Advanced manual

This manual covers more advanced topics, which are not of immediate interest to regular users, but more to developers and integration users.

Command line use

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Configuration

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Configuring display

Show start and stop codons and splice sites
This can be turned on and off in the menu File > Configuration > Structure view. There are several check boxes that allow you to configure how start/stop codons and splice sites are displayed.

Integration

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Communicating with GenomeView

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Creating a plug-in


Plugins are the standard extension mechanism for GenomeView. They allow you to add your own algorithms and functionality to GenomeView without modifying the core application.

To build your own custom modules you will need a recent version of GenomeView. This can be obtained from the Download link in the left menu.

A module consists of three parts:

We suggest you take a look at the two plug-ins we currently support for ideas how to go about implementing your own. If you decide to develop a plug-in, we would be very happy to help you out by improving the documentation.

Example plug-ins

DNA property plug-in source code

Export image to PDF plug-in source code

Integrating GenomeView as an editor

GenomeView can be integrated as an editor in a web platform.

There are a couple of configuration options that need to be set and you'll need to setup a web service to handle the database access.

First start by setting up GenomeView as a viewer for your data, remember that the URL that you give to GenomeView to load data from can be a complex URL that contains load of parameters, which may be useful to pass information around.

Configuration changes

First the default location where GenomeView will store data needs to be set. When this value is set in the configuration file, GenomeView will not pop-up a file chooser dialog when the user presses the save button, but will send the data to this location. If it is an URL, GenomeView will use HTTP-post to send the file.
save:defaultLocation=http://server/yourwebservice.php

The second option that needs to be set is the parser to use to format the file that is being saved. Valid options are EMBL or GFF
save:defaultParser=null

Setting up the webservice

You need to setup a web service that is capable of handling a HTTP-post request with a file upload.

GenomeView sends the data with an HTTP-post request to the URL that is specified in the save:defaultLocation parameter with HTTP headers.

The name of the uploaded file is "file". The web service will be responsible to apply the changes to the database, redo analysis that depend on annotations, etc.

We do not provide such a webservice as stand-alone software at this point.

We have a system set up, called BOGAS, for genome annotation and curation which we make available to collaborators.

Programming with GenomeView

GenomeView is completely open-source and this allows you to write program that manipulate GenomeView or re-use parts of GenomeView, in particular the visualization component.

This is not yet for the faint-hearted. We are still in the process of documenting the GenomeView API, so expect a lot of documentation to be minimal.

One important thing to remember is that GenomeView is completely multi-threaded and virtually none of the methods is blocking. Unfortunately, this also often means that returned data can be incomplete and developers should implement proper checks or use other tricks to make sure output is sufficiently complete.

Scripting GenomeView

In this section we explore how to manipulate GenomeView from within your program. In our example we'll load some data sets, move to each each gene and take a snapshot.

The documented source code is available from the code repository.

Embedding the GenomeView visualization component in other software

Documented source code is available from the code repository.

Security

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