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broad.core.annotation.BED Class Reference
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Public Member Functions

 BED (String name)
 
 BED (LightweightGenomicAnnotation anot)
 
 BED (String name, String chr, int start, int end)
 
 BED (BED anot)
 
 BED (Annotation anot)
 
 BED (String[] info) throws ParseException
 
String toString ()
 
String toString (boolean setNegativeScoresTo0)
 
String toShortString ()
 
String toWIGString ()
 
int[][] getBlockSizeStarts ()
 
void setBlockSizeStarts (int[][] blockSizeStarts)
 
List< GenomicAnnotation > getBlocks ()
 
String getRgb ()
 
void setRgb (String rgb)
 
int getThickEnd ()
 
void setThickEnd (int thickEnd)
 
int getThickStart ()
 
void setThickStart (int thickStart)
 
void addBlock (String name, int start, int end)
 
String toBED ()
 
String toBED (int r, int g, int b)
 
boolean mayHaveBlocks ()
 
boolean IntersectBlocks (GenomicAnnotation annot)
 
- Public Member Functions inherited from broad.core.annotation.BasicGenomicAnnotation
 BasicGenomicAnnotation (String name)
 
 BasicGenomicAnnotation (String name, String chr, int start, int end)
 
 BasicGenomicAnnotation (String name, String chr, int start, int end, Strand strand)
 
 BasicGenomicAnnotation (LightweightGenomicAnnotation ga)
 
 BasicGenomicAnnotation (Annotation ga)
 
 BasicGenomicAnnotation (GenomicAnnotation ga)
 
 BasicGenomicAnnotation (String[] info)
 
int getLength ()
 
String toString ()
 
String getId ()
 
void setId (String id)
 
void reduceToDifference (GenomicAnnotation other)
 
List< Annotation > disect (Annotation a)
 
List< Annotation > disect (List<?extends Annotation > disectors)
 
boolean isFlankedBy (TwoSubjectAnnotation twoSubjectAnnotation, int buffer)
 
int lastIdxWhereListSearchBroke ()
 
Sequence getSequence ()
 
void setSequence (Sequence sequence)
 
void setOrientation (boolean orientation)
 
void setThreePrimeBuffer (int bufferSize)
 
void setFivePrimeBuffer (int bufferSize)
 
int getFivePrimeBases ()
 
int getThreePrimeBases ()
 
int compareTo (GenomicAnnotation arg0)
 
int getOrientedEnd ()
 
int getOrientedStart ()
 
void addBlock (String name, int start, int end)
 
boolean mayHaveBlocks ()
 
- Public Member Functions inherited from broad.core.annotation.BasicLightweightAnnotation
 BasicLightweightAnnotation ()
 
 BasicLightweightAnnotation (String chr, int start, int end)
 
 BasicLightweightAnnotation (String chr, int start, int end, String orientation)
 
 BasicLightweightAnnotation (String chr, int start, int end, Strand orientation, String name)
 
 BasicLightweightAnnotation (String chr, int start, int end, String orientation, double Scr)
 
 BasicLightweightAnnotation (String chr, String start, String end)
 
 BasicLightweightAnnotation (LightweightGenomicAnnotation annotation)
 
 BasicLightweightAnnotation (Annotation annotation)
 
String getChromosomeString ()
 
int getDistanceTo (LightweightGenomicAnnotation other)
 
double getExtraScore (int i)
 
List< Double > getExtraScores ()
 
String getLocationString ()
 
long getMiddle ()
 
int getOverlap (LightweightGenomicAnnotation other)
 
double getScore ()
 
void setReversedOrientation (boolean isInReversedOrientation)
 
void setScore (double score)
 
boolean almostEqual (LightweightGenomicAnnotation other, int fudge)
 
boolean contains (LightweightGenomicAnnotation other)
 
boolean inReversedOrientation ()
 
boolean overlaps (Collection<?extends Annotation > others, int buffer)
 
boolean overlaps (Collection<?extends Annotation > others)
 
void addExtraScore (double score)
 
void removeExtraScores ()
 
void setBoundariesFromAnnoations (List<?extends GenomicAnnotation > annotations)
 
void stitchTo (LightweightGenomicAnnotation other)
 
void takeIntersection (LightweightGenomicAnnotation other)
 
void takeUnion (LightweightGenomicAnnotation other)
 
LightweightGenomicAnnotation intersect (LightweightGenomicAnnotation other)
 
Collection<?extends Annotation > intersect (Collection<?extends Annotation > annotations)
 
int hashCode ()
 
int length ()
 
String toUCSC ()
 
String toString ()
 
int compareTo (LightweightGenomicAnnotation b)
 
void setOrientation (String orientation)
 
String getChromosome ()
 
void setChromosome (String chr)
 
- Public Member Functions inherited from broad.core.annotation.LightweightGenomicAnnotation
int getStart ()
 
int getEnd ()
 
String getName ()
 
void setName (String name)
 
void setStart (int start)
 
void setEnd (int end)
 
- Public Member Functions inherited from umms.core.annotation.Annotation
int getSAMStart ()
 
int getSAMEnd ()
 
String getReferenceName ()
 
String getChr ()
 
Strand getStrand ()
 
boolean hasOrientation ()
 
boolean isNegativeStrand ()
 
int numBlocks ()
 
List<?extends Annotation > getBlocks (boolean oriented)
 
int getSize ()
 
int size ()
 
int getLengthOnReference ()
 
boolean isUnoriented ()
 
int getReferenceCoordinateAtPosition (int positionInAnnotation)
 
int getPositionAtReferenceCoordinate (int referenceCoordinate)
 
int getReferenceCoordinateAtPosition (int positionInAnnotation, boolean ignoreOrientation)
 
int getPositionAtReferenceCoordinate (int referenceCoordinate, boolean ignoreOrientation)
 
void setOrientation (char orientation)
 
void setOrientation (Strand orientation)
 
void setOrientedStart (int orientedStart)
 
void setOrientedEnd (int orientedEnd)
 
void setReferenceName (String refName)
 
boolean equals (Annotation other)
 
void expand (int deltaStart, int deltaEnd)
 
Annotation trim (int deltaStart, int deltaEnd)
 
void shift (int delta)
 
void moveToCoordinate (int coordinateInReference)
 
Annotation copy ()
 
Annotation minus (Annotation other)
 
Annotation minus (Collection<?extends Annotation > others)
 
int getDistanceTo (Annotation other)
 
String toShortBED ()
 
String toBEDGraph ()
 
String getFullInfoString ()
 
boolean overlaps (Annotation other, int buffer)
 
boolean overlaps (Annotation other)
 
boolean overlaps (Annotation other, int buffer, boolean considerOrientation)
 
boolean overlaps (Annotation other, boolean considerOrientation)
 
boolean overlapsStranded (Annotation other)
 
int getOverlap (Annotation other)
 
boolean contains (Annotation other)
 
Annotation union (Annotation other)
 
Annotation intersect (Annotation other)
 
List< Annotation > intersect (List<?extends Annotation > annotations)
 
int compareToAnnotation (Annotation b)
 
void stitchTo (Annotation next)
 
String toCigar ()
 
boolean fullyContains (Annotation annotation)
 
Annotation complement ()
 
boolean equals (Annotation other, boolean useOrientation)
 
Collection<?extends Annotation > getSpliceConnections ()
 
int getMidpoint ()
 
- Public Member Functions inherited from broad.core.annotation.GenomicAnnotation
void setReversedOrientation (boolean isInReversedOrientation)
 
void setOrientation (String orientationString)
 
Strand getOrientation ()
 
String getLocationString ()
 
- Public Member Functions inherited from broad.core.annotation.Feature
String getName ()
 
double getScore ()
 

Additional Inherited Members

- Static Public Member Functions inherited from broad.core.annotation.BasicLightweightAnnotation
static Collection
< BasicLightweightAnnotation > 		mergeAllOverlappers (TreeSet< BasicLightweightAnnotation > regions)
 
static LightweightGenomicAnnotation createFromUCSC (String ucsc)
 
static List< Annotation > stitchList (Collection<?extends Annotation > sortedList, int maxDistanceToStitch)
 
- Protected Member Functions inherited from broad.core.annotation.BasicGenomicAnnotation
 BasicGenomicAnnotation ()
 
- Protected Member Functions inherited from broad.core.annotation.BasicLightweightAnnotation
void setStart (String data)
 

Constructor & Destructor Documentation

broad.core.annotation.BED.BED ( String  name)
broad.core.annotation.BED.BED ( LightweightGenomicAnnotation  anot)
broad.core.annotation.BED.BED ( String  name,
String  chr,
int  start,
int  end 
)
broad.core.annotation.BED.BED ( BED  anot)
broad.core.annotation.BED.BED ( Annotation  anot)
broad.core.annotation.BED.BED ( String[]  info) throws ParseException

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Member Function Documentation

void broad.core.annotation.BED.addBlock ( String  name,
int  start,
int  end 
)

Adds a block to the annotation if it supports blocks

Implements broad.core.annotation.GenomicAnnotation.

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List<GenomicAnnotation> broad.core.annotation.BED.getBlocks ( )

Returns a list of blocks if the annotations has any (

See also
containsBlocks)

Implements broad.core.annotation.GenomicAnnotation.

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int [][] broad.core.annotation.BED.getBlockSizeStarts ( )
String broad.core.annotation.BED.getRgb ( )
int broad.core.annotation.BED.getThickEnd ( )

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int broad.core.annotation.BED.getThickStart ( )

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boolean broad.core.annotation.BED.IntersectBlocks ( GenomicAnnotation  annot)

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boolean broad.core.annotation.BED.mayHaveBlocks ( )

Returns true if the annotation (like a full BED or a RefSeq) has sub annotations like exons or blocks

Implements broad.core.annotation.GenomicAnnotation.

void broad.core.annotation.BED.setBlockSizeStarts ( int  blockSizeStarts[][])
void broad.core.annotation.BED.setRgb ( String  rgb)
void broad.core.annotation.BED.setThickEnd ( int  thickEnd)
void broad.core.annotation.BED.setThickStart ( int  thickStart)
String broad.core.annotation.BED.toBED ( )

Implements umms.core.annotation.Annotation.

String broad.core.annotation.BED.toBED ( int  r,
int  g,
int  b 
)

Implements umms.core.annotation.Annotation.

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String broad.core.annotation.BED.toShortString ( )

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String broad.core.annotation.BED.toString ( )

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String broad.core.annotation.BED.toString ( boolean  setNegativeScoresTo0)

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String broad.core.annotation.BED.toWIGString ( )

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The documentation for this class was generated from the following file:
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