Index (biojava-aa-prop 4.2.2 API)

A B C D E F G H I K L M N O P Q R S T U V W Y

A

A - Static variable in class org.biojava.nbio.aaproperties.Constraints
aa2CTerminalPka - Static variable in class org.biojava.nbio.aaproperties.Constraints
aa2ExtinctionCoefficient - Static variable in class org.biojava.nbio.aaproperties.Constraints
aa2Hydrophathicity - Static variable in class org.biojava.nbio.aaproperties.Constraints
aa2MolecularWeight - Static variable in class org.biojava.nbio.aaproperties.Constraints
aa2NTerminalPka - Static variable in class org.biojava.nbio.aaproperties.Constraints
aa2PKa - Static variable in class org.biojava.nbio.aaproperties.Constraints
AminoAcidComposition - Class in org.biojava.nbio.aaproperties.xml
AminoAcidComposition() - Constructor for class org.biojava.nbio.aaproperties.xml.AminoAcidComposition
AminoAcidComposition(String, String, String, List<Name2Count>, List<Name2Count>) - Constructor for class org.biojava.nbio.aaproperties.xml.AminoAcidComposition
AminoAcidCompositionTable - Class in org.biojava.nbio.aaproperties.xml
AminoAcidCompositionTable() - Constructor for class org.biojava.nbio.aaproperties.xml.AminoAcidCompositionTable
AminoAcidCompositionTable(List<AminoAcidComposition>) - Constructor for class org.biojava.nbio.aaproperties.xml.AminoAcidCompositionTable

B

BioJavaAADemo - Class in demo: Created by andreas on 8/9/14.
BioJavaAADemo() - Constructor for class demo.BioJavaAADemo

C

C - Static variable in class org.biojava.nbio.aaproperties.Constraints
CaseFreeAminoAcidCompoundSet - Class in org.biojava.nbio.aaproperties.xml: Set of proteinogenic amino acids.
CaseFreeAminoAcidCompoundSet() - Constructor for class org.biojava.nbio.aaproperties.xml.CaseFreeAminoAcidCompoundSet
checkSequence(String) - Static method in class org.biojava.nbio.aaproperties.Utils: Checks if the sequence contains invalid characters.
checkSequence(String, Set<Character>) - Static method in class org.biojava.nbio.aaproperties.Utils: Checks if the sequence contains invalid characters.
cleanSequence(String, Set<Character>) - Static method in class org.biojava.nbio.aaproperties.Utils: Returns a new sequence with all invalid characters being replaced by '-'.
CommandPrompt - Class in org.biojava.nbio.aaproperties
CommandPrompt() - Constructor for class org.biojava.nbio.aaproperties.CommandPrompt
CommandPrompt.PropertyName - Enum in org.biojava.nbio.aaproperties
compoundsEquivalent(AminoAcidCompound, AminoAcidCompound) - Method in class org.biojava.nbio.aaproperties.xml.CaseFreeAminoAcidCompoundSet
compoundsEquivalent(AminoAcidCompound, AminoAcidCompound) - Method in class org.biojava.nbio.aaproperties.xml.ModifiedAminoAcidCompoundSet
computeMolecularWeight(ElementTable) - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidCompositionTable: Computes and store the molecular weight of each amino acid by its symbol in aaSymbol2MolecularWeight.
Constraints - Class in org.biojava.nbio.aaproperties: This class is used to support the implementation of properties stated in IPeptideProperties.
Constraints() - Constructor for class org.biojava.nbio.aaproperties.Constraints
convert(char) - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Charge: Class for the conversion of protein sequence into charge
convert(char) - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Hydrophobicity: Class for the conversion of protein sequence into hydrophobicity
convert(char) - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2NormalizedVanDerWaalsVolume: Class for the conversion of protein sequence into normalized van der waals volume
convert(char) - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Polarity: Class for the conversion of protein sequence into polarity
convert(char) - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Polarizability: Class for the conversion of protein sequence into polarizability
convert(char) - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2SecondaryStructure: Class for the conversion of protein sequence into secondary structure
convert(char) - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2SolventAccessibility: Class for the conversion of protein sequence into solvent accessibility
convert(char) - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convertor: Returns the grouping of the amino acid character.
convert(ProteinSequence) - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convertor: Returns the converted sequence.
Convert2Charge - Class in org.biojava.nbio.aaproperties.profeat.convertor
Convert2Charge() - Constructor for class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Charge
Convert2Hydrophobicity - Class in org.biojava.nbio.aaproperties.profeat.convertor
Convert2Hydrophobicity() - Constructor for class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Hydrophobicity
Convert2NormalizedVanDerWaalsVolume - Class in org.biojava.nbio.aaproperties.profeat.convertor
Convert2NormalizedVanDerWaalsVolume() - Constructor for class org.biojava.nbio.aaproperties.profeat.convertor.Convert2NormalizedVanDerWaalsVolume
Convert2Polarity - Class in org.biojava.nbio.aaproperties.profeat.convertor
Convert2Polarity() - Constructor for class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Polarity
Convert2Polarizability - Class in org.biojava.nbio.aaproperties.profeat.convertor
Convert2Polarizability() - Constructor for class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Polarizability
Convert2SecondaryStructure - Class in org.biojava.nbio.aaproperties.profeat.convertor
Convert2SecondaryStructure() - Constructor for class org.biojava.nbio.aaproperties.profeat.convertor.Convert2SecondaryStructure
Convert2SolventAccessibility - Class in org.biojava.nbio.aaproperties.profeat.convertor
Convert2SolventAccessibility() - Constructor for class org.biojava.nbio.aaproperties.profeat.convertor.Convert2SolventAccessibility
Convertor - Class in org.biojava.nbio.aaproperties.profeat.convertor
Convertor() - Constructor for class org.biojava.nbio.aaproperties.profeat.convertor.Convertor
createOutput(String, String) - Method in class org.biojava.nbio.aaproperties.xml.SchemaGenerator

D

D - Static variable in class org.biojava.nbio.aaproperties.Constraints
demo - package demo
diAA2Instability - Static variable in class org.biojava.nbio.aaproperties.Constraints
doesSequenceContainInvalidChar(String, Set<Character>) - Static method in class org.biojava.nbio.aaproperties.Utils: Checks if given sequence contains invalid characters.

E

E - Static variable in class org.biojava.nbio.aaproperties.Constraints
Element - Class in org.biojava.nbio.aaproperties.xml: One way to model the elements
Element() - Constructor for class org.biojava.nbio.aaproperties.xml.Element
Element(String, String, int, List<Isotope>, double) - Constructor for class org.biojava.nbio.aaproperties.xml.Element
ElementTable - Class in org.biojava.nbio.aaproperties.xml
ElementTable() - Constructor for class org.biojava.nbio.aaproperties.xml.ElementTable
ElementTable(List<Element>) - Constructor for class org.biojava.nbio.aaproperties.xml.ElementTable

F

F - Static variable in class org.biojava.nbio.aaproperties.Constraints

G

G - Static variable in class org.biojava.nbio.aaproperties.Constraints
getAAComposition(ProteinSequence) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties: Returns the composition of the 20 standard amino acid in the sequence.
getAAComposition(String) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties: An adaptor method to return the composition of the 20 standard amino acid in the sequence.
getAAComposition(ProteinSequence) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
getAACompositionChar(String) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties: An adaptor method to return the composition of the 20 standard amino acid in the sequence.
getAACompositionString(String) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties: An adaptor method to return the composition of the 20 standard amino acid in the sequence.
getAbsorbance(ProteinSequence, boolean) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties: Returns the absorbance (optical density) of sequence.
getAbsorbance(String, boolean) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties: An adaptor method to returns the absorbance (optical density) of sequence.
getAbsorbance(ProteinSequence, boolean) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
getAllCompounds() - Method in class org.biojava.nbio.aaproperties.xml.CaseFreeAminoAcidCompoundSet
getAllCompounds() - Method in class org.biojava.nbio.aaproperties.xml.ModifiedAminoAcidCompoundSet
getAminoacid() - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidCompositionTable
getAminoAcidCompoundSet() - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidCompositionTable
getAminoAcidCompoundSet() - Static method in class org.biojava.nbio.aaproperties.xml.CaseFreeAminoAcidCompoundSet
getApliphaticIndex(ProteinSequence) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties: Returns the apliphatic index of sequence.
getApliphaticIndex(String) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties: An adaptor method to return the apliphatic index of sequence.
getApliphaticIndex(ProteinSequence) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
getAttribute() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Charge
getAttribute() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Hydrophobicity
getAttribute() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2NormalizedVanDerWaalsVolume
getAttribute() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Polarity
getAttribute() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Polarizability
getAttribute() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2SecondaryStructure
getAttribute() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2SolventAccessibility
getAttribute() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convertor: Return the attribute of the grouping
getAvgHydropathy(ProteinSequence) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties: Returns the average hydropathy value of sequence.
getAvgHydropathy(String) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties: An adaptor method to return the average hydropathy value of sequence.
getAvgHydropathy(ProteinSequence) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
getComposition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING) - Method in interface org.biojava.nbio.aaproperties.profeat.IProfeatProperties: Returns the composition of the specific grouping for the given attribute.
getComposition(ProteinSequence, IProfeatProperties.ATTRIBUTE) - Method in interface org.biojava.nbio.aaproperties.profeat.IProfeatProperties
getComposition(ProteinSequence) - Method in interface org.biojava.nbio.aaproperties.profeat.IProfeatProperties
getComposition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties: An adaptor method which returns the composition of the specific grouping for the given attribute.
getComposition(ProteinSequence, IProfeatProperties.ATTRIBUTE) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
getComposition(ProteinSequence) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
getComposition(String, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
getComposition(String, IProfeatProperties.ATTRIBUTE) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
getComposition(String) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
getComposition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING) - Method in class org.biojava.nbio.aaproperties.profeat.ProfeatPropertiesImpl
getComposition(ProteinSequence, IProfeatProperties.ATTRIBUTE) - Method in class org.biojava.nbio.aaproperties.profeat.ProfeatPropertiesImpl
getComposition(ProteinSequence) - Method in class org.biojava.nbio.aaproperties.profeat.ProfeatPropertiesImpl
getCompoundForString(String) - Method in class org.biojava.nbio.aaproperties.xml.CaseFreeAminoAcidCompoundSet
getCompoundForString(String) - Method in class org.biojava.nbio.aaproperties.xml.ModifiedAminoAcidCompoundSet
getCount() - Method in class org.biojava.nbio.aaproperties.xml.Name2Count
getDistributionPosition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING, IProfeatProperties.DISTRIBUTION) - Method in interface org.biojava.nbio.aaproperties.profeat.IProfeatProperties: Computes and return the position with respect to the sequence where the given distribution of the grouping can be found.
Example: "1111122222"
For the above example,
position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
getDistributionPosition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING) - Method in interface org.biojava.nbio.aaproperties.profeat.IProfeatProperties
getDistributionPosition(ProteinSequence, IProfeatProperties.ATTRIBUTE) - Method in interface org.biojava.nbio.aaproperties.profeat.IProfeatProperties
getDistributionPosition(ProteinSequence) - Method in interface org.biojava.nbio.aaproperties.profeat.IProfeatProperties
getDistributionPosition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING, IProfeatProperties.DISTRIBUTION) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties: An adaptor method which computes and return the position with respect to the sequence where the given distribution of the grouping can be found.
Example: "1111122222"
For the above example,
position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
getDistributionPosition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
getDistributionPosition(ProteinSequence, IProfeatProperties.ATTRIBUTE) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
getDistributionPosition(ProteinSequence) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
getDistributionPosition(String, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING, IProfeatProperties.DISTRIBUTION) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
getDistributionPosition(String, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
getDistributionPosition(String, IProfeatProperties.ATTRIBUTE) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
getDistributionPosition(String) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
getDistributionPosition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING, IProfeatProperties.DISTRIBUTION) - Method in class org.biojava.nbio.aaproperties.profeat.ProfeatPropertiesImpl
getDistributionPosition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING) - Method in class org.biojava.nbio.aaproperties.profeat.ProfeatPropertiesImpl
getDistributionPosition(ProteinSequence, IProfeatProperties.ATTRIBUTE) - Method in class org.biojava.nbio.aaproperties.profeat.ProfeatPropertiesImpl
getDistributionPosition(ProteinSequence) - Method in class org.biojava.nbio.aaproperties.profeat.ProfeatPropertiesImpl
getElement() - Method in class org.biojava.nbio.aaproperties.xml.ElementTable
getElement(String) - Method in class org.biojava.nbio.aaproperties.xml.ElementTable
getElementList() - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidComposition
getEnrichment(ProteinSequence, AminoAcidCompound) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties: Returns the composition of specified amino acid in the sequence.
getEnrichment(String, PeptideProperties.SingleLetterAACode) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties: An adaptor method to return the composition of specified amino acid in the sequence.
getEnrichment(String, char) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties: An adaptor method to return the composition of specified amino acid in the sequence.
getEnrichment(String, String) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties: An adaptor method to return the composition of specified amino acid in the sequence.
getEnrichment(ProteinSequence, AminoAcidCompound) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
getEquivalentCompounds(AminoAcidCompound) - Method in class org.biojava.nbio.aaproperties.xml.CaseFreeAminoAcidCompoundSet
getEquivalentCompounds(AminoAcidCompound) - Method in class org.biojava.nbio.aaproperties.xml.ModifiedAminoAcidCompoundSet
getExtinctionCoefficient(ProteinSequence, boolean) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties: Returns the extinction coefficient of sequence.
getExtinctionCoefficient(String, boolean) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties: An adaptor method to return the extinction coefficient of sequence.
getExtinctionCoefficient(ProteinSequence, boolean) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
getGrouping() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Charge
getGrouping() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Hydrophobicity
getGrouping() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2NormalizedVanDerWaalsVolume
getGrouping() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Polarity
getGrouping() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Polarizability
getGrouping() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2SecondaryStructure
getGrouping() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2SolventAccessibility
getGrouping() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convertor: Returns the groupings of the attribute
getInstabilityIndex(ProteinSequence) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties: Returns the instability index of sequence.
getInstabilityIndex(String) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties: An adaptor method to return the instability index of sequence.
getInstabilityIndex(ProteinSequence) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
getIsoelectricPoint(ProteinSequence, boolean) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties: Returns the isoelectric point of sequence.
getIsoelectricPoint(ProteinSequence) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties
getIsoelectricPoint(String, boolean) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties: An adaptor method to return the isoelectric point of sequence.
getIsoelectricPoint(String) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
getIsoelectricPoint(ProteinSequence, boolean) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
getIsoelectricPoint(ProteinSequence) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
getIsotope(String) - Method in class org.biojava.nbio.aaproperties.xml.ElementTable
getIsotopeList() - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidComposition
getIsotopes() - Method in class org.biojava.nbio.aaproperties.xml.Element
getMass() - Method in class org.biojava.nbio.aaproperties.xml.Element
getMass() - Method in class org.biojava.nbio.aaproperties.xml.Isotope
getMaxSingleCompoundStringLength() - Method in class org.biojava.nbio.aaproperties.xml.CaseFreeAminoAcidCompoundSet
getMaxSingleCompoundStringLength() - Method in class org.biojava.nbio.aaproperties.xml.ModifiedAminoAcidCompoundSet
getMolecularWeight(ProteinSequence) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties: Returns the molecular weight of sequence.
getMolecularWeight(ProteinSequence, File) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties: Returns the molecular weight of sequence.
getMolecularWeight(ProteinSequence, File, File) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties: Returns the molecular weight of sequence.
getMolecularWeight(String) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties: An adaptor method to return the molecular weight of sequence.
getMolecularWeight(String, File, File) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties: An adaptor method to return the molecular weight of sequence.
getMolecularWeight(String, File) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties: An adaptor method to return the molecular weight of sequence.
getMolecularWeight(ProteinSequence) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
getMolecularWeight(ProteinSequence, File) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
getMolecularWeight(ProteinSequence, File, File) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
getMolecularWeight(Character) - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidCompositionTable
getMolecularWeightBasedOnXML(ProteinSequence, AminoAcidCompositionTable) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties: Returns the molecular weight of sequence.
getMolecularWeightBasedOnXML(String, AminoAcidCompositionTable) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties: An adaptor method that returns the molecular weight of sequence.
getMolecularWeightBasedOnXML(ProteinSequence, AminoAcidCompositionTable) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
getName() - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidComposition
getName() - Method in class org.biojava.nbio.aaproperties.xml.Element
getName() - Method in class org.biojava.nbio.aaproperties.xml.Isotope
getName() - Method in class org.biojava.nbio.aaproperties.xml.Name2Count
getNetCharge(ProteinSequence, boolean, double) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties: Returns the net charge of sequence at pH 7.
getNetCharge(ProteinSequence, boolean) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties
getNetCharge(ProteinSequence) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties
getNetCharge(String, boolean, double) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties: An adaptor method to return the net charge of sequence at pH 7.
getNetCharge(String, boolean) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
getNetCharge(String) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
getNetCharge(ProteinSequence) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
getNetCharge(ProteinSequence, boolean) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
getNetCharge(ProteinSequence, boolean, double) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
getNeutronsNum() - Method in class org.biojava.nbio.aaproperties.xml.Isotope
getNumberOfInvalidChar(String, Set<Character>, boolean) - Static method in class org.biojava.nbio.aaproperties.Utils: Return the number of invalid characters in sequence.
getShorName() - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidComposition
getStringForCompound(AminoAcidCompound) - Method in class org.biojava.nbio.aaproperties.xml.CaseFreeAminoAcidCompoundSet
getStringForCompound(AminoAcidCompound) - Method in class org.biojava.nbio.aaproperties.xml.ModifiedAminoAcidCompoundSet
getSymbol() - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidComposition
getSymbolSet() - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidCompositionTable
getTransition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.TRANSITION) - Method in interface org.biojava.nbio.aaproperties.profeat.IProfeatProperties: Returns the number of transition between the specified groups for the given attribute with respect to the length of sequence.
getTransition(ProteinSequence, IProfeatProperties.ATTRIBUTE) - Method in interface org.biojava.nbio.aaproperties.profeat.IProfeatProperties
getTransition(ProteinSequence) - Method in interface org.biojava.nbio.aaproperties.profeat.IProfeatProperties
getTransition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.TRANSITION) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties: An adaptor method which returns the number of transition between the specified groups for the given attribute with respect to the length of sequence.
getTransition(ProteinSequence, IProfeatProperties.ATTRIBUTE) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
getTransition(ProteinSequence) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
getTransition(String, IProfeatProperties.ATTRIBUTE, IProfeatProperties.TRANSITION) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
getTransition(String, IProfeatProperties.ATTRIBUTE) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
getTransition(String) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
getTransition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.TRANSITION) - Method in class org.biojava.nbio.aaproperties.profeat.ProfeatPropertiesImpl
getTransition(ProteinSequence, IProfeatProperties.ATTRIBUTE) - Method in class org.biojava.nbio.aaproperties.profeat.ProfeatPropertiesImpl
getTransition(ProteinSequence) - Method in class org.biojava.nbio.aaproperties.profeat.ProfeatPropertiesImpl
group1 - Static variable in class org.biojava.nbio.aaproperties.profeat.convertor.Convertor: Based on Table 2 of http://nar.oxfordjournals.org/content/34/suppl_2/W32.full.pdf
An abstract class to convert a protein sequence into representation of different attribute with each attribute having 3 groups.
The seven different attributes are
Hydrophobicity (Polar, Neutral, Hydrophobicity)
Normalized van der Waals volume (Range 0 - 2.78, 2.95 - 4.0, 4.03 - 8.08)
Polarity (Value 4.9 - 6.2, 8.0 - 9.2, 10.4 - 13.0)
Polarizability (Value 0 - 1.08, 0.128 - 0.186, 0.219 - 0.409)
Charge (Positive, Neutral, Negative)
Secondary structure (Helix, Strand, Coil)
Solvent accessibility (Buried, Exposed, Intermediate)
group2 - Static variable in class org.biojava.nbio.aaproperties.profeat.convertor.Convertor
group3 - Static variable in class org.biojava.nbio.aaproperties.profeat.convertor.Convertor

H

H - Static variable in class org.biojava.nbio.aaproperties.Constraints
handleEvent(ValidationEvent) - Method in class org.biojava.nbio.aaproperties.xml.MyValidationEventHandler
hasCompound(AminoAcidCompound) - Method in class org.biojava.nbio.aaproperties.xml.CaseFreeAminoAcidCompoundSet
hasCompound(AminoAcidCompound) - Method in class org.biojava.nbio.aaproperties.xml.ModifiedAminoAcidCompoundSet

I

I - Static variable in class org.biojava.nbio.aaproperties.Constraints
initExtinctionCoefficient() - Static method in class org.biojava.nbio.aaproperties.Constraints: Does the initialization of extinction coefficient based on http://au.expasy.org/tools/protparam-doc.html
initMolecularWeight() - Static method in class org.biojava.nbio.aaproperties.Constraints: Does the initialization of molecular weights based on http://au.expasy.org/tools/findmod/findmod_masses.html#AA
IPeptideProperties - Interface in org.biojava.nbio.aaproperties: An interface to generate some basic physico-chemical properties of protein sequences.
The following properties could be generated:
Molecular weight
Absorbance
Extinction coefficient
Instability index
Apliphatic index
Average hydropathy value
Isoelectric point
Net charge at pH 7
Composition of specified amino acid
Composition of the 20 standard amino acid
IProfeatProperties - Interface in org.biojava.nbio.aaproperties.profeat
IProfeatProperties.ATTRIBUTE - Enum in org.biojava.nbio.aaproperties.profeat: Enumeration of the seven different attributes
IProfeatProperties.DISTRIBUTION - Enum in org.biojava.nbio.aaproperties.profeat: Enumeration of the distribution for the first, first 25%, first 50%, first 75% and 100% of the grouping
IProfeatProperties.GROUPING - Enum in org.biojava.nbio.aaproperties.profeat: Enumeration of the three different groupings for each attributes
IProfeatProperties.TRANSITION - Enum in org.biojava.nbio.aaproperties.profeat: Enumeration of the transition between groupA and groupB
isComplementable() - Method in class org.biojava.nbio.aaproperties.xml.CaseFreeAminoAcidCompoundSet
isComplementable() - Method in class org.biojava.nbio.aaproperties.xml.ModifiedAminoAcidCompoundSet
isCompoundStringLengthEqual() - Method in class org.biojava.nbio.aaproperties.xml.CaseFreeAminoAcidCompoundSet
isCompoundStringLengthEqual() - Method in class org.biojava.nbio.aaproperties.xml.ModifiedAminoAcidCompoundSet
Isotope - Class in org.biojava.nbio.aaproperties.xml
Isotope() - Constructor for class org.biojava.nbio.aaproperties.xml.Isotope
Isotope(String, int, double) - Constructor for class org.biojava.nbio.aaproperties.xml.Isotope
isValidSequence(Sequence<AminoAcidCompound>) - Method in class org.biojava.nbio.aaproperties.xml.CaseFreeAminoAcidCompoundSet
isValidSequence(Sequence<AminoAcidCompound>) - Method in class org.biojava.nbio.aaproperties.xml.ModifiedAminoAcidCompoundSet

K

K - Static variable in class org.biojava.nbio.aaproperties.Constraints

L

L - Static variable in class org.biojava.nbio.aaproperties.Constraints

M

M - Static variable in class org.biojava.nbio.aaproperties.Constraints
main(String[]) - Static method in class demo.BioJavaAADemo
main(String[]) - Static method in class org.biojava.nbio.aaproperties.CommandPrompt: The main method
ModifiedAminoAcidCompoundSet - Class in org.biojava.nbio.aaproperties.xml
ModifiedAminoAcidCompoundSet(List<AminoAcidComposition>, Map<Character, Double>) - Constructor for class org.biojava.nbio.aaproperties.xml.ModifiedAminoAcidCompoundSet
MyValidationEventHandler - Class in org.biojava.nbio.aaproperties.xml
MyValidationEventHandler() - Constructor for class org.biojava.nbio.aaproperties.xml.MyValidationEventHandler

N

N - Static variable in class org.biojava.nbio.aaproperties.Constraints
Name2Count - Class in org.biojava.nbio.aaproperties.xml
Name2Count() - Constructor for class org.biojava.nbio.aaproperties.xml.Name2Count
Name2Count(String, int) - Constructor for class org.biojava.nbio.aaproperties.xml.Name2Count

O

obtainAminoAcidCompositionTable(File) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties: This method would initialize amino acid composition table based on the input xml files and stores the table for usage in future calls to IPeptideProperties.getMolecularWeightBasedOnXML(ProteinSequence, AminoAcidCompositionTable).
obtainAminoAcidCompositionTable(File, File) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties: This method would initialize amino acid composition table based on the input xml files and stores the table for usage in future calls to IPeptideProperties.getMolecularWeightBasedOnXML(ProteinSequence, AminoAcidCompositionTable).
obtainAminoAcidCompositionTable(File) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties: An adaptor method would initialize amino acid composition table based on the input xml files and stores the table for usage in future calls to IPeptideProperties.getMolecularWeightBasedOnXML(ProteinSequence, AminoAcidCompositionTable).
obtainAminoAcidCompositionTable(File, File) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties: An adaptor method would initialize amino acid composition table based on the input xml files and stores the table for usage in future calls to IPeptideProperties.getMolecularWeightBasedOnXML(ProteinSequence, AminoAcidCompositionTable).
obtainAminoAcidCompositionTable(File) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
obtainAminoAcidCompositionTable(File, File) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
org.biojava.nbio.aaproperties - package org.biojava.nbio.aaproperties: Set of classes that responsible for providing APIs and Command Prompt access to generate some basic physico-chemical properties of protein sequences.
org.biojava.nbio.aaproperties.profeat - package org.biojava.nbio.aaproperties.profeat: Set of classes that responsible for providing APIs access to generate some PROFEAT properties of protein sequences.
org.biojava.nbio.aaproperties.profeat.convertor - package org.biojava.nbio.aaproperties.profeat.convertor: Set of classes that enable the conversion protein sequences into various attributes.
org.biojava.nbio.aaproperties.xml - package org.biojava.nbio.aaproperties.xml: Set of classes that handles the reading and writing of xml files.

P

P - Static variable in class org.biojava.nbio.aaproperties.Constraints
PeptideProperties - Class in org.biojava.nbio.aaproperties: This is an adaptor class which enable the ease of generating protein properties.
PeptideProperties() - Constructor for class org.biojava.nbio.aaproperties.PeptideProperties
PeptideProperties.SingleLetterAACode - Enum in org.biojava.nbio.aaproperties: Enumeration of 20 standard amino acid code
PeptidePropertiesImpl - Class in org.biojava.nbio.aaproperties: This class contains the actual implementation of IPeptideProperties and is wrapped around by PeptideProperties for ease of use.
PeptidePropertiesImpl() - Constructor for class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
populateMaps() - Method in class org.biojava.nbio.aaproperties.xml.ElementTable: Populate the Maps for quick retrieval
ProfeatProperties - Class in org.biojava.nbio.aaproperties.profeat: This is an adaptor class which enable the ease of generating profeat properties.
ProfeatProperties() - Constructor for class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
ProfeatPropertiesImpl - Class in org.biojava.nbio.aaproperties.profeat
ProfeatPropertiesImpl() - Constructor for class org.biojava.nbio.aaproperties.profeat.ProfeatPropertiesImpl

Q

Q - Static variable in class org.biojava.nbio.aaproperties.Constraints

R

R - Static variable in class org.biojava.nbio.aaproperties.Constraints
roundToDecimals(double, int) - Static method in class org.biojava.nbio.aaproperties.Utils: Returns a value with the desired number of decimal places.
run(String[]) - Static method in class org.biojava.nbio.aaproperties.CommandPrompt

S

S - Static variable in class org.biojava.nbio.aaproperties.Constraints
SchemaGenerator - Class in org.biojava.nbio.aaproperties.xml
SchemaGenerator(String) - Constructor for class org.biojava.nbio.aaproperties.xml.SchemaGenerator
setAminoacid(List<AminoAcidComposition>) - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidCompositionTable
setAtomicNumber(int) - Method in class org.biojava.nbio.aaproperties.xml.Element
setElement(List<Element>) - Method in class org.biojava.nbio.aaproperties.xml.ElementTable
setIsotopes(List<Isotope>) - Method in class org.biojava.nbio.aaproperties.xml.Element
setMass(double) - Method in class org.biojava.nbio.aaproperties.xml.Element
setMass(double) - Method in class org.biojava.nbio.aaproperties.xml.Isotope
setName(String) - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidComposition
setName(String) - Method in class org.biojava.nbio.aaproperties.xml.Element
setName(String) - Method in class org.biojava.nbio.aaproperties.xml.Isotope
setNeutronsNum(int) - Method in class org.biojava.nbio.aaproperties.xml.Isotope
setShortName(String) - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidComposition
setSymbol(String) - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidComposition
setSymbol(String) - Method in class org.biojava.nbio.aaproperties.xml.Element
standardAASet - Static variable in class org.biojava.nbio.aaproperties.PeptideProperties: Contains the 20 standard AA code in a set

T

T - Static variable in class org.biojava.nbio.aaproperties.Constraints
toString() - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidComposition
toString() - Method in class org.biojava.nbio.aaproperties.xml.Element

U

unknownGroup - Static variable in class org.biojava.nbio.aaproperties.profeat.convertor.Convertor
Utils - Class in org.biojava.nbio.aaproperties: This is a utility class that contains utility methods which will facilitates the coding of other methods
Utils() - Constructor for class org.biojava.nbio.aaproperties.Utils

V

V - Static variable in class org.biojava.nbio.aaproperties.Constraints
valueOf(String) - Static method in enum org.biojava.nbio.aaproperties.CommandPrompt.PropertyName: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.aaproperties.profeat.IProfeatProperties.ATTRIBUTE: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.aaproperties.profeat.IProfeatProperties.DISTRIBUTION: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.aaproperties.profeat.IProfeatProperties.GROUPING: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.aaproperties.profeat.IProfeatProperties.TRANSITION: Returns the enum constant of this type with the specified name.
values() - Static method in enum org.biojava.nbio.aaproperties.CommandPrompt.PropertyName: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.aaproperties.profeat.IProfeatProperties.ATTRIBUTE: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.aaproperties.profeat.IProfeatProperties.DISTRIBUTION: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.aaproperties.profeat.IProfeatProperties.GROUPING: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.aaproperties.profeat.IProfeatProperties.TRANSITION: Returns an array containing the constants of this enum type, in the order they are declared.

W

W - Static variable in class org.biojava.nbio.aaproperties.Constraints

Y

Y - Static variable in class org.biojava.nbio.aaproperties.Constraints

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