Package | Description |
---|---|
org.anchoranalysis.annotation.io |
Reading and writing annotations to the filesystem.
|
org.anchoranalysis.annotation.io.image.findable |
The outcome of searching for annotations or images on the file-system.
|
org.anchoranalysis.bean |
Defining, loading, initializing Anchor Beans.
|
org.anchoranalysis.bean.initializable |
Initializing beans with particular parameters, including recursively.
|
org.anchoranalysis.bean.initializable.property |
Initializating a bean with parameters.
|
org.anchoranalysis.core.identifier.provider.store |
Data structures like
NamedProvider with
supporting for adding new elements. |
org.anchoranalysis.core.log |
Interfaces to log messages, both information and error messages.
|
org.anchoranalysis.core.log.error |
Mechanism for reporting errors (exceptions/throwables) to the user.
|
org.anchoranalysis.core.system |
Utilities for interacting with the operating system or computer system generally
|
org.anchoranalysis.core.time |
Recording the execution-time of operations for profiling.
|
org.anchoranalysis.experiment.bean.log |
Different approaches to where messages on the progress/status of an experiment are logged to.
|
org.anchoranalysis.experiment.io |
Interfaces for replacing attributes of an experiment: input, output, task etc.
|
org.anchoranalysis.experiment.log |
Helpful classes for logging.
|
org.anchoranalysis.experiment.task |
Non-bean classes related to a
Task . |
org.anchoranalysis.experiment.task.processor |
Non-bean classes related to
JobProcessor . |
org.anchoranalysis.feature.bean.list |
A feature-list (custom list type for features) and associated providers.
|
org.anchoranalysis.feature.calculate.cache |
Classes to cache feature-results or parts of feature-results that occur repeatedly among features
or across calculations of the same feature.
|
org.anchoranalysis.feature.initialization |
Initialization parameters used for beans in
org.anchoranalysis.feature.bean . |
org.anchoranalysis.feature.session |
A defined context in which one or more features are provided inputs and produce results.
|
org.anchoranalysis.feature.session.cache |
Creates a
FeatureCalculationCache to use
during feature-calculations. |
org.anchoranalysis.feature.session.replace |
Strategies on whether to reuse or invalidate a feature-input's cache.
|
org.anchoranalysis.feature.shared |
Features shared for referencing among calculations.
|
org.anchoranalysis.image.bean.channel |
Base classes for performing operations on
Channel s. |
org.anchoranalysis.image.bean.nonbean.init |
Classes that aren't AnchorBeans that pertain to the initialization of image-related beans.
|
org.anchoranalysis.image.feature.calculator |
Implementations of
FeatureCalculatorMulti
related to images, especially to create tables of feature-calculations. |
org.anchoranalysis.image.feature.calculator.merged |
A particular implementation of
FeatureCalculatorMulti for feature-calculations based
upon pairs of image-objects. |
org.anchoranalysis.image.inference |
Inference of machine learning models on images.
|
org.anchoranalysis.image.inference.bean.segment.instance |
Instance-segmentation of a
Stack . |
org.anchoranalysis.image.io.bean.channel |
Beans pertaining to reading
Channel s as input. |
org.anchoranalysis.image.io.bean.stack.writer |
Bean classes for writing raster-files to the filesystem.
|
org.anchoranalysis.image.io.channel.input |
Non-bean classes for reading a
Channel from the
filesystem. |
org.anchoranalysis.image.io.channel.map |
Non-bean classes for a mapping of names to
Channel s. |
org.anchoranalysis.image.io.object.output.hdf5 |
Writing an
ObjectCollection to the filesystem in
HDF5 format. |
org.anchoranalysis.image.io.stack |
Non-bean classes for reading / writing a
Stack from
and to the filesystem. |
org.anchoranalysis.image.io.stack.input |
Non-bean classes for reading a
Stack from the
filesystem. |
org.anchoranalysis.image.io.stack.output.generator |
Base classes for generators that ultimately write a
Stack to the filesystem. |
org.anchoranalysis.inference.concurrency |
Specifying how many CPUs and GPUs can be allocated for some purpose.
|
org.anchoranalysis.io.generator |
Base-classes and utilities for generators, which write different types of objects to the file
system.
|
org.anchoranalysis.io.generator.serialized |
Generators for writing serialized objects.
|
org.anchoranalysis.io.generator.tabular |
Generators for writing tabular data, including CSV.
|
org.anchoranalysis.io.generator.text |
Generators for writing textual data, including strings.
|
org.anchoranalysis.io.generator.xml |
Generators for writing XML data.
|
org.anchoranalysis.io.input.bean |
Beans related to collecting inputs from the file-system for an experiment.
|
org.anchoranalysis.io.input.file |
Non-bean classes that relate to using files during inputting.
|
org.anchoranalysis.io.output.bean |
Beans for the framework around writing files to the file-system.
|
org.anchoranalysis.io.output.outputter |
Classes for outputting to particular directories.
|
org.anchoranalysis.io.output.writer |
Allows a generators to write element(s) to the filesystem.
|
org.anchoranalysis.launcher |
Parent package and entry-point classes for the Anchor command-line launcher application.
|
org.anchoranalysis.launcher.executor |
Runs a particular experiment after identifying necessary paths and input files.
|
org.anchoranalysis.launcher.run |
Parses command-line arguments and runs an experiment.
|
org.anchoranalysis.mpp.feature.addcriteria |
Criteria for adding edges during optimization of marked-point-processes.
|
org.anchoranalysis.mpp.feature.energy.marks |
Non-bean classes pertaining to calculating energy of {org.anchoranalysis.mpp.mark.Mark}s.
|
org.anchoranalysis.mpp.feature.energy.saved |
Saved snapshots of energy-calculations.
|
org.anchoranalysis.mpp.feature.energy.scheme |
Factorized form of storing the energy during an energy-minimization optimization scheme.
|
org.anchoranalysis.mpp.feature.mark |
Non-bean classes for calculating feature-values related to
Mark s. |
org.anchoranalysis.mpp.init |
Parameters used to initialize certain types of beans.
|
org.anchoranalysis.mpp.io.bean.report.feature |
Beans for communicating feature-values from data-structures in human-readable manner.
|
org.anchoranalysis.mpp.io.input |
Non-beans for reading data structures related to marked point processes from the file system.
|
org.anchoranalysis.mpp.mark |
Non-bean classes related to
Mark s. |
org.anchoranalysis.mpp.segment.bean.optimization.feedback |
Providing feedback on the progress of a
OptimizationScheme . |
org.anchoranalysis.mpp.segment.bean.optimization.kernel |
Base classes for kernels that transition a configuration of marks (a
MarkCollection ) into an altered version. |
org.anchoranalysis.mpp.segment.bean.optimization.termination |
In which circumstances to terminate an
OptimizationScheme that is underway. |
org.anchoranalysis.mpp.segment.optimization |
Non-bean classes used in
org.anchoranalysis.mpp.segment.bean.optimization |
org.anchoranalysis.mpp.segment.optimization.feedback |
Non-bean classes used in
org.anchoranalysis.mpp.segment.bean.optimization.feedback |
org.anchoranalysis.mpp.segment.transformer |
Mapping one type of optimization state to another.
|
org.anchoranalysis.plugin.image.bean.blur |
Filters that perform blurring.
|
org.anchoranalysis.plugin.image.feature.bean.object.combine |
Features from combinations of
ObjectMask s. |
org.anchoranalysis.plugin.image.intensity.level |
Non-beans for calculating a thresholding level from itensity values.
|
org.anchoranalysis.plugin.image.object.merge |
Merging
ObjectMask s. |
org.anchoranalysis.plugin.image.object.merge.condition |
Conditions for merging
ObjectMask s. |
org.anchoranalysis.plugin.image.object.merge.priority |
Assigning priority when merging
ObjectMask s. |
org.anchoranalysis.plugin.image.task.bean.format.convertstyle |
Different approaches for converting sets of channels (RGB, independently etc.) to another image
format.
|
org.anchoranalysis.plugin.image.task.feature |
Non-bean classes pertaining to
Feature s as used in tasks. |
org.anchoranalysis.plugin.image.task.stack |
Non-bean classes pertaining to stacks and channels as used in tasks.
|
org.anchoranalysis.plugin.io.bean.channel.map |
Implementations of
ChannelMapCreator . |
org.anchoranalysis.plugin.io.bean.input.stack |
Implementations of
InputManager that process Stack s. |
org.anchoranalysis.plugin.io.multifile |
Non-bean classes to help use multiple files to represent a single
Stack . |
org.anchoranalysis.plugin.mpp.experiment.bean.objects |
Tasks involving
ObjectMask s. |
org.anchoranalysis.plugin.mpp.experiment.objects |
Non-bean classes used in
org.anchoranalysis.plugin.mpp.experiment.bean.objects . |
org.anchoranalysis.plugin.mpp.experiment.shared |
Shared-state use across tasks in this JAR.
|
org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination |
Implementations of
TerminationCondition . |
org.anchoranalysis.plugin.mpp.segment.optimization |
Non-bean classes to help with optimization in
org.anchoranalysis.plugin.mpp.segment.bean.optimization and sub-packages. |
org.anchoranalysis.plugin.onnx.bean.object.segment.stack |
Segmenting a
Stack using the ONNX Runtime to produce
an ObjectCollection . |
org.anchoranalysis.plugin.opencv.bean.object.segment.stack |
Segmentation of a
Stack using OpenCV. |
org.anchoranalysis.test |
Testing utilities and fixtures with no greater downstream dependency than anchor-core.
|
org.anchoranalysis.test.experiment |
Testing utilities and fixtures with no greater downstream dependency than
anchor-experiment or anchor-mpp or anchor-mpp-io.
|
org.anchoranalysis.test.image |
Testing utilities and fixtures with no greater downstream dependency than anchor-image-io
or anchor-io-bioformats or anchor-imagej.
|
Class and Description |
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Logger
A logging-mechanism for both messages and errors.
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Class and Description |
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Logger
A logging-mechanism for both messages and errors.
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Logger
A logging-mechanism for both messages and errors.
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Logger
A logging-mechanism for both messages and errors.
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Class and Description |
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Logger
A logging-mechanism for both messages and errors.
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Class and Description |
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CommonContext
A logger with additional configuration that are coupled together widely in the code.
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Class and Description |
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Logger
A logging-mechanism for both messages and errors.
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MessageLogger
Logs messages (strings) somewhere.
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Class and Description |
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MessageLogger
Logs messages (strings) somewhere.
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Class and Description |
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MessageLogger
Logs messages (strings) somewhere.
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Class and Description |
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Logger
A logging-mechanism for both messages and errors.
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Class and Description |
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MessageLogger
Logs messages (strings) somewhere.
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Class and Description |
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CommonContext
A logger with additional configuration that are coupled together widely in the code.
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Logger
A logging-mechanism for both messages and errors.
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Class and Description |
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MessageLogger
Logs messages (strings) somewhere.
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Class and Description |
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Logger
A logging-mechanism for both messages and errors.
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MessageLogger
Logs messages (strings) somewhere.
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Class and Description |
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MessageLogger
Logs messages (strings) somewhere.
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Class and Description |
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Logger
A logging-mechanism for both messages and errors.
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Logger
A logging-mechanism for both messages and errors.
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Logger
A logging-mechanism for both messages and errors.
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Logger
A logging-mechanism for both messages and errors.
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Logger
A logging-mechanism for both messages and errors.
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Logger
A logging-mechanism for both messages and errors.
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Logger
A logging-mechanism for both messages and errors.
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Logger
A logging-mechanism for both messages and errors.
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Logger
A logging-mechanism for both messages and errors.
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Logger
A logging-mechanism for both messages and errors.
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Logger
A logging-mechanism for both messages and errors.
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Class and Description |
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Logger
A logging-mechanism for both messages and errors.
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Class and Description |
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Logger
A logging-mechanism for both messages and errors.
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Class and Description |
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Logger
A logging-mechanism for both messages and errors.
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Class and Description |
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Logger
A logging-mechanism for both messages and errors.
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Class and Description |
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Logger
A logging-mechanism for both messages and errors.
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Class and Description |
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Logger
A logging-mechanism for both messages and errors.
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Class and Description |
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Logger
A logging-mechanism for both messages and errors.
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Class and Description |
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Logger
A logging-mechanism for both messages and errors.
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Class and Description |
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Logger
A logging-mechanism for both messages and errors.
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Class and Description |
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Logger
A logging-mechanism for both messages and errors.
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Class and Description |
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Logger
A logging-mechanism for both messages and errors.
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Class and Description |
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Logger
A logging-mechanism for both messages and errors.
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Class and Description |
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Logger
A logging-mechanism for both messages and errors.
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Class and Description |
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Logger
A logging-mechanism for both messages and errors.
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Class and Description |
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Logger
A logging-mechanism for both messages and errors.
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Class and Description |
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Logger
A logging-mechanism for both messages and errors.
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Class and Description |
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Logger
A logging-mechanism for both messages and errors.
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Class and Description |
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Logger
A logging-mechanism for both messages and errors.
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Class and Description |
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Logger
A logging-mechanism for both messages and errors.
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Class and Description |
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CommonContext
A logger with additional configuration that are coupled together widely in the code.
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Logger
A logging-mechanism for both messages and errors.
|
MessageLogger
Logs messages (strings) somewhere.
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Class and Description |
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Logger
A logging-mechanism for both messages and errors.
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Class and Description |
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Logger
A logging-mechanism for both messages and errors.
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Class and Description |
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Logger
A logging-mechanism for both messages and errors.
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Class and Description |
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Logger
A logging-mechanism for both messages and errors.
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Class and Description |
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Logger
A logging-mechanism for both messages and errors.
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Class and Description |
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Logger
A logging-mechanism for both messages and errors.
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Class and Description |
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Logger
A logging-mechanism for both messages and errors.
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Class and Description |
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Logger
A logging-mechanism for both messages and errors.
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Class and Description |
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Logger
A logging-mechanism for both messages and errors.
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Class and Description |
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Logger
A logging-mechanism for both messages and errors.
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Class and Description |
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Logger
A logging-mechanism for both messages and errors.
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Class and Description |
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Logger
A logging-mechanism for both messages and errors.
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Class and Description |
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Logger
A logging-mechanism for both messages and errors.
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Class and Description |
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Logger
A logging-mechanism for both messages and errors.
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Class and Description |
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Logger
A logging-mechanism for both messages and errors.
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Class and Description |
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MessageLogger
Logs messages (strings) somewhere.
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Class and Description |
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Logger
A logging-mechanism for both messages and errors.
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Class and Description |
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MessageLogger
Logs messages (strings) somewhere.
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Class and Description |
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Logger
A logging-mechanism for both messages and errors.
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Class and Description |
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MessageLogger
Logs messages (strings) somewhere.
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Class and Description |
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Logger
A logging-mechanism for both messages and errors.
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Class and Description |
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MessageLogger
Logs messages (strings) somewhere.
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Class and Description |
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Logger
A logging-mechanism for both messages and errors.
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Class and Description |
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Logger
A logging-mechanism for both messages and errors.
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MessageLogger
Logs messages (strings) somewhere.
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Class and Description |
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Logger
A logging-mechanism for both messages and errors.
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Class and Description |
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Logger
A logging-mechanism for both messages and errors.
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Class and Description |
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Logger
A logging-mechanism for both messages and errors.
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Class and Description |
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Logger
A logging-mechanism for both messages and errors.
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Class and Description |
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Logger
A logging-mechanism for both messages and errors.
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Class and Description |
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Logger
A logging-mechanism for both messages and errors.
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Class and Description |
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Logger
A logging-mechanism for both messages and errors.
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Class and Description |
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Logger
A logging-mechanism for both messages and errors.
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Class and Description |
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Logger
A logging-mechanism for both messages and errors.
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Class and Description |
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MessageLogger
Logs messages (strings) somewhere.
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Class and Description |
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MessageLogger
Logs messages (strings) somewhere.
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Class and Description |
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Logger
A logging-mechanism for both messages and errors.
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Class and Description |
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Logger
A logging-mechanism for both messages and errors.
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Class and Description |
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Logger
A logging-mechanism for both messages and errors.
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Class and Description |
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Logger
A logging-mechanism for both messages and errors.
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MessageLogger
Logs messages (strings) somewhere.
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Class and Description |
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Logger
A logging-mechanism for both messages and errors.
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Class and Description |
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Logger
A logging-mechanism for both messages and errors.
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Copyright © 2010–2023 Owen Feehan, ETH Zurich, University of Zurich, Hoffmann-La Roche. All rights reserved.