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java.lang.Objectorg.biojava.bio.program.gff.GFFTools
Field Summary | |
static int |
NO_FRAME
Flag to indicate that there is no frame info. |
static double |
NO_SCORE
Flag to indicate that there is no score info. |
Constructor Summary | |
GFFTools()
|
Method Summary | |
static Sequence |
annotateSequence(Sequence seq,
GFFEntrySet ents)
Annotates a sequence with the features from a GFF entry set with sequence name matching this sequence. |
static Sequence |
annotateSequence(Sequence seq,
GFFEntrySet ents,
boolean checkSeqName)
Annotates a sequence with the features from a GFF entry set. |
static SequenceDB |
annotateSequences(SequenceDB seqs,
GFFEntrySet ents)
Annotates all sequences in a sequence DB with features from a GFF entry set. |
static GFFEntrySet |
gffFromSequence(Sequence seq)
Creates a GFFEntrySet containing one entry for each feature on a sequence. |
static GFFEntrySet |
readGFF(java.io.BufferedReader gffIn)
|
static GFFEntrySet |
readGFF(java.io.BufferedReader gffIn,
GFFRecordFilter recFilt)
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static GFFEntrySet |
readGFF(java.lang.String fileName)
Reads a GFFEntrySet from a file with no filtering |
static GFFEntrySet |
readGFF(java.lang.String fileName,
GFFRecordFilter recFilt)
Reads a GFFEntrySet from a file with the specified filter |
static void |
writeGFF(java.io.PrintWriter pw,
GFFEntrySet ents)
Writes a GFFEntrySet to a PrintWriter |
static void |
writeGFF(java.lang.String fileName,
GFFEntrySet ents)
Writes a GFFEntrySet to a file |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
public static double NO_SCORE
public static int NO_FRAME
Constructor Detail |
public GFFTools()
Method Detail |
public static GFFEntrySet readGFF(java.lang.String fileName) throws java.io.FileNotFoundException, ParserException, BioException, java.io.IOException
GFFEntrySet
from a file with no filtering
fileName
- the file containing the GFF
GFFEntrySet
encapsulating the records read from the file
java.io.FileNotFoundException
- if file is not found
ParserException
- if format is wrong
BioException
- if format is wrong
java.io.IOException
- if file reading error occurspublic static GFFEntrySet readGFF(java.lang.String fileName, GFFRecordFilter recFilt) throws java.io.FileNotFoundException, ParserException, BioException, java.io.IOException
fileName
- the file containing the GFFrecFilt
- the filter to use
GFFEntrySet
encapsulating the records read from the file
java.io.FileNotFoundException
- if file is not found
ParserException
- if format is wrong
BioException
- if format is wrong
java.io.IOException
- if file reading error occurspublic static GFFEntrySet readGFF(java.io.BufferedReader gffIn) throws ParserException, BioException, java.io.IOException
ParserException
BioException
java.io.IOException
public static GFFEntrySet readGFF(java.io.BufferedReader gffIn, GFFRecordFilter recFilt) throws ParserException, BioException, java.io.IOException
ParserException
BioException
java.io.IOException
public static void writeGFF(java.lang.String fileName, GFFEntrySet ents) throws java.io.IOException
fileName
- the file to write toents
- the entries to write
java.io.IOException
- if file writing failspublic static void writeGFF(java.io.PrintWriter pw, GFFEntrySet ents) throws java.io.IOException
pw
- the PrintWriter to write toents
- the entries to write
java.io.IOException
- if file writing failspublic static Sequence annotateSequence(Sequence seq, GFFEntrySet ents)
seq
- the Sequence
to annotate.ents
- the the GFF features to annotate it with.
public static Sequence annotateSequence(Sequence seq, GFFEntrySet ents, boolean checkSeqName)
seq
- the Sequence
to annotate.ents
- the the GFF features to annotate it with.
public static SequenceDB annotateSequences(SequenceDB seqs, GFFEntrySet ents) throws IllegalIDException, BioException
seqs
- the SequenceDB to annotateents
- the GFFEntrySet to annote with
IllegalIDException
BioException
public static GFFEntrySet gffFromSequence(Sequence seq) throws BioException
seq
- the Sequence to create features for
BioException
- if something went wrong GFF-ifying the sequences
features
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