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To see the directory structure for your project in NetBeans, select the Files tab (next to the Projects tab).

HelloWorld pom.xml

***Need explanation of what the app's pom.xml file is for***

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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>9.0.0</version>
    </parent>
    <groupId>org.lorainelab.igb</groupId>
    <artifactId>org.lorainelab.igb.menu.api.example</artifactId>
    <version>1.0.0</version>
    <packaging>bundle</packaging>

    <name>IGB Menubar Extension</name>
    
    <dependencies>
        <dependency>
            <groupId>biz.aQute.bnd</groupId>
            <artifactId>bndlib</artifactId>
            <scope>provided</scope>
        </dependency>
          <dependency>
            <groupId>org.lorainelab.igb</groupId>
            <artifactId>org.lorainelab.igb.menu.api</artifactId>
            <scope>provided</scope>
        </dependency>
    </dependencies>

    <build>
        <plugins>
            <plugin>
                <groupId>org.apache.felix</groupId>
                <artifactId>maven-bundle-plugin</artifactId>
                <extensions>true</extensions>
                <executions>
                    <execution>
                        <id>build plugin repository</id>
                        <goals>
                            <goal>
                                index
                            </goal>                       
                        </goals>
                        <phase>package</phase>
                        <configuration>
                            <obrRepository>${project.build.directory}</obrRepository>    
                            <mavenRepository>${project.build.directory}</mavenRepository>                      
                        </configuration>
                    </execution>
                </executions>
                <configuration>
                    <instructions>
                       <Bundle-SymbolicName>${project.artifactId}</Bundle-SymbolicName>
                        <Import-Package>*</Import-Package>
                        <Export-Package/>
                        <Service-Component>*</Service-Component>
                    </instructions>
                </configuration>
            </plugin>     
        </plugins>
    </build>
</project>

parent tag

<parent>
     <groupId>com.affymetrix</groupId>
     <artifactId>igb-project</artifactId>
     <version>8<version>9.60.0</version>
</parent>

This tag specifies packaging type - e.g., war or jar. In IGB, we use an OSGi-specific packaging structure called a "bundle," which is a jar file with additional metadata. This additional metadata transforms an ordinary jar file into a plug-able module in the OSGi runtime. The IGB project uses the Apache Felix Maven Bundle plugin (BND) to generate this metadata. The BND bundle defines the packaging type "bundle."

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<name>Hello<name>IGB Menubar World<Extension</name>

dependency tags (parent tag "dependencies")

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<dependency>
   <groupId>biz.aQute.bnd</groupId>
   <artifactId>bndlib</artifactId>
   <scope>provided</scope>
</dependency>

...

com.

...

affymetrix:

...

igb-

...

services

This module is an API module that contains most of the service interfaces which provide access (hooks) to functions in the IGB platform, such as identifying the currently selected feature or tracks.  

<dependency>
     <groupId>org  <groupId>com.slf4j<affymetrix</groupId>
    <artifactId>slf4j-api<   <artifactId>igb-services</artifactId>
       <scope>provided</scope>
</dependency> 

com.affymetrix:

...

igbSwingExt

This module is an API module that contains most of the service interfaces which provide access (hooks) to functions in the IGB platform, such as identifying the currently selected feature or tracks.  contains custom Swing components used in the IGB graphical user interface. In some cases the interfaces contained in the igb-services modules require the use of some of the custom swing components contained in this module.  We do this because we often have the need to add additional functions to basic swing components, such as the concept of "weights" for menu items to ensure that newly added menu options appear in the correct order. 

<dependency>
       <groupId>com.affymetrix</groupId>
       <artifactId>igb-services<<artifactId>igbSwingExt</artifactId>
       <scope>provided</scope>
</dependency> 

com.affymetrix:igbSwingExt

This module contains custom Swing components used in the IGB graphical user interface. In some cases the interfaces contained in the igb-services modules require the use of some of the custom swing components contained in this module.  We do this because we often have the need to add additional functions to basic swing components, such as the concept of "weights" for menu items to ensure that newly added menu options appear in the correct order. 

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...

build, plugins, and plugin tag

maven-bundle-plugin

This is the most important plugin to be aware of as an IGB module developer.  This plugin is known as the "Swiss army knife of OSGi" and is a wrapper around the BND project described in the previous section.

	<build>
        <plugins>
            <plugin>
                <groupId>org.apache.felix</groupId>
                <artifactId>maven-bundle-plugin</artifactId>
     <scope>provided</scope>
</dependency> 

build, plugins, and plugin tag

maven-bundle-plugin

This is the most important plugin to be aware of as an IGB module developer.  This plugin is known as the "Swiss army knife of OSGi" and is a wrapper around the BND project described in the previous section.

           <build><extensions>true</extensions>
        <plugins>
        <executions>
    <plugin>
                <groupId>org.apache.felix</groupId><execution>
                <artifactId>maven-bundle-plugin</artifactId>
          <id>build plugin     <extensions>true</extensions>repository</id>
                <executions>
        <goals>
            <execution>
                <goal>
        <id>build plugin repository</id>
                        <goals>index
                            <goal>
         </goal>                       index
                            </goal>goals>
                        <phase>package</phase>
                        </goals><configuration>
                          <phase>package</phase>
                        <configuration>
                            <obrRepository>${project.build.directory}</obrRepository>     
                            <mavenRepository>${project.build.directory}</mavenRepository>                       
                        </configuration>
                    </execution>
                </executions>
                <configuration>
                    <instructions>
                        <Bundle-SymbolicName>${project.artifactId}</Bundle-SymbolicName>
                        <Import-Package>*</Import-Package>
                        <Export-Package/>
                        <Service-Component>*</Service-Component>
                    </instructions>
                </configuration>
            </plugin>         
        </plugins>
    </build>

There are several important things to understand about the above configuration.

...

...

Adding a new item to the IGB Tools menu 

To demonstrate how an IGB plugin could hook into and expand the IGB toolbar, you will can write a new class that implements the IgbMenuItemProvider the MenuBarEntryProvider interface.

This interface is designed to allow App developers to add new menu items to the IGB application's top level menus.

IGB (as of this writing) has seven top-level menus, including:

The IgbMenuItemProvider The MenuBarEntryProvider interface contains the following methods, shown below. To add a new menu item to IGB, you'll create a class that implements this interface. In other words, you'll create a class that provides an IGB menu item to the OSGi run-time, which will add it to IGB as soon as it becomes available.

public interface IgbMenuItemProviderMenuBarEntryProvider {
    public IgbToolBarParentMenuOptional<List<MenuItem>> getParentMenugetMenuItems();
    	public JRPMenuItemMenuBarParentMenu getMenuItemgetMenuExtensionParent();
    public int getMenuItemWeight();
 }

package comorg.lorainelab.plugin;

import aQute.bnd.annotation.component.Component;
import com.affymetrix.igb.swing.JRPMenuItem;
import com.lorainelab.igb.services.window.menus.IgbMenuItemProvider;
import com.lorainelab.igb.services.window.menus.IgbToolBarParentMenu;
import java.awt.event.ActionEvent;
import javax.swing.AbstractAction;
import static javax.swing.Action.MNEMONIC_KEY;
import static javax.swing.Action.SHORT_DESCRIPTION;
import javax.swing.ImageIcon;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

// annotations processed by BND tool
@Component(name = IgbToolbarExtension.COMPONENT_NAME, immediate = true, provide = IgbMenuItemProvider.class)
public class IgbToolbarExtension implements IgbMenuItemProvider {
    public static final String COMPONENT_NAME = "IgbToolbarExtension";
    private static final Logger logger = LoggerFactory.getLogger(IgbToolbarExtension.class);
    private static final int MENU_ITEM_INDEX = 4;
    private final JRPMenuItem exampleMenuItem;
    public IgbToolbarExtension() {
        exampleMenuItem = new JRPMenuItem("exampleIgbToolbarMenuItem", new LogEventAction(), MENU_ITEM_INDEX);
    }

    @Override
    public JRPMenuItem getMenuItem() {
        return exampleMenuItem;
    }
 
    @Override
    public IgbToolBarParentMenu getParentMenu() {
        return IgbToolBarParentMenu.TOOLS;
    }
    @Override
    public int getMenuItemWeight() {
        return MENU_ITEM_INDEX;
    }
    private class LogEventAction extends AbstractAction {
        public LogEventAction() {
            this("Hello IGB Toolbar", null, "", null);
        }
        public LogEventAction(String text, ImageIcon icon,
                String desc, Integer mnemonicmenu.api.example;
import aQute.bnd.annotation.component.Component;
import java.util.Arrays;
import java.util.List;
import java.util.Optional;
import javax.swing.JOptionPane;
import org.lorainelab.igb.menu.api.MenuBarEntryProvider;
import org.lorainelab.igb.menu.api.model.MenuBarParentMenu;
import org.lorainelab.igb.menu.api.model.MenuItem;
@Component(immediate = true)
public class MenuBarExtensionExample implements MenuBarEntryProvider {

    @Override
    public Optional<List<MenuItem>> getMenuItems() {
        MenuItem menuItem = new super(text, icon);MenuItem("Hello World App", (Void t) -> {
            putValue(SHORT_DESCRIPTION, descJOptionPane.showMessageDialog(null, "Hello IGB World!");
            putValue(MNEMONIC_KEY, mnemonic)return t;
        }});
        @OverridemenuItem.setWeight(1000000000);
        public void actionPerformed(ActionEvent e) {return Optional.ofNullable(Arrays.asList(menuItem));
    }

    @Override
    logger.info("Hello Igb Toolbar menu item clicked");
public MenuBarParentMenu getMenuExtensionParent() {
          }return MenuBarParentMenu.TOOLS;
    }
}

@Component(name = IgbToolbarExtension.COMPONENT_NAME, immediate = true, provide = IgbMenuItemProvider.class)
public class IgbToolbarExtension implements IgbMenuItemProvider {...}