public class GFFTools
extends java.lang.Object
Modifier and Type | Field and Description |
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static int |
NO_FRAME
Flag to indicate that there is no frame info.
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static double |
NO_SCORE
Flag to indicate that there is no score info.
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Constructor and Description |
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GFFTools() |
Modifier and Type | Method and Description |
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static Sequence |
annotateSequence(Sequence seq,
GFFEntrySet ents)
Annotates a sequence with the features from a GFF entry set with sequence
name matching this sequence.
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static Sequence |
annotateSequence(Sequence seq,
GFFEntrySet ents,
boolean checkSeqName)
Annotates a sequence with the features from a GFF entry set.
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static SequenceDB |
annotateSequences(SequenceDB seqs,
GFFEntrySet ents)
Annotates all sequences in a sequence DB with features from a GFF entry set.
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static GFFEntrySet |
gffFromSeqDB(SequenceDB seqDB)
Creates a GFFEntrySet containing one entry for each feature on each
sequence of a SequenceDB.
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static GFFEntrySet |
gffFromSequence(Sequence seq)
Creates a GFFEntrySet containing one entry for each feature on a sequence.
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static GFFEntrySet |
readGFF(java.io.BufferedReader gffIn)
Read all GFF entries from a buffered reader.
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static GFFEntrySet |
readGFF(java.io.BufferedReader gffIn,
GFFRecordFilter recFilt)
Read all GFF entries matching a filter from a buffered reader.
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static GFFEntrySet |
readGFF(java.io.File inFile)
Reads a
GFFEntrySet from a file with no filtering. |
static GFFEntrySet |
readGFF(java.io.File inFile,
GFFRecordFilter recFilt)
Reads a GFFEntrySet from a file with the specified filter.
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static GFFEntrySet |
readGFF(java.lang.String fileName)
Deprecated.
use: readGff(File)
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static GFFEntrySet |
readGFF(java.lang.String fileName,
GFFRecordFilter recFilt)
Deprecated.
use: readGff(File,GFFRecordFilter)
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static void |
writeGFF(java.io.File outFile,
GFFEntrySet ents)
Writes a GFFEntrySet to a file.
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static void |
writeGFF(java.io.PrintWriter pw,
GFFEntrySet ents)
Writes a GFFEntrySet to a PrintWriter.
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static void |
writeGFF(java.lang.String fileName,
GFFEntrySet ents)
Writes a GFFEntrySet to a file.
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public static double NO_SCORE
public static int NO_FRAME
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 GFFGFFEntrySet
encapsulating the records read from the filejava.io.FileNotFoundException
- if file is not foundParserException
- if format is wrongBioException
- if format is wrongjava.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 useGFFEntrySet
encapsulating the records read from the filejava.io.FileNotFoundException
- if file is not foundParserException
- if format is wrongBioException
- if format is wrongjava.io.IOException
- if file reading error occurspublic static GFFEntrySet readGFF(java.io.File inFile) throws java.io.FileNotFoundException, ParserException, BioException, java.io.IOException
GFFEntrySet
from a file with no filtering.inFile
- the File containing the GFFGFFEntrySet
encapsulating the records read from the filejava.io.FileNotFoundException
- if file is not foundParserException
- if format is wrongBioException
- if format is wrongjava.io.IOException
- if file reading error occurspublic static GFFEntrySet readGFF(java.io.File inFile, GFFRecordFilter recFilt) throws java.io.FileNotFoundException, ParserException, BioException, java.io.IOException
inFile
- the File containing the GFFrecFilt
- the filter to useGFFEntrySet
encapsulating the records read from the filejava.io.FileNotFoundException
- if file is not foundParserException
- if format is wrongBioException
- if format is wrongjava.io.IOException
- if file reading error occurspublic static GFFEntrySet readGFF(java.io.BufferedReader gffIn) throws ParserException, BioException, java.io.IOException
gffIn
- the BufferedReader to read text fromparserException
- if the text could not be parsed as GFFBioException
- if there was some error reading the GFFjava.io.IOException
- if there was an error with the readerParserException
public static GFFEntrySet readGFF(java.io.BufferedReader gffIn, GFFRecordFilter recFilt) throws ParserException, BioException, java.io.IOException
gffIn
- the BufferedReader to read text fromparserException
- if the text could not be parsed as GFFBioException
- if there was some error reading the GFFjava.io.IOException
- if there was an error with the readerParserException
public static void writeGFF(java.lang.String fileName, GFFEntrySet ents) throws java.io.IOException
fileName
- the file to write toents
- the entries to writejava.io.IOException
- if file writing failspublic static void writeGFF(java.io.File outFile, GFFEntrySet ents) throws java.io.IOException
outFile
- the file to write toents
- the entry set to writejava.io.IOException
- if writing to the file failspublic static void writeGFF(java.io.PrintWriter pw, GFFEntrySet ents) throws java.io.IOException
pw
- the PrintWriter to write toents
- the entries to writejava.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.checkSeqName
- boolean flat, if true only annotate sequence with
features that have matching sequence names, otherwise annotate
all featurespublic static SequenceDB annotateSequences(SequenceDB seqs, GFFEntrySet ents) throws IllegalIDException, BioException
seqs
- the SequenceDB to annotateents
- the GFFEntrySet to annote withIllegalIDException
BioException
public static GFFEntrySet gffFromSequence(Sequence seq) throws BioException
seq
- the Sequence to create features forBioException
- if something went wrong GFF-ifying the sequences
featurespublic static GFFEntrySet gffFromSeqDB(SequenceDB seqDB) throws BioException
Note: This converts all features in the whole database to in-memorey GFFRecord instances. This will take up considerable memory for large databases.
seqDB
- the SequenceDB to create features forBioException
- if something went wrong GFF-ifying the sequences
features