Package org.biojava.nbio.core.sequence.io

Class GenbankReaderHelper

java.lang.Object

org.biojava.nbio.core.sequence.io.GenbankReaderHelper

public class GenbankReaderHelper
extends Object

Author:

Scooter Willis

Constructor Summary

Constructors

Constructor	Description
GenbankReaderHelper()

Method Summary

Modifier and Type	Method	Description
static LinkedHashMap<String,DNASequence>	readGenbankDNASequence(File file)
static LinkedHashMap<String,DNASequence>	readGenbankDNASequence(File file, boolean lazySequenceLoad)	Selecting lazySequenceLoad=true will parse the Genbank file and figure out the accessionid and offsets and return sequence objects that can in the future read the sequence from the disk.
static LinkedHashMap<String,DNASequence>	readGenbankDNASequence(InputStream inStream)	Read a Genbank DNA sequence
static LinkedHashMap<String,ProteinSequence>	readGenbankProteinSequence(File file)	Read a Genbank file containing amino acids with setup that would handle most cases.
static LinkedHashMap<String,ProteinSequence>	readGenbankProteinSequence(File file, boolean lazySequenceLoad)	Selecting lazySequenceLoad=true will parse the Genbank file and figure out the accessionid and offsets and return sequence objects that can in the future read the sequence from the disk.
static LinkedHashMap<String,ProteinSequence>	readGenbankProteinSequence(InputStream inStream)	Read a Genbank file containing amino acids with setup that would handle most cases.
static LinkedHashMap<String,RNASequence>	readGenbankRNASequence(File file)
static LinkedHashMap<String,RNASequence>	readGenbankRNASequence(File file, boolean lazySequenceLoad)	Selecting lazySequenceLoad=true will parse the Genbank file and figure out the accessionid and offsets and return sequence objects that can in the future read the sequence from the disk.
static LinkedHashMap<String,RNASequence>	readGenbankRNASequence(InputStream inStream)	Read a Genbank RNA sequence

Methods inherited from class java.lang.Object

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

Constructor Detail

GenbankReaderHelper

public GenbankReaderHelper()

Method Detail

readGenbankDNASequence

public static LinkedHashMap<String,DNASequence> readGenbankDNASequence(File file,
                                                                             boolean lazySequenceLoad)
                                                                      throws Exception

Selecting lazySequenceLoad=true will parse the Genbank file and figure out the accessionid and offsets and return sequence objects that can in the future read the sequence from the disk. This allows the loading of large Genbank files where you are only interested in one sequence based on accession id.

Parameters:

file -

lazySequenceLoad -

Returns:

Throws:

Exception

readGenbankProteinSequence

public static LinkedHashMap<String,ProteinSequence> readGenbankProteinSequence(File file,
                                                                                     boolean lazySequenceLoad)
                                                                              throws Exception

Selecting lazySequenceLoad=true will parse the Genbank file and figure out the accessionid and offsets and return sequence objects that can in the future read the sequence from the disk. This allows the loading of large Genbank files where you are only interested in one sequence based on accession id.

Parameters:

file -

lazySequenceLoad -

Returns:

Throws:

Exception

readGenbankRNASequence

public static LinkedHashMap<String,RNASequence> readGenbankRNASequence(File file,
                                                                             boolean lazySequenceLoad)
                                                                      throws Exception

Selecting lazySequenceLoad=true will parse the Genbank file and figure out the accessionid and offsets and return sequence objects that can in the future read the sequence from the disk. This allows the loading of large Genbank files where you are only interested in one sequence based on accession id.

Parameters:

file -

lazySequenceLoad -

Returns:

Throws:

Exception

readGenbankProteinSequence

public static LinkedHashMap<String,ProteinSequence> readGenbankProteinSequence(File file)
                                                                              throws Exception

Read a Genbank file containing amino acids with setup that would handle most cases.

Parameters:

file -

Returns:

Throws:

Exception

readGenbankProteinSequence

public static LinkedHashMap<String,ProteinSequence> readGenbankProteinSequence(InputStream inStream)
                                                                              throws Exception

Read a Genbank file containing amino acids with setup that would handle most cases. User is responsible for closing InputStream because you opened it

Parameters:

inStream -

Returns:

Throws:

Exception

readGenbankDNASequence

public static LinkedHashMap<String,DNASequence> readGenbankDNASequence(InputStream inStream)
                                                                      throws Exception

Read a Genbank DNA sequence

Parameters:

inStream -

Returns:

Throws:

Exception

readGenbankDNASequence

public static LinkedHashMap<String,DNASequence> readGenbankDNASequence(File file)
                                                                      throws Exception

Parameters:

file -

Returns:

Throws:

Exception

readGenbankRNASequence

public static LinkedHashMap<String,RNASequence> readGenbankRNASequence(InputStream inStream)
                                                                      throws Exception

Read a Genbank RNA sequence

Parameters:

inStream -

Returns:

Throws:

Exception

readGenbankRNASequence

public static LinkedHashMap<String,RNASequence> readGenbankRNASequence(File file)
                                                                      throws Exception

Parameters:

file -

Returns:

Throws:

Exception