Search Java Classes and Packages
#Org.jscience.biology Classes and Interfaces - 131 results found.
| Name | Description | Type | Package | Framework |
| AbstractTaxon | An abstract implementation of Taxon. | Class | org.jscience.biology.taxonomy | JScience |
| Adenine | A class representing the Adenine Base. | Class | org.jscience.biology.bases | JScience |
| ADP | A class representing an Adenosine Di Phosphate molecule. | Class | org.jscience.biology.molecules | JScience |
| Alanine | A class representing the Alanine molecule. | Class | org.jscience.biology.aminoacids | JScience |
| AlignmentBlock | This class is used by the CrochemoreLandauZivUkelson algorithm to store the information of an alignment block. | Class | org.jscience.biology.alignment | JScience |
| Alphabet | An class used to define the process by which mRNA is transformed (:translation) into a protein according to a given code. | Class | org.jscience.biology | JScience |
| AminoAcid | A class representing an Amino-Acid. | Class | org.jscience.biology | JScience |
| AminoAcidFactory | This class provides access to amino acids. | Class | org.jscience.biology | JScience |
| AMP | A class representing an Adenosine Mono Phosphate molecule. | Class | org.jscience.biology.molecules | JScience |
| AnimationGroup | AnimationGroup is made as collection of scaling and translation transformgroups which belong together. | Class | org.jscience.biology.lsystems.growing | JScience |
| Arginine | A class representing the Arginine molecule. | Class | org.jscience.biology.aminoacids | JScience |
| Asparagine | A class representing the Asparagine molecule. | Class | org.jscience.biology.aminoacids | JScience |
| AsparticAcid | A class representing the AsparticAcid molecule. | Class | org.jscience.biology.aminoacids | JScience |
| ATP | A class representing an Adenosine Tri Phosphate molecule. | Class | org.jscience.biology.molecules | JScience |
| Base | A class representing a DNA/RNA Base. | Class | org.jscience.biology | JScience |
| BasicScoringScheme | This class implements a basic scoring scheme. | Class | org.jscience.biology.alignment | JScience |
| BiologyConstants | A class representing useful constants in biology. | Class | org.jscience.biology | JScience |
| Branch | This class represents a branch of a plant. | Class | org.jscience.biology.lsystems.growing.shape | JScience |
| CapillarityUtils | The CapillarityUtils class provides useful vascular biology relatedConstructor SummaryCapillarityUtils() | Class | org.jscience.biology | JScience |
| Cell | A class representing a cell. | Class | org.jscience.biology | JScience |
| Chain | An interface used to catch the common system underlying DNA and RNA. | Class | org.jscience.biology | JScience |
| CharSequence | This class implements a sequence of characters stored as an array that provides random access to any position in constant time. | Class | org.jscience.biology.alignment | JScience |
| Cholesterol | A class representing the Cholesterol lipid molecule. | Class | org.jscience.biology.molecules.lipids | JScience |
| Citronellol | A class representing the Citronellol lipid molecule. | Class | org.jscience.biology.molecules.lipids | JScience |
| CO2 | A class representing the carbon dioxide (CO2). | Class | org.jscience.biology.molecules | JScience |
| Codons | A class representing the codons (the transcription of a sequence of three amino acids) for all known species. | Class | org.jscience.biology | JScience |
| Converter | This class holds methods for easier conversion of types. | Class | org.jscience.biology.lsystems.growing | JScience |
| CrochemoreLandauZivUkelson | This abstract class is the superclass of both global and local sequence alignment algorithms (with linear gap penalty function) due to Maxime Crochemore, Gad Landau and | Class | org.jscience.biology.alignment | JScience |
| CrochemoreLandauZivUkelsonGlobalAlignment | This class implements the global pairwise sequence alignment algorithm (with linear gap penalty function) due to Maxime Crochemore, Gad Landau and Michal | Class | org.jscience.biology.alignment | JScience |
| CrochemoreLandauZivUkelsonLocalAlignment | This class implements the local pairwise sequence alignment algorithm (with linear gap penalty function) due to Maxime Crochemore, Gad Landau and Michal | Class | org.jscience.biology.alignment | JScience |
| Cysteine | A class representing the Cysteine molecule. | Class | org.jscience.biology.aminoacids | JScience |
| Cytosine | A class representing the Cytosine Base. | Class | org.jscience.biology.bases | JScience |
| Deoxyribose | A class representing the Deoxyribose carbohydrate molecule. | Class | org.jscience.biology.molecules.carbohydrates | JScience |
| DNA | A class representing a DNA strain and accounting for chromosome information (the histones are missing). | Class | org.jscience.biology | JScience |
| EbiFormat | Class | org.jscience.biology.taxonomy | JScience | |
| Ecosystem | A class representing an ecosystem (interacting populations from different species). | Class | org.jscience.biology | JScience |
| Enzyme | A class representing an Enzyme. | Class | org.jscience.biology | JScience |
| Factor | This class is used by FactorSequence to create a linked list of factors of a text as induced by its Lempel-Ziv (LZ78) factorisation. | Class | org.jscience.biology.alignment | JScience |
| FactorSequence | This class builds a list of factors of a character sequence as induced by its Lempel-Ziv (LZ78) factorisation. | Class | org.jscience.biology.alignment | JScience |
| FixedPlantsDefinitions | All definitions used in the lsys package are stored in this class. | Class | org.jscience.biology.lsystems.fixed | JScience |
| Fructose | A class representing the Fructose carbohydrate molecule. | Class | org.jscience.biology.molecules.carbohydrates | JScience |
| Galactose | A class representing the Galactose carbohydrate molecule. | Class | org.jscience.biology.molecules.carbohydrates | JScience |
| GeneticsConstants | A class representing useful constants in genetics. | Class | org.jscience.biology.genetics | JScience |
| GeneticsUtils | A class representing some useful methods for population genetics. | Class | org.jscience.biology.genetics | JScience |
| Genome | A class representing the whole genome of an individual. | Class | org.jscience.biology | JScience |
| Glucose | A class representing the Glucose carbohydrate molecule. | Class | org.jscience.biology.molecules.carbohydrates | JScience |
| GlutamicAcid | A class representing the GlutamicAcid molecule. | Class | org.jscience.biology.aminoacids | JScience |
| Glutamine | A class representing the Glutamine molecule. | Class | org.jscience.biology.aminoacids | JScience |
| Glycine | A class representing the Glycine molecule. | Class | org.jscience.biology.aminoacids | JScience |
| GrowingPlantsDefinitions | All definitions used in the lsys package are stored in this class. | Class | org.jscience.biology.lsystems.growing | JScience |
| GrowthBehavior | This class makes the animation of growth of the plants in a scene. | Class | org.jscience.biology.lsystems.growing | JScience |
| Guanine | A class representing the Guanine Base. | Class | org.jscience.biology.bases | JScience |
| H2O | A class representing the water molecule (H2O). | Class | org.jscience.biology.molecules | JScience |
| Hemoglobin | A class representing the human Hemoglobin molecule. | Class | org.jscience.biology.molecules.proteins | JScience |
| Histidine | A class representing the Histidine molecule. | Class | org.jscience.biology.aminoacids | JScience |
| HistoricalIndividual | A class representing an individual as part of a genealogical tree. | Class | org.jscience.biology | JScience |
| Human | A class representing an individual from the Human species. | Class | org.jscience.biology.human | JScience |
| HumanSpecies | A class representing a well known specie. | Class | org.jscience.biology.human | JScience |
| IncompatibleScoringSchemeException | Signals that an scoring scheme is not compatible with the sequencesSee Also:ScoringScheme, | Class | org.jscience.biology.alignment | JScience |
| Individual | A class representing an individual from a specie. | Class | org.jscience.biology | JScience |
| Insulin | A class representing the human Insulin (precursor) molecule. | Class | org.jscience.biology.molecules.proteins | JScience |
| InvalidScoringMatrixException | Signals that the substitution matrix does not comply with the specification (see for details). | Class | org.jscience.biology.alignment | JScience |
| InvalidSequenceException | Signals that the sequence does not comply with the specification (seeSee Also:CharSequence, | Class | org.jscience.biology.alignment | JScience |
| Isoleucine | A class representing the Isoleucine molecule. | Class | org.jscience.biology.aminoacids | JScience |
| ItisSupport | and lookup services for taxonomic information. | Class | org.jscience.biology.taxonomy | JScience |
| ItisTaxon | A taxonomic entity, represented by a scientific name and corresponding to a particular taxonomic serial numer (tsn) from ITIS. | Class | org.jscience.biology.taxonomy | JScience |
| ItisXmlHandler | XML parsing routines that handle conversion of XML documents that are retrieved from ITIS into Java objects. | Class | org.jscience.biology.taxonomy | JScience |
| KeyBehavior | This class is a simple behavior that implements keyboard navigation. | Class | org.jscience.biology.lsystems.growing | JScience |
| Lactose | A class representing the Lactose carbohydrate molecule. | Class | org.jscience.biology.molecules.carbohydrates | JScience |
| LeafShape | This class builds a leaf with the points given in the passed array ofFields inherited from class javax. | Class | org.jscience.biology.lsystems.growing.shape | JScience |
| Leucine | A class representing the Leucine molecule. | Class | org.jscience.biology.aminoacids | JScience |
| LocalAlignmentBlock | This class is used by the CrochemoreLandauZivUkelsonLocalAlignment algorithm to store the information of an alignment block. | Class | org.jscience.biology.alignment | JScience |
| Log | This class handles all the error messages, warnings and infos. | Class | org.jscience.biology.lsystems.common | JScience |
| LSystem | This class represents an LSystem as we know it in text form. | Class | org.jscience.biology.lsystems.fixed | JScience |
| LSystem | This class represents an LSystem as we know it in text form. | Class | org.jscience.biology.lsystems.growing | JScience |
| Lysine | A class representing the Lysine molecule. | Class | org.jscience.biology.aminoacids | JScience |
| MapPanel | This class is the map of the scene on the GUI. | Class | org.jscience.biology.lsystems.growing.gui | JScience |
| Matrix | This interface defines a minimal set of operations that a matrix must implement. | Interface | org.jscience.biology.alignment | JScience |
| Methionine | A class representing the Methionine molecule. | Class | org.jscience.biology.aminoacids | JScience |
| mRNA | A class representing a message RNA or mRNA. | Class | org.jscience.biology | JScience |
| NAD | A class representing an nicotinamide adenine dinucleotide (NAD+)See Also:Serialized Form | Class | org.jscience.biology.molecules | JScience |
| NeedlemanWunsch | This class implements the classic global alignment algorithm (with linear gap penalty function) due to S. | Class | org.jscience.biology.alignment | JScience |
| O2 | A class representing the dioxygen (O2). | Class | org.jscience.biology.molecules | JScience |
| Organ | A class representing an organ. | Class | org.jscience.biology | JScience |
| OutMatrix | CrochemoreLandauZivUkelson and subclasses to enconde the OUT matrix from the input border and DIST matrix of an AlignmentBlock. | Class | org.jscience.biology.alignment | JScience |
| PairwiseAlignment | This class is the product of a pairwise alignment, generated by one subclasses of PairwiseAlignmentAlgorithm. | Class | org.jscience.biology.alignment | JScience |
| PairwiseAlignmentAlgorithm | This abstract class is the superclass of all classes implementing pairwise sequence alignment algorithms. | Class | org.jscience.biology.alignment | JScience |
| Phenylalanine | A class representing the Phenylalanine molecule. | Class | org.jscience.biology.aminoacids | JScience |
| PhosphatidylCholine | A class representing the PhosphatidylCholine lipid molecule. | Class | org.jscience.biology.molecules.lipids | JScience |
| Plant | This class represents a plant which can be built with a lindenmayerConstructor SummaryPlant(java. | Class | org.jscience.biology.lsystems.growing | JScience |
| Population | A class representing a population. | Class | org.jscience.biology | JScience |
| Primitive | Base class for all Java 3D primitives. | Class | org.jscience.biology.lsystems.common | JScience |
| Proline | A class representing the Proline molecule. | Class | org.jscience.biology.aminoacids | JScience |
| Protein | A class representing Protein. | Class | org.jscience.biology | JScience |
| Ribose | A class representing the Ribose carbohydrate molecule. | Class | org.jscience.biology.molecules.carbohydrates | JScience |
| RNA | A class representing RNA strain. | Class | org.jscience.biology | JScience |
| Rule | To represent a rule of an LSystem containing a predecessor a successor and a probability this class may be used. | Class | org.jscience.biology.lsystems.fixed | JScience |
| Rule | To represent a rule of an LSystem containing a predecessor a successor and a probability this class may be used. | Class | org.jscience.biology.lsystems.growing | JScience |
| Scene | This is the main class for the 3D scene. | Class | org.jscience.biology.lsystems.growing | JScience |
| ScoringMatrix | This class implements a scoring scheme based on a substitution matrix. | Class | org.jscience.biology.alignment | JScience |
| ScoringScheme | This abstract class is the superclass of all scoring schemes. | Class | org.jscience.biology.alignment | JScience |
| Serine | A class representing the Serine molecule. | Class | org.jscience.biology.aminoacids | JScience |
| Settings | Ths class holds all the functionality of the graphical user interface. | Class | org.jscience.biology.lsystems.growing.gui | JScience |
| SettingsGUI | This class holds all the information of the graphical elements of the settins interface. | Class | org.jscience.biology.lsystems.growing.gui | JScience |
| SimpleTaxon | A no-frills implementatation of Taxon. | Class | org.jscience.biology.taxonomy | JScience |
| SimpleTaxonFactory | Class | org.jscience.biology.taxonomy | JScience | |
| Smawk | This class implement the SMAWK algorithm to compute column maxima on a totally monotone matrix as described. | Class | org.jscience.biology.alignment | JScience |
| SmithWaterman | This class implement the classic local alignment algorithm (with linear gap penalty function) due to T. | Class | org.jscience.biology.alignment | JScience |
| Species | A class representing a specie. | Class | org.jscience.biology | JScience |
| Sucrose | A class representing the Sucrose carbohydrate molecule. | Class | org.jscience.biology.molecules.carbohydrates | JScience |
| SuffixFileFilter | A convenience implementation of FileFilter that filters out all files except for those type extensions that it knows about. | Class | org.jscience.biology.lsystems.growing | JScience |
| Taxon | A taxon within a classification. | Interface | org.jscience.biology.taxonomy | JScience |
| TaxonFactory | Factory for handling a particular implementation of a Taxon. | Interface | org.jscience.biology.taxonomy | JScience |
| TaxonParser | Interface | org.jscience.biology.taxonomy | JScience | |
| TextureBuilder | This class serves as a factory for Texture and ImageComponent2D objects. | Class | org.jscience.biology.lsystems.common | JScience |
| Threonine | A class representing the Threonine molecule. | Class | org.jscience.biology.aminoacids | JScience |
| Thymine | A class representing the Thymine Base. | Class | org.jscience.biology.bases | JScience |
| Tissue | A class representing a tissue (a group of connected cells). | Class | org.jscience.biology | JScience |
| Triacylglycerol | A class representing the Triacylglycerol lipid molecule. | Class | org.jscience.biology.molecules.lipids | JScience |
| Trie | This class implements a trie, or a digital search tree. | Class | org.jscience.biology.alignment | JScience |
| tRNA | A class representing transfert RNA or tRNA. | Class | org.jscience.biology | JScience |
| TruncatedCone | Truncated Cone is a geometry primitive defined with two radius and a height. | Class | org.jscience.biology.lsystems.common | JScience |
| Tryptophan | A class representing the Tryptophan molecule. | Class | org.jscience.biology.aminoacids | JScience |
| Turtle | This class is responsible for all the drawing of the LSystem. | Class | org.jscience.biology.lsystems.fixed | JScience |
| Tyrosine | A class representing the Tyrosine molecule. | Class | org.jscience.biology.aminoacids | JScience |
| Uracil | A class representing the Uracil Base. | Class | org.jscience.biology.bases | JScience |
| Valine | A class representing the Valine molecule. | Class | org.jscience.biology.aminoacids | JScience |
| Virus | A class representing a virus. | Class | org.jscience.biology | JScience |
| Vitamins | The class defines constants for molecules the (human) organism cannot synthetize, these are mostly vitamins and several minerals. | Class | org.jscience.biology | JScience |
| WeakTaxon | An implementation of Taxon that keeps only weak references to children, but full references to parents. | Class | org.jscience.biology.taxonomy | JScience |
| WeakTaxonFactory | An implementation of TaxonFactory that builds a weak in-memory Taxon tree. | Class | org.jscience.biology.taxonomy | JScience |