util.bio.parsers.gff
Class Gff3Feature

java.lang.Object
  util.bio.parsers.gff.Gff3Feature

All Implemented Interfaces:

java.lang.Cloneable, java.lang.Comparable

public class Gff3Feature

extends java.lang.Object

implements java.lang.Comparable, java.lang.Cloneable

A container for each of the values in a GFF3 line. See http://flybase.net/annot/gff3.html. Does not look for multiple values in the attributes tag=value1,value2,value3 keeps value as a single String.

Constructor Summary

Gff3Feature()

Gff3Feature(java.lang.String unParsedGff3Line)
Always check if the GFF3Feature is valid after instantiating with this constructor.

Method Summary

java.lang.Object	clone()
int	compareTo(java.lang.Object obj) Sorts by the sortBy field so set it before sorting.
java.lang.String	getAlias() Reserved Attribute.
java.lang.String	getAttributes()
java.lang.String[]	getCustomAttributes() Any Attribute that is not a reserve attribute is grouped here.
java.lang.String	getDbxref() Reserved Attribute.
int	getEnd()
java.lang.String	getGap() Reserved Attribute.
java.lang.String	getId() Reserved Attribute.
java.lang.String	getName() Reserved Attribute.
java.lang.String	getNote() Reserved Attribute.
java.lang.String	getOntologyTerm() Reserved Attribute.
java.lang.String	getParent() Reserved Attribute.
int	getPhase()
double	getScore()
java.lang.String	getSeqId()
java.lang.String	getSortBy()
java.lang.String	getSource()
int	getStart()
java.lang.String	getStrand()
java.lang.String	getTarget() Reserved Attribute.
java.lang.String	getType()
boolean	isEndSet()
boolean	isPhaseSet()
boolean	isScoreSet()
boolean	isStartSet()
boolean	isValid() Call to find out if the unparsed GFF line correctly parsed.
static void	loadAttribute(java.lang.StringBuffer sb, java.lang.String reserveWord, java.lang.String value)
static void	loadField(java.lang.StringBuffer sb, java.lang.String field)
static void	saveGFF3TextFile(Gff3Feature[] g, java.io.File newGFF3File) Prints an array of GFF3Features as a plain text file
void	setAlias(java.lang.String alias)
void	setCustomAttributes(java.lang.String[] customAttributes)
void	setDbxref(java.lang.String dbxref)
void	setEnd(int end)
void	setEndSet(boolean endSet)
void	setGap(java.lang.String gap)
void	setId(java.lang.String id)
void	setName(java.lang.String name)
void	setNote(java.lang.String note)
void	setOntologyTerm(java.lang.String ontologyTerm)
void	setParent(java.lang.String parent)
void	setPhase(int phase)
void	setPhaseSet(boolean phaseSet)
void	setScore(double score)
void	setScoreSet(boolean scoreSet)
void	setSeqId(java.lang.String seqId)
void	setSortBy(java.lang.String sortBy)
void	setSource(java.lang.String source)
void	setStart(int start)
void	setStartSet(boolean startSet)
void	setStrand(java.lang.String strand)
void	setTarget(java.lang.String target) Reserved Attribute.
void	setType(java.lang.String type)
void	setValid(boolean valid)
java.lang.String	sgrBundle() Returns a collection of sgr lines representing the gff feature: 1) seqId startMin1 0 2) seqId start score 3) seqId end score 4) seqId endPlus1 0 Does not include a final return, thus println(gff.sgrBundle()).
java.lang.String	toString() Generates a GFF3 line.
java.lang.String	toStringNoAttributes() Generates a GFF3 line.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

Gff3Feature

public Gff3Feature()

Gff3Feature

public Gff3Feature(java.lang.String unParsedGff3Line)

Always check if the GFF3Feature is valid after instantiating with this constructor. Invalid cases arise from not having 9 tab delimited columns or having an attribute that does not split in two on '='. Escaped characters are OK. Will also fail if numbers could not be parsed correctly.

Method Detail

compareTo

public int compareTo(java.lang.Object obj)

Sorts by the sortBy field so set it before sorting.

Specified by:

compareTo in interface java.lang.Comparable

clone

public java.lang.Object clone()

toString

public java.lang.String toString()

Generates a GFF3 line.

toStringNoAttributes

public java.lang.String toStringNoAttributes()

Generates a GFF3 line.

sgrBundle

public java.lang.String sgrBundle()

Returns a collection of sgr lines representing the gff feature: 1) seqId startMin1 0 2) seqId start score 3) seqId end score 4) seqId endPlus1 0 Does not include a final return, thus println(gff.sgrBundle()).

loadAttribute

public static void loadAttribute(java.lang.StringBuffer sb,
                                 java.lang.String reserveWord,
                                 java.lang.String value)

loadField

public static void loadField(java.lang.StringBuffer sb,
                             java.lang.String field)

saveGFF3TextFile

public static void saveGFF3TextFile(Gff3Feature[] g,
                                    java.io.File newGFF3File)

Prints an array of GFF3Features as a plain text file

getAlias

public java.lang.String getAlias()

Reserved Attribute.

setAlias

public void setAlias(java.lang.String alias)

getCustomAttributes

public java.lang.String[] getCustomAttributes()

Any Attribute that is not a reserve attribute is grouped here. Ie {"cat= dog", "tag=value1, value2, value3"}.

setCustomAttributes

public void setCustomAttributes(java.lang.String[] customAttributes)

getDbxref

public java.lang.String getDbxref()

Reserved Attribute.

setDbxref

public void setDbxref(java.lang.String dbxref)

getEnd

public int getEnd()

setEnd

public void setEnd(int end)

getGap

public java.lang.String getGap()

Reserved Attribute.

setGap

public void setGap(java.lang.String gap)

getId

public java.lang.String getId()

Reserved Attribute.

setId

public void setId(java.lang.String id)

getName

public java.lang.String getName()

Reserved Attribute.

setName

public void setName(java.lang.String name)

getNote

public java.lang.String getNote()

Reserved Attribute.

setNote

public void setNote(java.lang.String note)

getOntologyTerm

public java.lang.String getOntologyTerm()

Reserved Attribute.

setOntologyTerm

public void setOntologyTerm(java.lang.String ontologyTerm)

getParent

public java.lang.String getParent()

Reserved Attribute.

setParent

public void setParent(java.lang.String parent)

getPhase

public int getPhase()

setPhase

public void setPhase(int phase)

getScore

public double getScore()

setScore

public void setScore(double score)

getSeqId

public java.lang.String getSeqId()

setSeqId

public void setSeqId(java.lang.String seqId)

getSource

public java.lang.String getSource()

setSource

public void setSource(java.lang.String source)

getStart

public int getStart()

setStart

public void setStart(int start)

getStrand

public java.lang.String getStrand()

setStrand

public void setStrand(java.lang.String strand)

getTarget

public java.lang.String getTarget()

Reserved Attribute.

setTarget

public void setTarget(java.lang.String target)

Reserved Attribute.

getType

public java.lang.String getType()

setType

public void setType(java.lang.String type)

isValid

public boolean isValid()

Call to find out if the unparsed GFF line correctly parsed.

setValid

public void setValid(boolean valid)

isEndSet

public boolean isEndSet()

setEndSet

public void setEndSet(boolean endSet)

isPhaseSet

public boolean isPhaseSet()

setPhaseSet

public void setPhaseSet(boolean phaseSet)

isScoreSet

public boolean isScoreSet()

setScoreSet

public void setScoreSet(boolean scoreSet)

isStartSet

public boolean isStartSet()

setStartSet

public void setStartSet(boolean startSet)

getSortBy

public java.lang.String getSortBy()

setSortBy

public void setSortBy(java.lang.String sortBy)

getAttributes

public java.lang.String getAttributes()