#Cipres MrBayes Plugin

##mrBayesPlugin Package

###CipresMrBayesPlugin.java

1. Geneious plugin initiallizer that calls CipresMrBayes
2. Load icons

###CipresMrBayesToolbar.java

1. getActionOption()

• Determine the placement of the GUI

2. getOptions()

• Load the option GUI

3. performOperation()

• Implement code to prompt users to login.
• Login is located under "Tools" tab named "Cipres MrBayes"

###CipresMrBayesTree.java

1. getActionOption()

• Determine the placement of the GUI

2. getOption()

• Load the option GUI

3. performOperation()

• Implement code to show the options and actions for pre-job submission of a job

##mrBayesPlugin.model Package

###UserModel.java

1. Cipres User model, includes all getter and setter methods

##mrBayesPlugin.ui Package

###JobManagePanel.java

1. Customizable GUI that displays all of the jobs binded to the Cipres user.
2. Currently set to be displayed after user login

###LoginOptions.java

1. User Login GUI
2. Simple GUI that asks for user's username and password to their Cipres account

###MrBayesOptions.java

1. getJsonInterface()

• Get the input parameters from the interface 2 MrBayesOptions()
• Constructor of the GUI
• Determine the interface outline and default values

##mrBayesPlugin.utilities Package

###CipresUtilities.java All of these methods are utilizing methods from directclient.jar/package

1. clientCheck()

• Call myClient.listJobs() to check if there's an exception, if error then client does not exist.

2. listJobs()

• Add the list of jobs retrieved to the user model

3. getJobs()

• Get the list of jobs binded to the user account

4. updateList()

• Update the list of jobs, return the them in a JSON

5. deleteJobs

• Delte the selected Job

6. submitJob()

• Submit job to MrBayes's server.

###DataHandlingUtilities.java

1. Getter and Setters for users and their jobs
2. getClient()

• Fetch the user client from CiClient

3. getUserJSON()

• Fetch user data in a JSON format, fields of the data can be seened within the method.

###MrBayesUtilities.java

1. Mocking the existing MrBayes plugin

• Save the input parameter values into a JSON to be sent as a parameter in submitJob()

2. getMetaData()

• Get the metadata of the user

3. getVParams()

• Get the param from JSON data

##Geneious Files

Geneious' plugin libraries

##MrBayesPlugin_2_1_3

The example code for the current MrBayes Plugin

##java_umbrelaa

Contains "directclient", Cipres's APIs for client, user and job handling functions.

##Note

All of these code were developed on a Mac, so there may require some configurations if it is to be tested in a different OS.

Useful resources:

1. https://biomatters.zendesk.com/forums/21579261-Plugin-Development-Forum

• Forum to post questions related to Geneious
• Click "Add article" instead of submit a request
• Bookmark the article you posted so you can go back to it easily, there's no history binded to your accounts

2. http://assets.geneious.com/developer/geneious/javadoc/latest/index.html

• Genious Public API documentation

###Questions I have asked

1. https://biomatters.zendesk.com/entries/98823428-How-to-trigger-a-plugin-by-right-clicking-listed-items

2.https://biomatters.zendesk.com/entries/99219167-How-to-obtain-Sequence-Alignment-file-paths

3.https://biomatters.zendesk.com/entries/100167627-Handling-of-returned-MrBayes-files