org.biojava3.core.sequence
Class TranscriptSequence

java.lang.Object
  extended by org.biojava3.core.sequence.template.AbstractSequence<NucleotideCompound>
      extended by org.biojava3.core.sequence.DNASequence
          extended by org.biojava3.core.sequence.TranscriptSequence
All Implemented Interfaces:
Iterable<NucleotideCompound>, Accessioned, Sequence<NucleotideCompound>

public class TranscriptSequence
extends DNASequence

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

Author:
Scooter Willis

Nested Class Summary
 
Nested classes/interfaces inherited from class org.biojava3.core.sequence.DNASequence
DNASequence.DNAType
 
Nested classes/interfaces inherited from class org.biojava3.core.sequence.template.AbstractSequence
AbstractSequence.AnnotationType
 
Constructor Summary
TranscriptSequence(GeneSequence parentDNASequence, int begin, int end)
           
 
Method Summary
 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)
           
 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()
           
 StopCodonSequence getStopCodonSequence()
           
 Strand getStrand()
           
 CDSSequence removeCDS(String accession)
          Remove a CDS or coding sequence from the transcript sequence
 
Methods inherited from class org.biojava3.core.sequence.DNASequence
getComplement, getDNAType, getGCCount, getReverse, getReverseComplement, getRNASequence, getRNASequence, getRNASequence, getRNASequence, main, setDNAType
 
Methods inherited from class org.biojava3.core.sequence.template.AbstractSequence
addFeature, addFeature, addNote, countCompounds, getAccession, getAnnotationType, getAsList, getBioBegin, getBioEnd, getCompoundAt, getCompoundSet, getDatabaseReferences, getDescription, getFeatures, getFeatures, getFeatures, getFeaturesByType, getFeaturesKeyWord, getIndexOf, getInverse, getLastIndexOf, getNotesList, getOriginalHeader, getParentSequence, getProxySequenceReader, getSequenceAsString, getSequenceAsString, getSequenceScore, getSource, getSubSequence, getTaxonomy, getUserCollection, iterator, removeFeature, removeNote, setAccession, setAnnotationType, setBioBegin, setBioEnd, setCompoundSet, setDatabaseReferences, setDescription, 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
 

Constructor Detail

TranscriptSequence

public TranscriptSequence(GeneSequence parentDNASequence,
                          int begin,
                          int end)
Parameters:
parentDNASequence -
begin -
end - inclusive of end
Method Detail

getLength

public int getLength()
Description copied from interface: Sequence
Returns the length of the Sequence

Specified by:
getLength in interface Sequence<NucleotideCompound>
Overrides:
getLength in class AbstractSequence<NucleotideCompound>

getStrand

public Strand getStrand()
Returns:
the strand

removeCDS

public CDSSequence removeCDS(String accession)
Remove a CDS or coding sequence from the transcript sequence

Parameters:
accession -
Returns:

getCDSSequences

public LinkedHashMap<String,CDSSequence> getCDSSequences()
Get the CDS sequences that have been added to the TranscriptSequences

Returns:

addCDS

public CDSSequence addCDS(AccessionID accession,
                          int begin,
                          int end,
                          int phase)
                   throws Exception
Add a Coding Sequence region with phase to the transcript sequence

Parameters:
accession -
begin -
end -
phase - 0,1,2
Returns:
Throws:
Exception

getProteinCDSSequences

public 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. This can be used to map a CDS/exon region of a protein sequence back to the DNA sequence If you have a protein sequence and a predicted gene you can take the predict CDS protein sequences and align back to the protein sequence. If you have errors in mapping the predicted protein CDS regions to an the known protein sequence then you can identify possible errors in the prediction

Returns:

getDNACodingSequence

public DNASequence getDNACodingSequence()
Get the stitched together CDS sequences then maps to the cDNA

Returns:

getProteinSequence

public ProteinSequence getProteinSequence()
Get the protein sequence

Returns:

getProteinSequence

public ProteinSequence getProteinSequence(TranscriptionEngine engine)
Get the protein sequence with user defined TranscriptEngine

Parameters:
engine -
Returns:

getStartCodonSequence

public StartCodonSequence getStartCodonSequence()
Returns:
the startCodonSequence

addStartCodonSequence

public void addStartCodonSequence(AccessionID accession,
                                  int begin,
                                  int end)
Parameters:
startCodonSequence - the startCodonSequence to set

getStopCodonSequence

public StopCodonSequence getStopCodonSequence()
Returns:
the stopCodonSequence

addStopCodonSequence

public void addStopCodonSequence(AccessionID accession,
                                 int begin,
                                 int end)
Parameters:
stopCodonSequence - the stopCodonSequence to set