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MolecularFaces

Javadoc Maven Central Sonatype Nexus (Snapshots) Maven Build Maven dependency check

MolecularFaces is a collection of reusable UI components for Java Server Faces (JSF) featuring input and output plugins, validators and converters for chemistry and biochemistry data. It is a spin-off project of CRIMSy (Cloud Resource & Information Management System).

UI library for chemistry

UI library for biology and biochemistry

Maven coordinates

The artifacts are available on Maven Central. To include MolecularFaces into your JSF project, add the following dependency to your project's pom.xml:

<dependency>
  <groupId>de.ipb-halle</groupId>
  <artifactId>molecularfaces</artifactId>
  <version>0.4.0</version>
</dependency>

Version 1.0.0 and above require JakartaEE. Use versions 0.x.y for JavaEE 7 projects. Snapshots can be included via

<repository>
  <id>snapshots-repo</id>
  <url>https://s01.oss.sonatype.org/content/repositories/snapshots/</url>
  <releases><enabled>false</enabled></releases>
  <snapshots><enabled>true</enabled></snapshots>
</repository>
...
<dependency>
  <groupId>de.ipb-halle</groupId>
  <artifactId>molecularfaces</artifactId>
  <version>0.5.0-SNAPSHOT</version>
</dependency>

Usage

XML Namespace

xmlns:mol="http://github.com/ipb-halle/MolecularFaces"

Usage example

JSF view:

<?xml version='1.0' encoding='UTF-8' ?>
<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml"
  xmlns:h="http://xmlns.jcp.org/jsf/html"
  xmlns:mol="http://github.com/ipb-halle/MolecularFaces">
  <h:head>
    <title>MolecularFaces</title>
  </h:head>
  <h:body>
    <h:form>
      <mol:molecule value="#{myBean.structure}" pluginType="OpenChemLibJS" />
      <br />
      <mol:openVectorEditor value="#{myBean.sequence}" />
    </h:form>
  </h:body>
</html>

JSF backing bean:

@Named
@RequestScoped
public class MyBean {

// structure in MDL Molfile V2000 format
private String structure = "";

// DNA/RNA sequence in JSON format
private String sequence = "";

// getters/setters
...
}

Configuring resources via web.xml

MolecularFaces tries to include as much resources (JavaScript, CSS, images) of the third-party plugins in its jar as possible and loads them when required. Alternatively, you can configure the URL of the resources (relative to the application's context root) via a context-param in your project's web.xml.

Example:

<context-param>
  <param-name>de.ipb-halle.molecularfaces.OPENCHEMLIBJS_URL</param-name>
  <param-value>openchemlib-full.js</param-value>
</context-param>