util.bio.parsers.gff
Class GadFlyGffExtractor

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

public class GadFlyGffExtractor

extends java.lang.Object

Class for building annotation objects from GffFeatures, basically a converter, specific to the old dmel GadFly annotation. GffFeature object are built from the following type of gff file. Assumes a specific order of incoming features: (exon(s), translation(optional), transcript) many then a gene/transposon/rRNA etc example gff gadfly format 2R gadfly exon 67118 67499 . + . genegrp=CG8416; transgrp=CG8416-RD; name=CG8416:8 2R gadfly exon 68758 68907 . + . genegrp=CG8416; transgrp=CG8416-RD; name=CG8416:3 2R gadfly exon 69442 69522 . + . genegrp=CG8416; transgrp=CG8416-RD; name=CG8416:4 2R gadfly exon 69585 70954 . + . genegrp=CG8416; transgrp=CG8416-RD; name=CG8416:6 2R gadfly translation 67344 69773 . + . genegrp=CG8416; transgrp=CG8416-RD 2R gadfly transcript 67118 70954 . + . genegrp=CG8416; transgrp=CG8416-RD; name=CG8416-RD 2R gadfly gene 66411 70954 . + . genegrp=CG8416; name=CG8416; dbxref=GO:0016318; dbxref=GO:0007391; dbxref=GO:0007391; dbxref=GO:0007391; dbxref=GO:0007010; dbxref=GO:0003931; dbxref=GO:0016318; dbxref=GO:0007369; dbxref=GO:0007254; dbxref=GO:0007164; dbxref=GO:0003931; dbxref=GO:0003924; dbxref=GO:0003931; dbxref=GO:0007405; dbxref=GO:0030239; dbxref=GO:0016203; symbol=Rho1; dbxref=FlyBase:FBgn0014020; cytorange=52E3-52E4; cdna_clone=GH20776; cdna_clone=LD03419 2L gadfly exon 47514 52519 . + . genegrp=TE19092; transgrp=TE19092-RA; name=TE19092:1 2L gadfly transcript 47514 52519 . + . genegrp=TE19092; transgrp=TE19092-RA; name=TE19092-RA 2L gadfly transposable_element 47514 52519 . + . genegrp=TE19092; name=TE19092; symbol=jockey{}277; dbxref=FlyBase:FBti0019092; cytorange=21A3-21A3 2L gadfly exon 1791017 1792026 . - . genegrp=CR31930; transgrp=CR31930-RA; name=CR31930:1 2L gadfly exon 1790806 1790958 . - . genegrp=CR31930; transgrp=CR31930-RA; name=CR31930:2 2L gadfly transcript 1790806 1792026 . - . genegrp=CR31930; transgrp=CR31930-RA; name=CR31930-RA 2L gadfly pseudogene 1790806 1792026 . - . genegrp=CR31930; name=CR31930; symbol=Gr22d; dbxref=FlyBase:FBgn0045498; cytorange=22B2-22B2 Assumes that there is at least one exon and transcript per gene/transposon/rRNA etc. Assumes that start is always less than end/stop. Use orientation to get 1 or -1, (+ or -)

Constructor Summary

GadFlyGffExtractor(java.io.File gffFile, int startNt, int stopNt)

Method Summary

void	buildExon(GffFeature f)
void	buildGeneGrp(GffFeature f)
void	buildGenericFeature(GffFeature f)
void	buildTranscript(GffFeature f)
void	buildTransGrp()
void	buildTranslation(GffFeature f)
java.util.ArrayList	getGeneGrps()
java.util.LinkedHashSet	getGenericFeatureHash() Contains all the feature types that were not recognized by the GadFlyGFFExtractor.
java.util.ArrayList	getGenericFeatures()
boolean	isGenericFeaturesFound()
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

GadFlyGffExtractor

public GadFlyGffExtractor(java.io.File gffFile,
                          int startNt,
                          int stopNt)

Method Detail

toString

public java.lang.String toString()

getGenericFeatureHash

public java.util.LinkedHashSet getGenericFeatureHash()

Contains all the feature types that were not recognized by the GadFlyGFFExtractor. Should be user added items like CRMs, enhancers, etc.

getGenericFeatures

public java.util.ArrayList getGenericFeatures()

buildGenericFeature

public void buildGenericFeature(GffFeature f)

buildExon

public void buildExon(GffFeature f)

buildTranslation

public void buildTranslation(GffFeature f)

buildTranscript

public void buildTranscript(GffFeature f)

buildTransGrp

public void buildTransGrp()

buildGeneGrp

public void buildGeneGrp(GffFeature f)

getGeneGrps

public java.util.ArrayList getGeneGrps()

isGenericFeaturesFound

public boolean isGenericFeaturesFound()