% PANDORA Toolbox Classes
% The following classes are designed as generic templates that can be
% subclassed to take specific tasks. They should not be modified for
% more specialized tasks.
% Basic data wrapper classes that define the measurements:
% trace - A voltage/current trace.
% spikes - Spike times of a trace.
% spike_shape - Averaged spike shape from a trace.
% period - Defines time periods to operate on trace or spikes objects.
% Classes specialized for CIP experiments tests:
% cip_trace - A voltage trace with a CIP applied.
% Profile classes that hold test results:
% result_profile - Base class that holds a results structure.
% trace_profile - Generic example class for holding a trace profile.
% cip_trace_profile - Holds cip_trace results. Template class designed
% only for subclassing.
% - Created by cip_trace/getProfileAllSpikes, contains statistics
% of spike shape measures from individual spikes.
% params_tests_profile- Collects both intermediate and result data structures
% from analysis of a params_tests_db.
% Dataset classes that point to or hold raw data:
% params_tests_dataset - Base class for datasets.
% params_tests_fileset - Holds a list of filenames and associated information,
% capable of creating a params_tests_db.
% params_cip_trace_fileset - Fileset from which cip_trace objects can be created.
% physiol_cip_traceset - Dataset of a traceset from a single file.
% physiol_cip_traceset_fileset - Dataset of a tracesets from many files.
% Database classes created from datasets:
% tests_db - Base class for databases. Contains many utilities.
% params_tests_db - DB extended to hold parameter values
% associated with results.
% spikes_db - Holds measures from each individual spike in a trace.
% test_3D_db - 3D database of tests that vary with a third variable.
% corrcoefs_db - Holds correlation coefficients.
% histogram_db - Holds histogram bins.
% stats_db - Holds statistical measurements.
% ranked_db - Database ranked for a criterion, holds error values or distances.
% Bundle classes that bridge the gap between database and it's ancestral dataset:
% dataset_db_bundle - Base class of bundles. Puts a processed and raw DBs with datasets.
% model_ct_bundle - Bundle for model databases.
% physiol_bundle - Bundle for physiology databases.
% Plotting classes:
% plot_abstract - Base class that holds information sufficient to generate any plot.
% plot_simple - Simple extension that works for most simple plots.
% plot_stack - Holds horizontal or vertical stack of plot_abstract objects.
% plot_inset - Places multiple plots at absolute locations in a figure. Good for insets, etc.
% plot_superpose - Allows superposing different plot_abstract's in the same axis.
% plot_bars - Multi-axis bar plot with extended errorbars.
% plot_errorbar - Errorbar plot.
% plot_errorbars - Multi-axis errorbar plot.
% Classes for generating formatted printable or presentable documents:
% doc_generate - Base class for all document classes.
% doc_plot - Holds a plot_abstract and captions, etc.
% doc_multi - Combines multiple doc_generate objects.
% Script control classes for cluster computing:
% script_factory - Generates a set of scripts based on a recipe.
% script_array - Designed to execute an array job serially on a computer.
% script_array_for_cluster - Executes an array job on a cluster computer.
% See also: subclasses under classes/cengiz
% Author: Cengiz Gunay <email@example.com>, 2004/09/14