wiki:PluginOverview

Overview of GRITS plugins

Dependency diagram of the entire application.

All in one dependency diagram of GRITS

Main application (edu.uga.ccrc.simiantools)

=> Detailed information

The main application is the base plugin providing the basic framework for all other plugins. It contains the Application class and the Advisor classes to control the main application. It also provides the toolbar and main menu. In addition this plugin exposes a set of shared classes and functionality that can be reused by the other plugins. The main application also provides access to the general data model, workspace folder, configuration folder and application preferences.

Project explorer (edu.uga.ccrc.simiantools.display.view.projectexplorer)

=> Detailed information?

The project explorer plugin only contains the source code for the project explorer view typical visible on the left side of the application window. It also provides the context menu which can be extended by other plugins.

Experiment Designer (org.grits.toolbox.editor.experimentdesigner)

= > Detailed Information

Experiment Designer plugin provides a user interface for creating an experiment design for an analyte (thus it has Sample Entry plugin as one of its dependencies). It provides a graphical editor to create a graph of Protocols used in the experiments. Protocols may have parameters and/or parameter groups. Possible parameters, parameter groups and protocol templates are stored in an ontology. An experiment design can be created by copying from a previously saved design template and can also re-use protocols created and saved in other experiment designs.

MS Table Data Model and Preferences (edu.uga.ccrc.simiantools.datamodel.ms)

= > Detailed Information?

The MS table data model plugin provides a translation from the mass spectrometry specific elements in the GRITS object model to spreadsheet formatted model. It is to be used in instances of the NatTable Extension Control. It provides human readable descriptors for fields in the object model, a data structure for storing instances of the object model in a two-dimensional table format, and provides the interfaces for storing and loading user preferences for the table view. At this level, the table data model stores the location of peak IDs, m/z, and peak intensity columns for use in user applications.

MS Annotation Table Data Model and Preferences (edu.uga.ccrc.simiantools.datamodel.ms.annotation)

= > Detailed Information?

The MS annotation table data model extends the functionality of the MS table data model by adding elements for generic annotation of mass spectrometry data in the GRITS object model. This includes storing the location of feature IDs, annotation IDs, sequences, and which rows are unannotated.

MS Glycan Annotation Table Data Model and Preferences (edu.uga.ccrc.simiantools.datamodel.ms.annotation.glycan)

= > Detailed Information?

The MS annotation table data model extends the functionality of the MS annotation table data model by adding elements for glycan annotation of mass spectrometry data in the GRITS object model. This includes the addition of glycan "cartoon" support (with preferences). Here we also add the "Summary" table data object for use in the Glycan Summary View. Here we store the location of the cartoon columns in the table model.

MS Glycan Annotation Report Table Data Model and Preferences (edu.uga.ccrc.simiantools.datamodel.ms.annotation.glycan.report)

= > Detailed Information?

The MS glycan annotation report table data model plugin extends the MS Glycan Annotation Table Data Model by adding elements specific to merge reports of glycan annotations of mass spectrometry data in the GRITS object model. The merge report has 2 column headers, so here we store the location of column group indices.

MS Spectrum Control (edu.uga.ccrc.simiantools.display.control.spectrum)

= > Detailed Information?

The MS spectrum control plugin provides a generic interface for displaying MS spectral data (X-axis = m/z values, Y-axis is peak intensity). It uses the jfree library for generating graphs and other plugins use the API to supply the data to be graphed.

NatTable Extension Control (edu.uga.ccrc.simiantools.display.control.table)

= > Detailed Information?

The NatTable extension control is the base plugin for displaying data in tabular format in the GRITS editors. It provides the basis viewer preferences that the data model plugin extends for particular data types. It provides the processor that reads in data from a particular format (e.g. GRITS object model) and converts it into the table data model. It also provides default implementation for event handling.

MS Entry Plugin (edu.uga.ccrc.simiantools.entry.ms)

= > Detailed Information?

The MS entry plugin is responsible for creating an MS entry object in the project explorer window and the creation and viewing of mass spectrometry data using the NatTable extension control and the spectrum control. It utilizes the MS table data model and the GRITS object model for reading and formatting the data. MS-specific preferences are also manipulated here.

MS Annotation Entry Plugin (edu.uga.ccrc.simiantools.entry.ms.annotation)

= > Detailed Information?

The MS annotation entry plugin extends the MS entry plugin for the creating and viewing the results of generic annotation of mass spectrometry data. Note that this plugin is not instantiated directly. Its purpose is like that of an interface and must be extended by classes in additional plugins for specific annotation types. While generic editors and viewers exist and are specified in the plugin.xml, no menu items are added, so this plugin essentially makes no contribution to the GUI.

MS Glycan Annotation Entry Plugin (edu.uga.ccrc.simiantools.entry.ms.annotation.glycan)

= > Detailed Information?

The MS glycan annotation entry plugin extends the MS annotation entry plugin for the creating and viewing the results of glycan annotation of mass spectrometry data. Most of the editors and viewers extend those in the annotation plugin, except that the Glycan Summary View is added. Menu items are added in plugin.xml to allow users to filter and export MS glycan results.

MS Glycan Annotation Report Entry Plugin(edu.uga.ccrc.simiantools.entry.ms.annotation.glycan.report)

= > Detailed Information?

The MS glycan annotation report entry plugin extends much of the functionality in the glycan annotation plugin, but the views here are unique and specific for creating and viewing read-only reports from merging results from 1 or more glycan annotation analyses. This plugin adds menu items for exporting the reports.

Project Entry Plugin (edu.uga.ccrc.simiantools.entry.project)

= > Detailed Information?

Sample Entry Plugin (edu.uga.ccrc.simiantools.entry.sample)

= > Detailed Information The Sample Entry Plugin provides an user interface for creating and managing analytes and its components. Multiple components can be added to an analyte. Each component is described using descriptors and descriptor groups. The descriptors and descriptor groups and other ontological information are stored inside an ontology. One can also create components by using a template or by copying from a previously created component.

MS Importer (edu.uga.ccrc.simiantools.importer.ms)

= > Detailed Information

MS GAG Id Annotation Importer (edu.uga.ccrc.simiantools.importer.ms.annotation.gagid)

= > Detailed Information?

MS Glycan GELATO Annotation Importer (edu.uga.ccrc.simiantools.importer.ms.annotation.glycan.simiansearch)

= > Detailed Information?

MS Annotation I/O Plugin (edu.uga.ccrc.simiantools.io.ms.annotation)

= > Detailed Information?

MS Glycan Annotation I/O Plugin (edu.uga.ccrc.simiantools.io.ms.annotation.glycan)

= > Detailed Information?

MS Glycan Annotation Report I/O Plugin (edu.uga.ccrc.simiantools.io.ms.annotation.glycan.report)

= > Detailed Information?

GRITS Annotation Libraries (edu.uga.ccrc.simiantools.lib)

= > Detailed Information?

GRITS Merge Report Creator (edu.uga.ccrc.simiantools.merge)

= > Detailed Information?

MS Glycan GELATO Annotation Creator (edu.uga.ccrc.simiantools.ms.annotation)

= > Detailed Information?

GRITS Object Model Plugin (edu.uga.ccrc.simiantools.ms.om)

= > Detailed Information?

General Utility Classes (edu.uga.ccrc.simiantools.utils)

= > Detailed Information?

Last modified 8 years ago Last modified on 12/11/2014 10:17:55 PM

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