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- The IGB Toolbar menu contains a menu option labeled Configure Web Links. This is the first hook.
- Selecting Configure Web Links opens the Web links configuration window. IGB includes several built-in linkout patterns in the top section. The middle section contains user-defined Custom Web Links.
- When users right-click an annotation, a context menu appears that contains menu items for each matching Web Link pattern. This is the second hook. Note that if only one Web Link pattern matches, it appears in the main menu, not in sub menus as shown below.
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Web links project and directory structure
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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">
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>com.affymetrix</groupId>
<artifactId>igb-project</artifactId>
<version>8.6.0</version>
<relativePath>../../pom.xml</relativePath>
</parent>
<groupId>org.lorainelab.igb</groupId>
<artifactId>weblinks</artifactId>
<packaging>bundle</packaging>
<name>WebLinks</name>
<dependencies>
<dependency>
<groupId>biz.aQute.bnd</groupId>
<artifactId>bndlib</artifactId>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>com.affymetrix</groupId>
<artifactId>genometry</artifactId>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>com.affymetrix</groupId>
<artifactId>igb-services</artifactId>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>com.affymetrix</groupId>
<artifactId>igbSwingExt</artifactId>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
<scope>provided</scope>
</dependency>
<!--Start of logging dependencies-->
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
<scope>provided</scope>
</dependency>
<!--End of logging dependencies-->
<dependency>
<groupId>org.lorainelab.igb</groupId>
<artifactId>igb-preferences</artifactId>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>com.jidesoft</groupId>
<artifactId>jide-ultimate</artifactId>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>com.affymetrix</groupId>
<artifactId>affymetrix-common</artifactId>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.lorainelab.igb</groupId>
<artifactId>igb-genoviz-extensions</artifactId>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.lorainelab.igb</groupId>
<artifactId>synonym-lookup</artifactId>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.lorainelab.igb</groupId>
<artifactId>context-menu-api</artifactId>
<scope>provided</scope>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<artifactId>maven-clean-plugin</artifactId>
<configuration>
<filesets>
<fileset>
<directory>${project.parent.basedir}/bundles/dynamic</directory>
<includes>
<include>${project.build.finalName}.jar</include>
</includes>
<followSymlinks>false</followSymlinks>
</fileset>
</filesets>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<executions>
<execution>
<id>copy</id>
<phase>install</phase>
<goals>
<goal>copy</goal>
</goals>
<configuration>
<artifactItems>
<artifactItem>
<groupId>${project.groupId}</groupId>
<artifactId>${project.artifactId}</artifactId>
<version>${project.version}</version>
</artifactItem>
</artifactItems>
<outputDirectory>${project.parent.basedir}/bundles/dynamic</outputDirectory>
<overWriteReleases>true</overWriteReleases>
<overWriteSnapshots>true</overWriteSnapshots>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.felix</groupId>
<artifactId>maven-bundle-plugin</artifactId>
<extensions>true</extensions>
<configuration>
<instructions>
<Bundle-SymbolicName>${project.artifactId}</Bundle-SymbolicName>
<Import-Package>*</Import-Package>
<Export-Package/>
<Service-Component>*</Service-Component>
<Bundle-Description>${bundleDescription}</Bundle-Description>
</instructions>
</configuration>
</plugin>
<plugin>
<groupId>org.lorainelab.igb</groupId>
<artifactId>bundle-markdown-encoder</artifactId>
<executions>
<execution>
<goals>
<goal>encodeMarkdown</goal>
</goals>
</execution>
</executions>
<configuration>
<manifestFile>${project.build.outputDirectory}/META-INF/MANIFEST.MF</manifestFile>
</configuration>
</plugin>
</plugins>
</build>
</project>
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Parent Tag
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<parent> <groupId>com.affymetrix</groupId> <artifactId>igb-project</artifactId> <version>8.6.0</version> <relativePath>../../pom.xml</relativePath> </parent> |
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<packaging>bundle</packaging> |
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We are using packaging type of "bundle" to take advantage of the plug-able architecture of Maven itself and the custom packaging type which is defined in the Apache Felix Maven Bundle Plugin. Throughout the IGB project we use this maven plugin to generate all of the OSGi meta-data which makes the jar file into a module that can be managed in the IGB OSGi runtime.
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| Code Block | ||
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<dependency> <groupId>biz.aQute.bnd</groupId> <artifactId>bndlib</artifactId> <scope>provided</scope> </dependency> |
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com.affymetrix:genometry
Contains data models and utility methods used throughout the project. When the user right-clicks a item to select it, the Web Links module obtains a reference to the selected data model and uses it to create linkouts to external resources. The genometry module defines these data models and their interfaces.
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| Code Block | ||
|---|---|---|
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<dependency>
<groupId>com.affymetrix</groupId>
<artifactId>igb-services</artifactId>
<scope>provided</scope>
</dependency> |
com.affymetrix:igbSwingExt
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| Code Block | ||
|---|---|---|
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<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
<scope>provided</scope>
</dependency> |
org.lorainelab.igb:context-menu-api
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| Code Block | ||
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<dependency> <groupId>org.lorainelab.igb</groupId> <artifactId>context-menu-api</artifactId> <scope>provided</scope> </dependency> |
Build and plugins section
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Note that this design facilitates moving IGB from using Swing to JavaFX, a newer GUI toolkit that is replacing Swing in Java applications. framework handles the work of creating
IgbMenuItemProvider
This interface, defined in the IGB Services module, is designed to allow module developers to hook into the applications main toolbar.
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public interface IgbMenuItemProvider {
public String getParentMenuName();
public JRPMenuItem getMenuItem();
public int getMenuItemWeight();
} |
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