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 and 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

Constructor and 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 and Description
AbstractSequence<NucleotideCompound>	ABITrace.getSequence() Returns the original programmatically determined (unedited) sequence as a AbstractSequence.
AbstractSequence<AminoAcidCompound>	ProteinSequenceCreator.getSequence(String sequence, long index)
AbstractSequence<AminoAcidCompound>	CasePreservingProteinSequenceCreator.getSequence(String sequence, long index)
AbstractSequence<NucleotideCompound>	DNASequenceCreator.getSequence(String sequence, long index)
AbstractSequence<NucleotideCompound>	RNASequenceCreator.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<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>	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.
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.
LinkedHashMap<String,S>	GenbankReader.process() The parsing is done in this method.
LinkedHashMap<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.

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 and 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 and Description
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.
void	StringProxySequenceReader.setContents(String sequence)
void	SequenceFileProxyLoader.setContents(String sequence)
void	StringProxySequenceReader.setContents(String sequence, ArrayList features)

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

Constructor and 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(Document document, CompoundSet<C> compoundSet) The xml is passed in as a DOM object so we know everything about the protein.
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.

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

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

Constructor and 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 and Description
void	SequenceReader.setContents(String sequence)

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

Constructor and 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 and 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 and Description
Sequence<?>	SequenceTools.getSequenceFromString(String sequence)

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