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java.lang.Objectorg.biojava.bio.program.gff.GFFTools
public class GFFTools
Field Summary | |
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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 | |
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GFFTools()
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Method Summary | |
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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. |
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 |
gffFromSeqDB(SequenceDB seqDB)
Creates a GFFEntrySet containing one entry for each feature on each sequence of a SequenceDB. |
static GFFEntrySet |
gffFromSequence(Sequence seq)
Creates a GFFEntrySet containing one entry for each feature on a sequence. |
static GFFEntrySet |
readGFF(java.io.BufferedReader gffIn)
Read all GFF entries from a buffered reader. |
static GFFEntrySet |
readGFF(java.io.BufferedReader gffIn,
GFFRecordFilter recFilt)
Read all GFF entries matching a filter from a buffered reader. |
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. |
static GFFEntrySet |
readGFF(java.lang.String fileName)
Deprecated. use: readGff(File) |
static GFFEntrySet |
readGFF(java.lang.String fileName,
GFFRecordFilter recFilt)
Deprecated. use: readGff(File,GFFRecordFilter) |
static void |
writeGFF(java.io.File outFile,
GFFEntrySet ents)
Writes a GFFEntrySet to a file. |
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 |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public static double NO_SCORE
public static int NO_FRAME
Constructor Detail |
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public GFFTools()
Method Detail |
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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.File inFile) throws java.io.FileNotFoundException, ParserException, BioException, java.io.IOException
GFFEntrySet
from a file with no filtering.
inFile
- 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.io.File inFile, GFFRecordFilter recFilt) throws java.io.FileNotFoundException, ParserException, BioException, java.io.IOException
inFile
- 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
gffIn
- the BufferedReader to read text from
parserException
- if the text could not be parsed as GFF
BioException
- if there was some error reading the GFF
java.io.IOException
- if there was an error with the reader
ParserException
public static GFFEntrySet readGFF(java.io.BufferedReader gffIn, GFFRecordFilter recFilt) throws ParserException, BioException, java.io.IOException
gffIn
- the BufferedReader to read text from
parserException
- if the text could not be parsed as GFF
BioException
- if there was some error reading the GFF
java.io.IOException
- if there was an error with the reader
ParserException
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.File outFile, GFFEntrySet ents) throws java.io.IOException
outFile
- the file to write toents
- the entry set to write
java.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 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.checkSeqName
- boolean flat, if true only annotate sequence with
features that have matching sequence names, otherwise annotate
all features
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
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 for
BioException
- if something went wrong GFF-ifying the sequences
features
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