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

 GFF ()
 
 GFF (String name)
 
 GFF (LightweightGenomicAnnotation annotation)
 
 GFF (Annotation annotation)
 
 GFF (GFF gff)
 
 GFF (String[] rawFields)
 
void setAttributes (String rawAttributeData)
 
Strand getStrand ()
 
void setStrand (String strand)
 
String getFeature ()
 
void setFeature (String feature)
 
int getFrame ()
 
void setFrame (int frame)
 
String getSource ()
 
void addAttribute (String attributeName, String attributeValue)
 
void clearAttribute (String attributeName)
 
void addAttributeValues (String attributeName, List< String > values)
 
Map< String, List< String > > getAttributes ()
 
List< String > getValues (String attributeName)
 
String getFirstValue (String attributeName)
 
String getSequenceName ()
 
void setSource (String source)
 
String toString ()
 
String toString (boolean quoteValues)
 
String toString (boolean quoteValues, boolean useEqualSign)
 
String toCufflinksString (boolean quoteValues)
 
String getGroup ()
 
void setGroup (String group)
 
- 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 ()
 
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 toBED ()
 
String toBED (int r, int g, int b)
 
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 ()
 
List<?extends Annotation > getBlocks ()
 
- Public Member Functions inherited from broad.core.annotation.Feature
String getName ()
 
double getScore ()
 

Static Public Member Functions

static String getGTFAttr (String rawFields, String attrName)
 
static String getGTFAttr (String[] attributeArray, String attrName)
 
- 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)
 

Additional Inherited Members

- 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.GFF.GFF ( )
broad.core.annotation.GFF.GFF ( String  name)
broad.core.annotation.GFF.GFF ( LightweightGenomicAnnotation  annotation)

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broad.core.annotation.GFF.GFF ( Annotation  annotation)

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broad.core.annotation.GFF.GFF ( GFF  gff)

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broad.core.annotation.GFF.GFF ( String[]  rawFields)

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Member Function Documentation

void broad.core.annotation.GFF.addAttribute ( String  attributeName,
String  attributeValue 
)

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void broad.core.annotation.GFF.addAttributeValues ( String  attributeName,
List< String >  values 
)
void broad.core.annotation.GFF.clearAttribute ( String  attributeName)
Map<String, List<String> > broad.core.annotation.GFF.getAttributes ( )
String broad.core.annotation.GFF.getFeature ( )

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String broad.core.annotation.GFF.getFirstValue ( String  attributeName)

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int broad.core.annotation.GFF.getFrame ( )
String broad.core.annotation.GFF.getGroup ( )
static String broad.core.annotation.GFF.getGTFAttr ( String  rawFields,
String  attrName 
)
static

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static String broad.core.annotation.GFF.getGTFAttr ( String[]  attributeArray,
String  attrName 
)
static
String broad.core.annotation.GFF.getSequenceName ( )
String broad.core.annotation.GFF.getSource ( )

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Strand broad.core.annotation.GFF.getStrand ( )
Returns
orientation or strand

Implements umms.core.annotation.Annotation.

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List<String> broad.core.annotation.GFF.getValues ( String  attributeName)
void broad.core.annotation.GFF.setAttributes ( String  rawAttributeData)

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void broad.core.annotation.GFF.setFeature ( String  feature)

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void broad.core.annotation.GFF.setFrame ( int  frame)

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void broad.core.annotation.GFF.setGroup ( String  group)
void broad.core.annotation.GFF.setSource ( String  source)

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void broad.core.annotation.GFF.setStrand ( String  strand)

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String broad.core.annotation.GFF.toCufflinksString ( boolean  quoteValues)

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

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String broad.core.annotation.GFF.toString ( boolean  quoteValues)

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String broad.core.annotation.GFF.toString ( boolean  quoteValues,
boolean  useEqualSign 
)

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The documentation for this class was generated from the following file:
Generated on Fri Aug 15 2014 15:10:51 for ESAT by   doxygen 1.8.7