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Merge branch 'refactor'
* refactor: Major refactor. Switched to new JsInterop. Simplified code
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‎.gitignore

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target/
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*.class
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# Package Files #
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*.jar
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*.war
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# gwt caches and compiled units #
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war/gwt_bree/
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gwt-unitCache/
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# boilerplate generated classes #
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.apt_generated/
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# more caches and things from deploy #
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war/WEB-INF/deploy/
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war/WEB-INF/classes/

‎CHANGELOG

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August 31, 2015 - Release 1.0.0
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* Major refactor. Moved to GWT 2.8.0 and new JsInterop
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* Upgraded to ProcessingJS library 1.0.0
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* Added unit tests
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March 26, 2014 - Release 0.4.9
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* pom.xml: GWT version updated to 2.5.1 and dependencies updated to latest version
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‎README

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‎README.md

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## What is GeneViewer?
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GeneViewer is a Google Web Toolkit (GWT) widget containing a [processingjs][0] sketch for visualizing gene models.
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![GeneViewer](https://raw.githubusercontent.com/timeu/GeneViewer/master/geneviewer.png "GeneViewer")
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## How do I use it?
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Following steps are required:
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```JAVA
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GeneViewer geneviewer = new GeneViewer();
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geneviewer.load(new Runnable() {
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@Override
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public void run() {
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GWT.log("GeneViewer loaded");
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// Interact with sketch
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JsArrayMixed data = getData();
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geneviewer.setGeneData(data);
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}
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});
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```
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To display the gene models the user has to call the `setGEneData(JsArrayMixed data)` function.
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The `JsArrayMixed` data consists of a list of genes in JSON format. There are 2 visualization modes:
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1. Simple gene models without any features (See [sample data][1]).
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2. Gene Models with features (see [sample data][2] and screenshot).
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Example of data with features:
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```JSON
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[
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[10421840,10424113,1,"AT2G24530.1",
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[
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[10422416,10422596,1,"five_prime_UTR"],
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[10422272,10422312,1,"five_prime_UTR"],
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[10421840,10421930,1,"five_prime_UTR"],
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[10422416,10424113,1,"exon"],
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[10423820,10424113,1,"three_prime_UTR"],
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[10422272,10422312,1,"exon"],
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[10421840,10421930,1,"exon"],
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[10422596,10423820,1,"CDS"]
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]
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]
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]
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```
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The data can be loaded this way:
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```JAVA
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final String jsonData = GET_FROM_CLIENTBUNDLE OR AJAX CALL
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JsArrayMixed data = JsonUtils.safeEval(jsonData);
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```
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## How do I install it?
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If you're using Maven, you can add the following to your `<dependencies>`
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section:
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```xml
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<dependency>
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<groupId>com.github.timeu.gwtlibs.geneviewer</groupId>
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<artifactId>geneviewer</artifactId>
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<version>1.0.0</version>
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</dependency>
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```
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GeneViewer uses [GWT 2.7's][3] new [JSInterop feature][4] and thus it has to be enabled in the GWT compiler args.
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For maven:
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```xml
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<compilerArgs>
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<compilerArg>-XjsInteropMode</compilerArg>
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<compilerArg>JS</compilerArg>
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</compilerArgs>
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```
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or passing it to the compiler via `-XjsInteropMode`
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You can also download the [jar][5] directly or check out the source using git
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from <https://github.com/timeu/geneviewer.git> and build it yourself. Once
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you've installed LDViewer, be sure to inherit the module in your .gwt.xml
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file like this:
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```xml
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<inherits name='com.github.timeu.gwtlibs.geneviewer.GeneViewer'/>
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```
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## Where can I learn more?
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* Check out the [sample app][6] ([Source Code][7]) for a full example of using GeneViewer.
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[0]: http://processingjs.org
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[1]: https://github.com/timeu/GeneViewer/blob/master/geneviewer-sample/src/main/resources/sample/client/data/genes.json
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[2]: https://github.com/timeu/GeneViewer/blob/master/geneviewer-sample/src/main/resources/sample/client/data/genes_with_features.json
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[3]: http://www.gwtproject.org/release-notes.html#Release_Notes_2_7_0_RC1
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[4]: https://docs.google.com/document/d/1tir74SB-ZWrs-gQ8w-lOEV3oMY6u6lF2MmNivDEihZ4/edit#
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[5]:
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[6]: http://timeu.github.io/GeneViewer
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[7]: https://github.com/timeu/GeneViewer/tree/master/geneviewer-sample

‎geneviewer-sample/pom.xml

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<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
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<modelVersion>4.0.0</modelVersion>
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<parent>
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<groupId>com.github.timeu.gwt-libs.geneviewer</groupId>
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<artifactId>geneviewer-parent</artifactId>
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<version>1.0.0-SNAPSHOT</version>
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</parent>
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<artifactId>geneviewer-sample</artifactId>
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<packaging>gwt-app</packaging>
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<name>GeneViewer Sample Application</name>
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<build>
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<plugins>
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<plugin>
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<groupId>net.ltgt.gwt.maven</groupId>
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<artifactId>gwt-maven-plugin</artifactId>
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<configuration>
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<moduleName>${gwt.module}</moduleName>
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<moduleShortName>${gwt.shortName}</moduleShortName>
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</configuration>
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</plugin>
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<plugin>
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<groupId>com.github.github</groupId>
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<artifactId>site-maven-plugin</artifactId>
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<version>0.12</version>
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<configuration>
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<message>Creating site for ${project.version}</message>
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<outputDirectory>${project.build.directory}/${artifactId}-${version}/${gwt.shortName}</outputDirectory>
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</configuration>
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<executions>
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<execution>
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<goals>
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<goal>site</goal>
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</goals>
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<phase>site</phase>
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</execution>
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</executions>
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</plugin>
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</plugins>
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</build>
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<dependencies>
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<dependency>
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<groupId>com.google.gwt</groupId>
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<artifactId>gwt-user</artifactId>
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</dependency>
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<dependency>
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<groupId>com.google.gwt</groupId>
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<artifactId>gwt-dev</artifactId>
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<scope>provided</scope>
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</dependency>
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<dependency>
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<groupId>com.github.timeu.gwt-libs.geneviewer</groupId>
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<artifactId>geneviewer</artifactId>
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<type>gwt-lib</type>
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</dependency>
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</dependencies>
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</project>

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