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:

java.lang.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.template.AbstractSequence
  AbstractSequence.AnnotationType
- Nested classes/interfaces inherited from class org.biojava.nbio.core.sequence.DNASequence
  DNASequence.DNAType

Constructor Summary

Constructors
Constructor	Description
`ChromosomeSequence()`	Empty constructor used by tools that need a proper Bean that allows the actual sequence data to be set after construction.
`ChromosomeSequence(java.lang.String seqString)`	String is king and assume DNA
`ChromosomeSequence(java.lang.String seqString, CompoundSet<NucleotideCompound> compoundSet)`	Allows the creation of a ChromosomeSequence using String for the sequence with a custom CompoundSet
`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

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	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(java.lang.String accession)`	Get the gene based on accession.
`java.util.LinkedHashMap<java.lang.String,GeneSequence>`	`getGeneSequences()`	Get the list of genes that have been added to the ChromosomeSequence where accession.toString is the key.
`GeneSequence`	`removeGeneSequence(java.lang.String accession)`
`void`	`setChromosomeNumber(int chromosomeNumber)`

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 org.biojava.nbio.core.sequence.DNASequence
getComplement, getDNAType, getGCCount, getReverse, getReverseComplement, getRNASequence, getRNASequence, getRNASequence, getRNASequence, main, setDNAType

Methods inherited from interface java.lang.Iterable
forEach, spliterator

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- 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(java.lang.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(java.lang.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 java.util.LinkedHashMap<java.lang.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(java.lang.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(java.lang.String accession)
```
    Get the gene based on accession. Will return null if not found
    
    Parameters:
    
    accession -
    
    Returns:

Class ChromosomeSequence

Nested Class Summary

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

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

Constructor Summary

Method Summary

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

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

Methods inherited from interface java.lang.Iterable

Methods inherited from class java.lang.Object

Constructor Detail

ChromosomeSequence

ChromosomeSequence

ChromosomeSequence

ChromosomeSequence

ChromosomeSequence

Method Detail

getChromosomeNumber

setChromosomeNumber

getGeneSequences

removeGeneSequence

addGene

getGene