https://github.com/timeu/geneviewer
A GWT Canvas Widget to display genes
https://github.com/timeu/geneviewer
Last synced: 11 months ago
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A GWT Canvas Widget to display genes
- Host: GitHub
- URL: https://github.com/timeu/geneviewer
- Owner: timeu
- License: mit
- Created: 2011-02-11T15:25:23.000Z (over 15 years ago)
- Default Branch: master
- Last Pushed: 2020-10-13T10:09:54.000Z (almost 6 years ago)
- Last Synced: 2025-07-18T05:37:42.169Z (about 1 year ago)
- Language: Java
- Homepage:
- Size: 1.49 MB
- Stars: 3
- Watchers: 1
- Forks: 0
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG
- License: LICENSE
Awesome Lists containing this project
README
## What is GeneViewer?
GeneViewer is a Google Web Toolkit (GWT) widget containing a [processingjs][0] sketch for visualizing gene models.
## How do I use it?
Following steps are required:
```JAVA
GeneViewer geneviewer = new GeneViewer();
geneviewer.load(new Runnable() {
@Override
public void run() {
GWT.log("GeneViewer loaded");
// Interact with sketch
JsArrayMixed data = getData();
geneviewer.setGeneData(data);
}
});
```
To display the gene models the user has to call the `setGEneData(JsArrayMixed data)` function.
The `JsArrayMixed` data consists of a list of genes in JSON format. There are 2 visualization modes:
1. Simple gene models without any features (See [sample data][1]).
2. Gene Models with features (see [sample data][2] and screenshot).
**Example of data with features:**
```JSON
[
[10421840,10424113,1,"AT2G24530.1",
[
[10422416,10422596,1,"five_prime_UTR"],
[10422272,10422312,1,"five_prime_UTR"],
[10421840,10421930,1,"five_prime_UTR"],
[10422416,10424113,1,"exon"],
[10423820,10424113,1,"three_prime_UTR"],
[10422272,10422312,1,"exon"],
[10421840,10421930,1,"exon"],
[10422596,10423820,1,"CDS"]
]
],
[
[
]
]
]
```
The data can be loaded this way:
```JAVA
final String jsonData = GET_FROM_CLIENTBUNDLE OR AJAX CALL
JsArrayMixed data = JsonUtils.safeEval(jsonData);
```
## How do I install it?
If you're using Maven, you can add the following to your ``
section:
```xml
com.github.timeu.gwtlibs.geneviewer
geneviewer
1.0.0
```
GeneViewer uses [GWT 2.8's][3] new [JSInterop feature][4] and thus it has to be enabled in the GWT compiler args.
For maven:
```xml
-generateJsInteropExports
```
or passing it to the compiler via `-generateJsInteropExports`
You can also download the [jar][5] directly or check out the source using git
from and build it yourself. Once
you've installed LDViewer, be sure to inherit the module in your .gwt.xml
file like this:
```xml
```
## Where can I learn more?
* Check out the [sample app][6] ([Source Code][7]) for a full example of using GeneViewer.
[0]: http://processingjs.org
[1]: https://github.com/timeu/GeneViewer/blob/master/geneviewer-sample/src/main/resources/sample/client/data/genes.json
[2]: https://github.com/timeu/GeneViewer/blob/master/geneviewer-sample/src/main/resources/sample/client/data/genes_with_features.json
[3]: http://www.gwtproject.org/release-notes.html#Release_Notes_2_8_0_BETA1
[4]: https://docs.google.com/document/d/10fmlEYIHcyead_4R1S5wKGs1t2I7Fnp_PaNaa7XTEk0/edit#heading=h.o7amqk9edhb9
[5]: https://github.com/timeu/GeneViewer/releases
[6]: http://timeu.github.io/GeneViewer
[7]: https://github.com/timeu/GeneViewer/tree/master/geneviewer-sample