org.biojava.nbio.core.sequence

Class ChromosomeSequence

java.lang.Object

org.biojava.nbio.core.sequence.template.AbstractSequence<NucleotideCompound>

org.biojava.nbio.core.sequence.DNASequence

org.biojava.nbio.core.sequence.ChromosomeSequence

All Implemented Interfaces:

Iterable<NucleotideCompound>, Accessioned, Sequence<NucleotideCompound>

public class ChromosomeSequence
extends DNASequence

A ChromosomeSequence is a DNASequence but keeps track of geneSequences

Author:

Scooter Willis

Nested Class Summary

Nested classes/interfaces inherited from class org.biojava.nbio.core.sequence.DNASequence

DNASequence.DNAType

Nested classes/interfaces inherited from class org.biojava.nbio.core.sequence.template.AbstractSequence

AbstractSequence.AnnotationType

Constructor Summary

Constructors

Constructor and Description
ChromosomeSequence() Empty constructor used by tools that need a proper Bean that allows the actual sequence data to be set after construction.
ChromosomeSequence(SequenceReader<NucleotideCompound> proxyLoader) Fairly important constructor given the size of a ChromsomeSequence where the ProxySequenceReader could load from disk via RandomAccessFile so that the sequence doesn't need to be kept in memory.
ChromosomeSequence(SequenceReader<NucleotideCompound> proxyLoader, CompoundSet<NucleotideCompound> compoundSet) Allows the creation of a ChromosomeSequence using a ProxyResequenceReader for the sequence with a custom CompoundSet
ChromosomeSequence(String seqString) String is king and assume DNA
ChromosomeSequence(String seqString, CompoundSet<NucleotideCompound> compoundSet) Allows the creation of a ChromosomeSequence using String for the sequence with a custom CompoundSet

Method Summary

Modifier and Type	Method and Description
GeneSequence	addGene(AccessionID accession, int bioBegin, int bioEnd, Strand strand) Add a gene to the chromosome sequence using bioIndexing starts at 1 instead of 0.
int	getChromosomeNumber()
GeneSequence	getGene(String accession) Get the gene based on accession.
LinkedHashMap<String,GeneSequence>	getGeneSequences() Get the list of genes that have been added to the ChromosomeSequence where accession.toString is the key.
GeneSequence	removeGeneSequence(String accession)
void	setChromosomeNumber(int chromosomeNumber)

Methods inherited from class org.biojava.nbio.core.sequence.DNASequence

getComplement, getDNAType, getGCCount, getReverse, getReverseComplement, getRNASequence, getRNASequence, getRNASequence, getRNASequence, main, setDNAType

Methods inherited from class org.biojava.nbio.core.sequence.template.AbstractSequence

addFeature, addFeature, addNote, countCompounds, getAccession, getAnnotationType, getAsList, getBioBegin, getBioEnd, getCompoundAt, getCompoundSet, getDatabaseReferences, getDescription, getFeatureRetriever, getFeatures, getFeatures, getFeatures, getFeaturesByType, getFeaturesKeyWord, getIndexOf, getInverse, getLastIndexOf, getLength, getNotesList, getOriginalHeader, getParentSequence, getProxySequenceReader, getSequenceAsString, getSequenceAsString, getSequenceScore, getSource, getSubSequence, getTaxonomy, getUserCollection, iterator, removeFeature, removeNote, setAccession, setAnnotationType, setBioBegin, setBioEnd, setCompoundSet, setDatabaseReferences, setDescription, setFeatureRetriever, setFeaturesKeyWord, setNotesList, setOriginalHeader, setParentSequence, setProxySequenceReader, setSequenceScore, setSource, setTaxonomy, setUserCollection, toString

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Constructor Detail

ChromosomeSequence

public ChromosomeSequence()

Empty constructor used by tools that need a proper Bean that allows the actual sequence data to be set after construction. Not recommended

ChromosomeSequence

public ChromosomeSequence(String seqString)
                   throws CompoundNotFoundException

String is king and assume DNA

Parameters:

seqString -

Throws:

CompoundNotFoundException

ChromosomeSequence

public ChromosomeSequence(SequenceReader<NucleotideCompound> proxyLoader)

Fairly important constructor given the size of a ChromsomeSequence where the ProxySequenceReader could load from disk via RandomAccessFile so that the sequence doesn't need to be kept in memory. Could also be a NCBI proxy to load sequence data as needed from remote web server.

Parameters:

proxyLoader -

ChromosomeSequence

public ChromosomeSequence(String seqString,
                          CompoundSet<NucleotideCompound> compoundSet)
                   throws CompoundNotFoundException

Allows the creation of a ChromosomeSequence using String for the sequence with a custom CompoundSet

Parameters:

seqString -

compoundSet -

Throws:

CompoundNotFoundException

ChromosomeSequence

public ChromosomeSequence(SequenceReader<NucleotideCompound> proxyLoader,
                          CompoundSet<NucleotideCompound> compoundSet)

Allows the creation of a ChromosomeSequence using a ProxyResequenceReader for the sequence with a custom CompoundSet

Parameters:

proxyLoader -

compoundSet -

Method Detail

getChromosomeNumber

public int getChromosomeNumber()

Returns:

the chromosomeNumber

setChromosomeNumber

public void setChromosomeNumber(int chromosomeNumber)

Parameters:

chromosomeNumber - the chromosomeNumber to set

getGeneSequences

public LinkedHashMap<String,GeneSequence> getGeneSequences()

Get the list of genes that have been added to the ChromosomeSequence where accession.toString is the key. The list retains the order the genes are added

Returns:

removeGeneSequence

public GeneSequence removeGeneSequence(String accession)

Parameters:

accession -

Returns:

addGene

public GeneSequence addGene(AccessionID accession,
                            int bioBegin,
                            int bioEnd,
                            Strand strand)

Add a gene to the chromosome sequence using bioIndexing starts at 1 instead of 0. The GeneSequence that is returned will have a reference to parent chromosome sequence which actually contains the sequence data. Strand is important for positive and negative direction where negative strand means we need reverse complement. If negative strand then bioBegin will be greater than bioEnd

Parameters:

accession -

begin -

end -

strand -

Returns:

getGene

public GeneSequence getGene(String accession)

Get the gene based on accession. Will return null if not found

Parameters:

accession -

Returns: