java.lang.Iterable<NucleotideCompound>
, Accessioned
, Sequence<NucleotideCompound>
public class ChromosomeSequence extends DNASequence
AbstractSequence.AnnotationType
DNASequence.DNAType
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
|
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) |
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
getComplement, getDNAType, getGCCount, getReverse, getReverseComplement, getRNASequence, getRNASequence, getRNASequence, getRNASequence, main, setDNAType
public ChromosomeSequence()
public ChromosomeSequence(java.lang.String seqString) throws CompoundNotFoundException
seqString
- CompoundNotFoundException
public ChromosomeSequence(SequenceReader<NucleotideCompound> proxyLoader)
proxyLoader
- public ChromosomeSequence(java.lang.String seqString, CompoundSet<NucleotideCompound> compoundSet) throws CompoundNotFoundException
seqString
- compoundSet
- CompoundNotFoundException
public ChromosomeSequence(SequenceReader<NucleotideCompound> proxyLoader, CompoundSet<NucleotideCompound> compoundSet)
proxyLoader
- compoundSet
- public int getChromosomeNumber()
public void setChromosomeNumber(int chromosomeNumber)
chromosomeNumber
- the chromosomeNumber to setpublic java.util.LinkedHashMap<java.lang.String,GeneSequence> getGeneSequences()
public GeneSequence removeGeneSequence(java.lang.String accession)
accession
- public GeneSequence addGene(AccessionID accession, int bioBegin, int bioEnd, Strand strand)
accession
- begin
- end
- strand
- public GeneSequence getGene(java.lang.String accession)
accession
-