public class AlignmentParser extends Object
id name { 0, 1 } seqstart seqend refstart refend [ sstart send rstart rend ... ]These fields are respectively:
Note that the id fields in this file are meant to correspond to ids in a matching sequence data file.
The aligment data is collected into a set of Mappings. Each Mapping refers to
a Sequence and a collection of Spans of that sequence. Each Span models a
contiguous portion of a sequence that corresponds to a contiguous portion of
some reference space. Often, that reference space is a consensus sequence.
,
com.affymetrix.genoviz.datamodel
Constructor and Description |
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AlignmentParser() |
Modifier and Type | Method and Description |
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static Vector |
getAlignments(BufferedReader chars)
gets the alignment data by parsing a stream of characters.
|
static Vector |
getAlignments(BufferedReader chars,
Hashtable seqhash)
gets the alignment data by parsing a stream of bytes.
|
static Vector |
getAlignments(URL url)
gets the alignment data from the net.
|
static Vector |
getAlignments(URL url,
Hashtable seqhash)
gets the alignment data from the net.
|
public static Vector getAlignments(URL url)
url
- from whence the data come.Mapping
public static Vector getAlignments(BufferedReader chars)
chars
- the BufferedReader holding the character streamMapping
public static Vector getAlignments(URL url, Hashtable seqhash)
url
- from whence the data come.seqhash
- a collection of matching sequence data keyed by the same
ids as are in the alignment data to be parsed.Mapping
public static Vector getAlignments(BufferedReader chars, Hashtable seqhash) throws IOException
chars
- the BufferedReader holding the character streamseqhash
- a collection of matching sequence data keyed by the same
ids as are in the alignment data to be parsed.IOException
Mapping
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