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java.lang.Objectorg.biojava3.core.sequence.template.AbstractSequence<NucleotideCompound>
org.biojava3.core.sequence.DNASequence
org.biojava3.core.sequence.ChromosomeSequence
public class ChromosomeSequence
A ChromosomeSequence is a DNASequence but keeps track of geneSequences
Nested Class Summary |
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Nested classes/interfaces inherited from class org.biojava3.core.sequence.DNASequence |
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DNASequence.DNAType |
Nested classes/interfaces inherited from class org.biojava3.core.sequence.template.AbstractSequence |
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AbstractSequence.AnnotationType |
Constructor Summary | |
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ChromosomeSequence()
Empty constructor used by tools that need a proper Bean that allows the actual sequence data to be set after construction. |
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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. |
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ChromosomeSequence(SequenceReader<NucleotideCompound> proxyLoader,
CompoundSet<NucleotideCompound> compoundSet)
Allows the creation of a ChromosomeSequence using a ProxyResequenceReader for the sequence with a custom CompoundSet |
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ChromosomeSequence(String seqString)
String is king and assume DNA |
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ChromosomeSequence(String seqString,
CompoundSet<NucleotideCompound> compoundSet)
Allows the creation of a ChromosomeSequence using String for the sequence with a custom CompoundSet |
Method Summary | |
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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()
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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)
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void |
setChromosomeNumber(int chromosomeNumber)
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Methods inherited from class org.biojava3.core.sequence.DNASequence |
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getComplement, getDNAType, getGCCount, getReverse, getReverseComplement, getRNASequence, getRNASequence, getRNASequence, getRNASequence, main, setDNAType |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Constructor Detail |
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public ChromosomeSequence()
public ChromosomeSequence(String seqString)
seqString
- public ChromosomeSequence(SequenceReader<NucleotideCompound> proxyLoader)
proxyLoader
- public ChromosomeSequence(String seqString, CompoundSet<NucleotideCompound> compoundSet)
seqString
- compoundSet
- public ChromosomeSequence(SequenceReader<NucleotideCompound> proxyLoader, CompoundSet<NucleotideCompound> compoundSet)
proxyLoader
- compoundSet
- Method Detail |
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public int getChromosomeNumber()
public void setChromosomeNumber(int chromosomeNumber)
chromosomeNumber
- the chromosomeNumber to setpublic LinkedHashMap<String,GeneSequence> getGeneSequences()
public GeneSequence removeGeneSequence(String accession)
accession
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public GeneSequence addGene(AccessionID accession, int bioBegin, int bioEnd, Strand strand)
accession
- begin
- end
- strand
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public GeneSequence getGene(String accession)
accession
-
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