org.utgenome.format.gff3
Class GFF3Reader

java.lang.Object
  org.utgenome.format.gff3.GFF3Reader

public class GFF3Reader
extends Object

GFF3 Format has

 Undefined fields are replaced with the "." character, as described in
  the original GFF spec.
 
  Column 1: "seqid"
 
  The ID of the landmark used to establish the coordinate system for the
  current feature. IDs may contain any characters, but must escape any
  characters not in the set [a-zA-Z0-9.:ˆ*$@!+_?-|].  In particular, IDs
  may not contain unescaped whitespace and must not begin with an
  unescaped ">".
 
  Column 2: "source"
 
  The source is a free text qualifier intended to describe the algorithm
  or operating procedure that generated this feature.  Typically this is
  the name of a piece of software, such as "Genescan" or a database
  name, such as "Genbank."  In effect, the source is used to extend the
  feature ontology by adding a qualifier to the type creating a new
  composite type that is a subclass of the type in the type column.
 
  Column 3: "type"
 
  The type of the feature (previously called the "method").  This is
  constrained to be either: (a) a term from the "lite" sequence
  ontology, SOFA; or (b) a SOFA accession number.  The latter
  alternative is distinguished using the syntax SO:000000.
 
  Columns 4 & 5: "start" and "end"
 
  The start and end of the feature, in 1-based integer coordinates,
  relative to the landmark given in column 1.  Start is always less than
  or equal to end.
 
  For zero-length features, such as insertion sites, start equals end
  and the implied site is to the right of the indicated base in the
  direction of the landmark.
 
  Column 6: "score"
 
  The score of the feature, a floating point number.  As in earlier
  versions of the format, the semantics of the score are ill-defined.
  It is strongly recommended that E-values be used for sequence
  similarity features, and that P-values be used for ab initio gene
  prediction features.
 
  Column 7: "strand"
 
  The strand of the feature.  + for positive strand (relative to the
  landmark), - for minus strand, and . for features that are not
  stranded.  In addition, ? can be used for features whose strandedness
  is relevant, but unknown.
 
  Column 8: "phase"
 
  For features of type "CDS", the phase indicates where the feature
  begins with reference to the reading frame.  The phase is one of the
  integers 0, 1, or 2, indicating the number of bases that should be
  removed from the beginning of this feature to reach the first base of
  the next codon. In other words, a phase of "0" indicates that the next
  codon begins at the first base of the region described by the current
  line, a phase of "1" indicates that the next codon begins at the
  second base of this region, and a phase of "2" indicates that the
  codon begins at the third base of this region. This is NOT to be
  confused with the frame, which is simply start modulo 3.
 
  For forward strand features, phase is counted from the start
  field. For reverse strand features, phase is counted from the end
  field.
 
  The phase is REQUIRED for all CDS features.
 
  Column 9: "attributes"
 
  A list of feature attributes in the format tag=value.  Multiple
  tag=value pairs are separated by semicolons.  URL escaping rules are
  used for tags or values containing the following characters: ",=;".
  Spaces are allowed in this field, but tabs must be replaced with the
  %09 URL escape.
 
  These tags have predefined meanings:
 
  ID       Indicates the name of the feature.  IDs must be unique
  within the scope of the GFF file.
 
  Name   Display name for the feature.  This is the name to be
  displayed to the user.  Unlike IDs, there is no requirement
  that the Name be unique within the file.
 
  Alias  A secondary name for the feature.  It is suggested that
  this tag be used whenever a secondary identifier for the
  feature is needed, such as locus names and
  accession numbers.  Unlike ID, there is no requirement
  that Alias be unique within the file.
 
  Parent Indicates the parent of the feature.  A parent ID can be
  used to group exons into transcripts, transcripts into
  genes, an so forth.  A feature may have multiple parents.
  Parent can *only* be used to indicate a partof 
  relationship.
 
  Target Indicates the target of a nucleotide-to-nucleotide or
  protein-to-nucleotide alignment.  The format of the
  value is "target_id start end [strand]", where strand
  is optional and may be "+" or "-".  If the target_id 
  contains spaces, they must be escaped as hex escape %20.
 
  Gap   The alignment of the feature to the target if the two are
  not collinear (e.g. contain gaps).  The alignment format is
  taken from the CIGAR format described in the 
  Exonerate documentation.
  (http://cvsweb.sanger.ac.uk/cgi-bin/cvsweb.cgi/exonerate
  ?cvsroot=Ensembl).  See "THE GAP ATTRIBUTE" for a description
  of this format.
 
  Derives_from  
  Used to disambiguate the relationship between one
  feature and another when the relationship is a temporal
  one rather than a purely structural "part of" one.  This
  is needed for polycistronic genes.  See "PATHOLOGICAL CASES"
  for further discussion.
 
  Note   A free text note.
 
  Dbxref A database cross reference.  See the section
  "Ontology Associations and Db Cross References" for
  details on the format.
 
  Ontology_term  A cross reference to an ontology term.  See
  the section "Ontology Associations and Db Cross References"
  for details.
 
  Multiple attributes of the same type are indicated by separating the
  values with the comma "," character, as in:
 
  Parent=AF2312,AB2812,abc-3
 
  Note that attribute names are case sensitive.  "Parent" is not the
  same as "parent".
 
  All attributes that begin with an uppercase letter are reserved for
  later use.  Attributes that begin with a lowercase letter can be used
  freely by applications.
 
 
 

Author:

leo

Constructor Summary

GFF3Reader(Reader input)

Method Summary

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

GFF3Reader

public GFF3Reader(Reader input)