Strand orientation) | umms.core.annotation.Annotation | |
| broad::core::annotation::GenomicAnnotation.setOrientation(String orientationString) | broad.core.annotation.GenomicAnnotation | |
| setOrientedEnd(int orientedEnd) | umms.core.annotation.Annotation | |
| setOrientedStart(int orientedStart) | umms.core.annotation.Annotation | |
| setReferenceName(String refName) | umms.core.annotation.Annotation | |
| broad::core::annotation::BasicLightweightAnnotation.setReversedOrientation(boolean isInReversedOrientation) | broad.core.annotation.BasicLightweightAnnotation | |
| broad::core::annotation::GenomicAnnotation.setReversedOrientation(boolean isInReversedOrientation) | broad.core.annotation.GenomicAnnotation | |
| setScore(double score) | broad.core.annotation.BasicLightweightAnnotation | |
| setScores(List< Double > values) | broad.pda.datastructures.Alignments | |
| setSequence(Sequence sequence) | broad.core.annotation.BasicGenomicAnnotation | |
| setStart(String data) | broad.core.annotation.BasicLightweightAnnotation | protected |
| broad::core::annotation::LightweightGenomicAnnotation.setStart(int start) | broad.core.annotation.LightweightGenomicAnnotation | |
| setThreePrimeBuffer(int bufferSize) | broad.core.annotation.BasicGenomicAnnotation | |
| shift(int delta) | umms.core.annotation.Annotation | |
| size() | umms.core.annotation.Annotation | |
| stitchList(Collection<?extends Annotation > sortedList, int maxDistanceToStitch) | broad.core.annotation.BasicLightweightAnnotation | static |
| stitchTo(LightweightGenomicAnnotation other) | broad.core.annotation.BasicLightweightAnnotation | |
| umms::core::annotation::Annotation.stitchTo(Annotation next) | umms.core.annotation.Annotation | |
| takeIntersection(LightweightGenomicAnnotation other) | broad.core.annotation.BasicLightweightAnnotation | |
| takeUnion(LightweightGenomicAnnotation other) | broad.core.annotation.BasicLightweightAnnotation | |
| toBED() | umms.core.annotation.Annotation | |
| toBED(int r, int g, int b) | umms.core.annotation.Annotation | |
| toBEDGraph() | umms.core.annotation.Annotation | |
| toCigar() | umms.core.annotation.Annotation | |
| toFileName() | broad.pda.datastructures.Alignments | |
| toShortBED() | umms.core.annotation.Annotation | |
| toString() | broad.pda.datastructures.Alignments | |
| toStringNum() | broad.pda.datastructures.Alignments | |
| toStringWithScores() | broad.pda.datastructures.Alignments | |
| toUCSC() | broad.pda.datastructures.Alignments | |
| trim(int deltaStart, int deltaEnd) | umms.core.annotation.Annotation | |
| union(Annotation other) | umms.core.annotation.Annotation | |
| within(Alignments bigger) | broad.pda.datastructures.Alignments | |
| write(String save, Collection< Alignments > alignments) | broad.pda.datastructures.Alignments | static |
| write(String save, Collection< Alignments > alignments, boolean sort) | broad.pda.datastructures.Alignments | static |
| write(String save, Collection< Alignments > alignments, final int sortOnScore) | broad.pda.datastructures.Alignments | static |
| write(BufferedWriter writer, Collection< Alignments > alignments) | broad.pda.datastructures.Alignments | static |
| write(BufferedWriter writer, Collection< Alignments > alignments, boolean sort) | broad.pda.datastructures.Alignments | static |
1.8.7
