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java.lang.Objectorg.biojava3.core.sequence.template.AbstractSequence<NucleotideCompound>
org.biojava3.core.sequence.DNASequence
org.biojava3.core.sequence.TranscriptSequence
public class TranscriptSequence
This is the sequence if you want to go from a gene sequence to a protein sequence. Need to start with a ChromosomeSequence then getting a GeneSequence and then a TranscriptSequence
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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TranscriptSequence(GeneSequence parentDNASequence,
int begin,
int end)
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Method Summary | |
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CDSSequence |
addCDS(AccessionID accession,
int begin,
int end,
int phase)
Add a Coding Sequence region with phase to the transcript sequence |
void |
addStartCodonSequence(AccessionID accession,
int begin,
int end)
|
void |
addStopCodonSequence(AccessionID accession,
int begin,
int end)
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LinkedHashMap<String,CDSSequence> |
getCDSSequences()
Get the CDS sequences that have been added to the TranscriptSequences |
DNASequence |
getDNACodingSequence()
Get the stitched together CDS sequences then maps to the cDNA |
int |
getLength()
Returns the length of the Sequence |
ArrayList<ProteinSequence> |
getProteinCDSSequences()
Return a list of protein sequences based on each CDS sequence where the phase shift between two CDS sequences is assigned to the CDS sequence that starts the triplet. |
ProteinSequence |
getProteinSequence()
Get the protein sequence |
ProteinSequence |
getProteinSequence(TranscriptionEngine engine)
Get the protein sequence with user defined TranscriptEngine |
StartCodonSequence |
getStartCodonSequence()
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StopCodonSequence |
getStopCodonSequence()
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Strand |
getStrand()
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CDSSequence |
removeCDS(String accession)
Remove a CDS or coding sequence from the transcript sequence |
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 TranscriptSequence(GeneSequence parentDNASequence, int begin, int end)
parentDNASequence
- begin
- end
- inclusive of endMethod Detail |
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public int getLength()
Sequence
getLength
in interface Sequence<NucleotideCompound>
getLength
in class AbstractSequence<NucleotideCompound>
public Strand getStrand()
public CDSSequence removeCDS(String accession)
accession
-
public LinkedHashMap<String,CDSSequence> getCDSSequences()
public CDSSequence addCDS(AccessionID accession, int begin, int end, int phase) throws Exception
accession
- begin
- end
- phase
- 0,1,2
Exception
public ArrayList<ProteinSequence> getProteinCDSSequences()
public DNASequence getDNACodingSequence()
public ProteinSequence getProteinSequence()
public ProteinSequence getProteinSequence(TranscriptionEngine engine)
engine
-
public StartCodonSequence getStartCodonSequence()
public void addStartCodonSequence(AccessionID accession, int begin, int end)
startCodonSequence
- the startCodonSequence to setpublic StopCodonSequence getStopCodonSequence()
public void addStopCodonSequence(AccessionID accession, int begin, int end)
stopCodonSequence
- the stopCodonSequence to set
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