Class GenbankReaderHelper
- java.lang.Object
-
- org.biojava.nbio.core.sequence.io.GenbankReaderHelper
-
public class GenbankReaderHelper extends java.lang.Object
- Author:
- Scooter Willis
-
-
Constructor Summary
Constructors Constructor Description GenbankReaderHelper()
-
Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static void
main(java.lang.String[] args)
static java.util.LinkedHashMap<java.lang.String,DNASequence>
readGenbankDNASequence(java.io.File file)
static java.util.LinkedHashMap<java.lang.String,DNASequence>
readGenbankDNASequence(java.io.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 java.util.LinkedHashMap<java.lang.String,DNASequence>
readGenbankDNASequence(java.io.InputStream inStream)
Read a Genbank DNA sequencestatic java.util.LinkedHashMap<java.lang.String,ProteinSequence>
readGenbankProteinSequence(java.io.File file)
Read a Genbank file containing amino acids with setup that would handle most cases.static java.util.LinkedHashMap<java.lang.String,ProteinSequence>
readGenbankProteinSequence(java.io.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 java.util.LinkedHashMap<java.lang.String,ProteinSequence>
readGenbankProteinSequence(java.io.InputStream inStream)
Read a Genbank file containing amino acids with setup that would handle most cases.static java.util.LinkedHashMap<java.lang.String,RNASequence>
readGenbankRNASequence(java.io.File file)
static java.util.LinkedHashMap<java.lang.String,RNASequence>
readGenbankRNASequence(java.io.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 java.util.LinkedHashMap<java.lang.String,RNASequence>
readGenbankRNASequence(java.io.InputStream inStream)
Read a Genbank RNA sequence
-
-
-
Method Detail
-
readGenbankDNASequence
public static java.util.LinkedHashMap<java.lang.String,DNASequence> readGenbankDNASequence(java.io.File file, boolean lazySequenceLoad) throws java.lang.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:
java.lang.Exception
-
readGenbankProteinSequence
public static java.util.LinkedHashMap<java.lang.String,ProteinSequence> readGenbankProteinSequence(java.io.File file, boolean lazySequenceLoad) throws java.lang.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:
java.lang.Exception
-
readGenbankRNASequence
public static java.util.LinkedHashMap<java.lang.String,RNASequence> readGenbankRNASequence(java.io.File file, boolean lazySequenceLoad) throws java.lang.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:
java.lang.Exception
-
readGenbankProteinSequence
public static java.util.LinkedHashMap<java.lang.String,ProteinSequence> readGenbankProteinSequence(java.io.File file) throws java.lang.Exception
Read a Genbank file containing amino acids with setup that would handle most cases.- Parameters:
file
-- Returns:
- Throws:
java.lang.Exception
-
readGenbankProteinSequence
public static java.util.LinkedHashMap<java.lang.String,ProteinSequence> readGenbankProteinSequence(java.io.InputStream inStream) throws java.lang.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:
java.lang.Exception
-
readGenbankDNASequence
public static java.util.LinkedHashMap<java.lang.String,DNASequence> readGenbankDNASequence(java.io.InputStream inStream) throws java.lang.Exception
Read a Genbank DNA sequence- Parameters:
inStream
-- Returns:
- Throws:
java.lang.Exception
-
readGenbankDNASequence
public static java.util.LinkedHashMap<java.lang.String,DNASequence> readGenbankDNASequence(java.io.File file) throws java.lang.Exception
- Parameters:
file
-- Returns:
- Throws:
java.lang.Exception
-
readGenbankRNASequence
public static java.util.LinkedHashMap<java.lang.String,RNASequence> readGenbankRNASequence(java.io.InputStream inStream) throws java.lang.Exception
Read a Genbank RNA sequence- Parameters:
inStream
-- Returns:
- Throws:
java.lang.Exception
-
readGenbankRNASequence
public static java.util.LinkedHashMap<java.lang.String,RNASequence> readGenbankRNASequence(java.io.File file) throws java.lang.Exception
- Parameters:
file
-- Returns:
- Throws:
java.lang.Exception
-
main
public static void main(java.lang.String[] args) throws java.lang.Exception
- Throws:
java.lang.Exception
-
-