Uses of Class
org.biojava.nbio.core.exceptions.CompoundNotFoundException

Packages that use CompoundNotFoundException

Package	Description
demo
org.biojava.nbio.core.sequence
org.biojava.nbio.core.sequence.io
org.biojava.nbio.core.sequence.io.template
org.biojava.nbio.core.sequence.loader
org.biojava.nbio.core.sequence.storage
org.biojava.nbio.core.sequence.template
org.biojava.nbio.core.sequence.views
org.biojava.nbio.core.util
org.biojava.nbio.genome.io.fastq	FASTQ and variants sequence format I/O.
org.biojava.nbio.genome.util
org.biojava.nbio.structure.align.multiple.util
org.biojava.nbio.structure.cluster
org.biojava.nbio.structure.io	Input and Output of Structures

Uses of CompoundNotFoundException in demo

Methods in demo that throw CompoundNotFoundException

Modifier and Type	Method	Description
static void	BioJavaAADemo.main(String[] args)

Uses of CompoundNotFoundException in org.biojava.nbio.core.sequence

Constructors in org.biojava.nbio.core.sequence that throw CompoundNotFoundException

Modifier	Constructor	Description
	BasicSequence(String sequence, CompoundSet<C> compoundSet)
	ChromosomeSequence(String seqString)	String is king and assume DNA
	ChromosomeSequence(String seqString, CompoundSet<NucleotideCompound> compoundSet)	Allows the creation of a ChromosomeSequence using String for the sequence with a custom CompoundSet
	DNASequence(String seqString)	String is king and create a sequence from DNA with default DNA compound set
	DNASequence(String seqString, CompoundSet<NucleotideCompound> compoundSet)	Create a sequence from a string with user defined compound set
	ProteinSequence(String seqString)	Create a protein from a string
	ProteinSequence(String seqString, CompoundSet<AminoAcidCompound> compoundSet)	Create a protein from a string with a user defined set of amino acids
	RNASequence(String seqString)	Create a RNA sequence from a String
	RNASequence(String seqString, CompoundSet<NucleotideCompound> compoundSet)	Create a RNA sequence from a string with a user defined RNA compound set

Uses of CompoundNotFoundException in org.biojava.nbio.core.sequence.io

Methods in org.biojava.nbio.core.sequence.io that throw CompoundNotFoundException

Modifier and Type	Method	Description
AbstractSequence<NucleotideCompound>	ABITrace.getSequence()	Returns the original programmatically determined (unedited) sequence as a AbstractSequence<NucleotideCompound>.
AbstractSequence<AminoAcidCompound>	CasePreservingProteinSequenceCreator.getSequence(String sequence, long index)
AbstractSequence<NucleotideCompound>	DNASequenceCreator.getSequence(String sequence, long index)
AbstractSequence<NucleotideCompound>	FileProxyDNASequenceCreator.getSequence(String sequence, long index)	Even though we are passing in the sequence we really only care about the length of the sequence and the offset index in the fasta file.
AbstractSequence<AminoAcidCompound>	FileProxyProteinSequenceCreator.getSequence(String sequence, long index)	Even though we are passing in the sequence we really only care about the length of the sequence and the offset index in the fasta file.
AbstractSequence<NucleotideCompound>	FileProxyRNASequenceCreator.getSequence(String sequence, long index)	Even though we are passing in the sequence we really only care about the length of the sequence and the offset index in the fasta file.
AbstractSequence<AminoAcidCompound>	ProteinSequenceCreator.getSequence(String sequence, long index)
AbstractSequence<NucleotideCompound>	RNASequenceCreator.getSequence(String sequence, long index)
int[]	ABITrace.getTrace(String base)	Returns one of the four traces - all of the y-coordinate values, each of which correspond to a single x-coordinate relative to the position in the array, so that if element 4 in the array is 972, then x is 4 and y is 972 for that point.
Map<String,S>	GenbankReader.process()	The parsing is done in this method. This method will return all the available Genbank records in the File or InputStream, closes the underlying resource, and return the results in LinkedHashMap. You don't need to call GenbankReader.close() after calling this method.
Map<String,S>	GenbankReader.process(int max)	This method tries to parse maximum max records from the open File or InputStream, and leaves the underlying resource open. Subsequent calls to the same method continue parsing the rest of the file. This is particularly useful when dealing with very big data files, (e.g.

Uses of CompoundNotFoundException in org.biojava.nbio.core.sequence.io.template

Methods in org.biojava.nbio.core.sequence.io.template that throw CompoundNotFoundException

Modifier and Type	Method	Description
AbstractSequence<C>	SequenceCreatorInterface.getSequence(String sequence, long index)

Uses of CompoundNotFoundException in org.biojava.nbio.core.sequence.loader

Methods in org.biojava.nbio.core.sequence.loader that throw CompoundNotFoundException

Modifier and Type	Method	Description
void	SequenceFileProxyLoader.setContents(String sequence)
void	StringProxySequenceReader.setContents(String sequence)
void	StringProxySequenceReader.setContents(String sequence, List features)
void	UniprotProxySequenceReader.setContents(String sequence)	Once the sequence is retrieved set the contents and make sure everything this is valid Some uniprot records contain white space in the sequence.

Constructors in org.biojava.nbio.core.sequence.loader that throw CompoundNotFoundException

Modifier	Constructor	Description
	GenbankProxySequenceReader(String genbankDirectoryCache, String accessionID, CompoundSet<C> compoundSet)
	SequenceFileProxyLoader(File file, SequenceParserInterface sequenceParser, long sequenceStartIndex, int sequenceLength, CompoundSet<C> compoundSet)
	StringProxySequenceReader(String sequence, CompoundSet<C> compoundSet)
	UniprotProxySequenceReader(String accession, CompoundSet<C> compoundSet)	The UniProt id is used to retrieve the UniProt XML which is then parsed as a DOM object so we know everything about the protein.
	UniprotProxySequenceReader(Document document, CompoundSet<C> compoundSet)	The xml is passed in as a DOM object so we know everything about the protein.

Uses of CompoundNotFoundException in org.biojava.nbio.core.sequence.storage

Methods in org.biojava.nbio.core.sequence.storage that throw CompoundNotFoundException

Modifier and Type	Method	Description
void	ArrayListSequenceReader.setContents(String sequence)
void	BitSequenceReader.setContents(String sequence)	Class is immutable, so this is unsupported
void	JoiningSequenceReader.setContents(String sequence)
void	SingleCompoundSequenceReader.setContents(String sequence)	Unsupported

Constructors in org.biojava.nbio.core.sequence.storage that throw CompoundNotFoundException

Modifier	Constructor	Description
	ArrayListSequenceReader(String sequence, CompoundSet<C> compoundSet)

Uses of CompoundNotFoundException in org.biojava.nbio.core.sequence.template

Methods in org.biojava.nbio.core.sequence.template that throw CompoundNotFoundException

Modifier and Type	Method	Description
protected void	AbstractSequence.initSequenceStorage(String seqString)
void	SequenceReader.setContents(String sequence)

Constructors in org.biojava.nbio.core.sequence.template that throw CompoundNotFoundException

Modifier	Constructor	Description
	AbstractSequence(String seqString, CompoundSet<C> compoundSet)	Create a Sequence from a simple string where the values should be found in compoundSet

Uses of CompoundNotFoundException in org.biojava.nbio.core.sequence.views

Methods in org.biojava.nbio.core.sequence.views that throw CompoundNotFoundException

Modifier and Type	Method	Description
void	RnaSequenceView.setContents(String sequence)

Uses of CompoundNotFoundException in org.biojava.nbio.core.util

Methods in org.biojava.nbio.core.util that throw CompoundNotFoundException

Modifier and Type	Method	Description
Sequence<?>	SequenceTools.getSequenceFromString(String sequence)	Attempts to parse String as a DNA sequence first. If this fails it tries to parse as a ProteinSequence.

Uses of CompoundNotFoundException in org.biojava.nbio.genome.io.fastq

Methods in org.biojava.nbio.genome.io.fastq that throw CompoundNotFoundException

Modifier and Type	Method	Description
static DNASequence	FastqTools.createDNASequence(Fastq fastq)	Create and return a new DNASequence from the specified FASTQ formatted sequence.
static DNASequence	FastqTools.createDNASequenceWithErrorProbabilities(Fastq fastq)	Create and return a new DNASequence with error probabilities from the specified FASTQ formatted sequence.
static DNASequence	FastqTools.createDNASequenceWithQualityScores(Fastq fastq)	Create and return a new DNASequence with quality scores from the specified FASTQ formatted sequence.
static DNASequence	FastqTools.createDNASequenceWithQualityScoresAndErrorProbabilities(Fastq fastq)	Create and return a new DNASequence with quality scores and error probabilities from the specified FASTQ formatted sequence.

Uses of CompoundNotFoundException in org.biojava.nbio.genome.util

Methods in org.biojava.nbio.genome.util that throw CompoundNotFoundException

Modifier and Type	Method	Description
static ProteinSequence	ProteinMappingTools.convertDNAtoProteinSequence(String dnaSequence)	Converts the DNA sequence to protein sequence.
static ProteinSequence	ProteinMappingTools.convertDNAtoProteinSequence(DNASequence dnaSequence)	Converts the DNA sequence to protein sequence.

Uses of CompoundNotFoundException in org.biojava.nbio.structure.align.multiple.util

Methods in org.biojava.nbio.structure.align.multiple.util that throw CompoundNotFoundException

Modifier and Type	Method	Description
static org.forester.phylogeny.Phylogeny	MultipleAlignmentTools.getHSDMTree(MultipleAlignment msta)	Calculate a phylogenetic tree of the MultipleAlignment using dissimilarity scores (DS), based in SDM Substitution Matrix (ideal for distantly related proteins, structure-derived) and the Neighbor Joining algorithm from forester.
static org.forester.phylogeny.Phylogeny	MultipleAlignmentTools.getKimuraTree(MultipleAlignment msta)	Calculate a phylogenetic tree of the MultipleAlignment using Kimura distances and the Neighbor Joining algorithm from forester.
static MultipleSequenceAlignment<ProteinSequence,AminoAcidCompound>	MultipleAlignmentTools.toProteinMSA(MultipleAlignment msta)	Convert a MultipleAlignment into a MultipleSequenceAlignment of AminoAcid residues.

Uses of CompoundNotFoundException in org.biojava.nbio.structure.cluster

Methods in org.biojava.nbio.structure.cluster that throw CompoundNotFoundException

Modifier and Type	Method	Description
ProteinSequence	Subunit.getProteinSequence()	Get the protein sequence of the Subunit.
boolean	SubunitCluster.mergeSequence(SubunitCluster other, SubunitClustererParameters params)	Merges the other SubunitCluster into this one if their representatives sequences are similar (according to the criteria in params).
boolean	SubunitCluster.mergeSequence(SubunitCluster other, SubunitClustererParameters params, Alignments.PairwiseSequenceAlignerType alignerType, GapPenalty gapPenalty, SubstitutionMatrix<AminoAcidCompound> subsMatrix)	Merges the other SubunitCluster into this one if their representatives sequences are similar (according to the criteria in params).

Uses of CompoundNotFoundException in org.biojava.nbio.structure.io

Methods in org.biojava.nbio.structure.io that throw CompoundNotFoundException

Modifier and Type	Method	Description
static AFPChain	FastaAFPChainConverter.cpFastaToAfpChain(String first, String second, Structure structure, int cpSite)
static AFPChain	FastaAFPChainConverter.fastaStringToAfpChain(String sequence1, String sequence2, Structure structure1, Structure structure2)	Returns an AFPChain corresponding to the alignment between structure1 and structure2, which is given by the gapped protein sequences sequence1 and sequence2.
static AFPChain	FastaAFPChainConverter.fastaToAfpChain(String sequence1, String sequence2, Structure structure1, Structure structure2)	TODO Write comment