The goal of this quickstart is to introduce you to the the context menu api, so you will be able to add context menu extensions in your IGB Apps.

Getting Started

Clone the quickstart project
- git clone https://bitbucket.org/lorainelab/context-menu-api-quickstart.git

What is a context menu?

Info

title	Wikipedia

"A context menu (also called contextual, shortcut, and popup or pop-up menu) is a menu in a graphical user interface (GUI) that appears upon user interaction, such as a right-click mouse operation. A context menu offers a limited set of choices that are available in the current state, or context, of the operating system or application. Usually the available choices are actions related to the selected object."

Example Context Menu on OS X 10.9

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IGB Context Menu

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Context Menu API Overview

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Interface

Code Block

theme	Midnight

package org.lorainelab.igb.context.menu.menu.api;

import java.util.List;
import java.util.Optional;
import org.lorainelab.igb.contextmenu.menuapi.model.AnnotationContextEvent;
import org.lorainelab.igb.contextmenu.menuapi.model.ContextMenuItem;

/**
 *
 * @author dcnorris
 */
public interface AnnotationContextMenuProvider {public interface AnnotationContextMenuProvider {
   
    public Optional<ContextMenuItem>Optional<List<ContextMenuItem>> buildMenuItem(AnnotationContextEvent event);
    public MenuSection getMenuSection();
}}

Data Model

AnnotationContextEvent

Code Block

theme	Midnight

package org.lorainelab.igb.contextmenu.menuapi.model;
import com.affymetrix.genometry.symmetry.impl.SeqSymmetry;
import java.util.List;
/**
 *
 * @author dcnorris
 */
public class AnnotationContextEvent {
    private final List<SeqSymmetry> selectedItems;
    public AnnotationContextEvent(List<SeqSymmetry> selectedItems) {
        this.selectedItems = selectedItems;
    }

    public List<SeqSymmetry> getSelectedItems() {
        return selectedItems;
    }
}

ContextMenuItem

Code Block

theme	Midnight

package org.lorainelab.igb.context.menu.api.quickstartmodel;

import aQutejava.bnd.annotation.component.Componentutil.Set;
import java.util.Optionalfunction.Function;
import org.lorainelab.igb.context.menu.AnnotationContextMenuProvider;
import org.lorainelab.igb.context.menu.MenuSection;
import org.lorainelab.igb.context.menu.model.AnnotationContextEvent;
import org.lorainelab.igb.context.menu.model.ContextMenuItem;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
 *
 * @author dcnorris
 */
@Component(immediate = true)
public class ContextMenuExtension implements AnnotationContextMenuProvider {
    private static final Logger logger = LoggerFactory.getLogger(ContextMenuExtension.class

public class ContextMenuItem extends MenuItem {
    private ContextMenuSection menuSection = ContextMenuSection.APP;
    public ContextMenuItem(String menuLabel, Set<MenuItem> subMenuItems) {
        super(menuLabel, subMenuItems);
    }
    public ContextMenuItem(String menuLabel, Function<Void, Void> action) {
        super(menuLabel, action);
    @Override}
    public Optional<ContextMenuItem>void buildMenuItemsetMenuSection(AnnotationContextEventContextMenuSection eventmenuSection) {
        ContextMenuItemthis.menuSection contextMenuItem = new ContextMenuItem("Log Selection ids", (Void t) -> {menuSection;
    }
    public        event.getSelectedItems().stream().map(selectedSym -> selectedSym.getID()).forEach(logger::info);
    ContextMenuSection getMenuSection() {
        return tmenuSection;
        });
        return Optional.ofNullable(contextMenuItem);
    }
    @Override
    public MenuSection getMenuSection()}
}

MenuIcon

Code Block

theme	Midnight

package org.lorainelab.igb.menu.api.model;
import com.google.common.io.BaseEncoding;
import java.io.InputStream;
import org.apache.commons.io.IOUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;


public class MenuIcon {
    private String encodedImage;
  return MenuSection.INFORMATION;
 private static  }
}

MenuIcon

Code Block

theme	Midnight

package org.lorainelab.igb.context.menu.model;
import com.google.common.io.BaseEncoding;
import java.io.InputStream;
import org.apache.commons.io.IOUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
 *
 * @author dcnorris
 */
public class MenuIconfinal Logger logger = LoggerFactory.getLogger(MenuIcon.class);
    public MenuIcon(InputStream resourceAsStream) {
        try {
    private String encodedImage;
    private static final Logger logger = LoggerFactory.getLogger(MenuIcon.class);
    public MenuIcon(InputStream resourceAsStream) {
        try {
            encodedImage encodedImage = BaseEncoding.base64().encode(IOUtils.toByteArray(resourceAsStream));
        } catch (Exception ex) {
            logger.error(ex.getMessage(), ex);
        }
    }
    public byte[] getEncodedImage() {
        return BaseEncoding.base64().decode(encodedImage);
    }
}

...

ContextMenuSection

Code Block

theme	Midnight

package org.lorainelab.igb.menu.contextapi.menumodel;
/**
 *
 * @author dcnorris
 */
public enum MenuSectionContextMenuSection {
    INFORMATION,
    SEQUENCE,
    APP,
    UI_ACTION;
}

Context Menu Sections

...

Context Menu Quickstart Code

ContextMenuExtension

Code Block

theme	Midnight

<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>
        <relativePath>../../pom.xml</relativePath>
    </parent>
    <groupId>org.lorainelab.igb</groupId>
    <artifactId>context-menu-api</artifactId>
    <packaging>bundle</packaging>
    <name>Context Menu API</name>
    
    <dependencies>package org.lorainelab.igb.context.menu.api.quickstart;

import aQute.bnd.annotation.component.Component;
import java.io.InputStream;
import java.util.Arrays;
import java.util.List;
import java.util.Optional;
import org.lorainelab.igb.menu.api.AnnotationContextMenuProvider;
import org.lorainelab.igb.menu.api.model.AnnotationContextEvent;
import org.lorainelab.igb.menu.api.model.ContextMenuItem;
import org.lorainelab.igb.menu.api.model.ContextMenuSection;
import org.lorainelab.igb.menu.api.model.MenuIcon;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

@Component(immediate = true)
public class ContextMenuExtension implements AnnotationContextMenuProvider {
    private static final Logger LOG = LoggerFactory.getLogger(ContextMenuExtension.class);
    private static final String ICONPATH = "terminal.png";
    @Override
    public Optional<List<ContextMenuItem>> buildMenuItem(AnnotationContextEvent event) {
        ContextMenuItem contextMenuItem = new ContextMenuItem("Log Selection ids", (Void t) -> {
            event.getSelectedItems().stream().map(selectedSym -> selectedSym.getID()).forEach(LOG::info);
        <dependency>
    return t;
       <groupId>biz.aQute.bnd</groupId> });
        try (InputStream resourceAsStream  <artifactId>bndlib</artifactId>= ContextMenuExtension.class.getClassLoader().getResourceAsStream(ICONPATH)) {
            <scope>provided</scope> contextMenuItem.setMenuIcon(new MenuIcon(resourceAsStream));
        </dependency>
} catch (Exception      <dependency>ex) {
            <groupId>com.affymetrix</groupId>LOG.error(ex.getMessage(), ex);
            <artifactId>genometry</artifactId>}
            <scope>provided</scope>contextMenuItem.setMenuSection(ContextMenuSection.INFORMATION);
        </dependency>  return Optional.ofNullable(Arrays.asList(contextMenuItem));
        <dependency>
  }
}

pom.xml

Code Block

theme	Midnight

<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
          <groupId>com.affymetrix</groupId>
  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>
      <artifactId>igb-services</artifactId>  <groupId>org.lorainelab.igb</groupId>
            <scope>provided</scope><artifactId>igb-project</artifactId>
        </dependency>      <version>9.0.0</version>
        <dependency></parent>
            <groupId>com.google.guava<<groupId>org.lorainelab.igb</groupId>
    <artifactId>org.lorainelab.igb.menu.api.quickstart</artifactId>
    <version>1.0.0</version>
    <artifactId>guava<<packaging>bundle</artifactId>packaging>
    <name>Context Menu       <scope>provided</scope>Extension Quickstart</name>
    
    </dependency><dependencies>
        <!--Start of logging dependencies-->
<dependency>
           <dependency>
            <groupId>org.slf4j< <groupId>biz.aQute.bnd</groupId>
            <artifactId>slf4j-api<<artifactId>bndlib</artifactId>
            <scope>provided</scope>
        </dependency>
        <!--End of logging dependencies-->
        <dependency>
            <groupId>com<groupId>org.lorainelab.affymetrix<igb</groupId>
            <artifactId>affymetrix-common<<artifactId>genometry</artifactId>
            <scope>provided</scope>
        </dependency>   
        </dependency>!--Start of logging dependencies-->
        <dependency>
            <groupId>commons-io<<groupId>org.slf4j</groupId>
            <artifactId>commons<artifactId>slf4j-io<api</artifactId>
            <scope>provided</scope>       
        </dependency>
    </dependencies>
    <build>
   <!--End of logging dependencies-->
     <plugins>
     <dependency>
       <plugin>
     <groupId>org.lorainelab.igb</groupId>
           <artifactId>maven-clean-plugin< <artifactId>org.lorainelab.igb.menu.api</artifactId>
            <<scope>provided</plugin>scope>
        </dependency>
    <plugin></dependencies>
    <build>
        <plugins>
    <groupId>org.apache.maven.plugins</groupId>
        <plugin>
        <artifactId>maven-dependency-plugin</artifactId>
            </plugin>          
            <plugin>
                <groupId>org.apache.felix</groupId>
                <artifactId>maven-bundle-plugin</artifactId>
                <extensions>true</extensions>
                <configuration><executions>
                    <instructions><execution>
                         <Bundle-SymbolicName>${project.artifactId}</Bundle-SymbolicName><id>build plugin repository</id>
                        <Import-Package>*</Import-Package><goals>
                        <Export-Package>
    <goal>
                        ${project.groupId}.context.menu,
        index
                    ${project.groupId}.context.menu.model
        </goal>                </Export-Package>       
                        <Service-Component>*</Service-Component>
goals>
                        <<phase>package</instructions>
phase>
                        </configuration><configuration>
            </plugin>    
        </plugins>
    <obrRepository>${project.build.directory}</build>
</project>

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>
                        <Bundle-Description>${bundleDescription}</Bundle-Description>
                    </instructions>
                </configuration>
            </plugin>     
            <plugin>
                <groupId>org.lorainelab</groupId>
                <artifactId>bundle-markdown-encoder</artifactId>
                <executions>
                    <execution>
                        <goals>
                            <goal>encodeMarkdown</goal>
                        </goals>
                    </execution> 
                </executions>
                <configuration>
                    <manifestFile>${project.build.outputDirectory}/META-INF/MANIFEST.MF</manifestFile>
                </configuration>
            </plugin>       
        </plugins>
    </build>
</project>

(Optional) Add README.md

Add a README.md markdown file to the root of the project for a customized APP manager display of your new app.

Example

Code Block

theme	Midnight

# Context Menu API Quickstart
A small example context menu extension that logs the ids of all selected SeqSymmetry objects

```java
package org.lorainelab.igb.context.menu.api.quickstart;
import aQute.bnd.annotation.component.Component;
import java.io.InputStream;
import java.util.Optional;
import org.lorainelab.igb.context.menu.AnnotationContextMenuProvider;
import org.lorainelab.igb.context.menu.MenuSection;
import org.lorainelab.igb.context.menu.model.AnnotationContextEvent;
import org.lorainelab.igb.context.menu.model.ContextMenuItem;
import org.lorainelab.igb.context.menu.model.MenuIcon;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
 *
 * @author dcnorris
 */
@Component(immediate = true)
public class ContextMenuExtension implements AnnotationContextMenuProvider {
    private static final Logger logger = LoggerFactory.getLogger(ContextMenuExtension.class);
    private static final String ICONPATH = "terminal.png";
    @Override
    public Optional<ContextMenuItem> buildMenuItem(AnnotationContextEvent event) {
        ContextMenuItem contextMenuItem = new ContextMenuItem("Log Selection ids", (Void t) -> {
            event.getSelectedItems().stream().map(selectedSym -> selectedSym.getID()).forEach(logger::info);
            return t;
        });
        try (InputStream resourceAsStream = ContextMenuExtension.class.getClassLoader().getResourceAsStream(ICONPATH)) {
            contextMenuItem.setMenuIcon(new MenuIcon(resourceAsStream));
        } catch (Exception ex) {
            logger.error(ex.getMessage(), ex);
        }
        return Optional.ofNullable(contextMenuItem);
    }
    @Override
    public MenuSection getMenuSection() {
        return MenuSection.INFORMATION;
    }
}
```

Building the Example

Navigate to the root of the project (e.g. the cloned repository https://bitbucket.org/lorainelab/context-menu-api-quickstart.git)
use maven to build the project

Code Block
mvn clean install

The build process will result in a new folder being added into your project directory (i.e. the target folder)
Add the target directory as a new IGB App repository
- IGB App Manger Tab -> Launch App Manager -> Manage Repositories -> Add...
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- Select and add the target directory
- Use the IGB App Manager to Install the new plugin
  - Image Added

Results

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Page tree

Versions Compared

Old Version 10

New Version Current

Key

Getting Started

What is a context menu?

Example Context Menu on OS X 10.9

Context Menu API Overview

Interface

Data Model

AnnotationContextEvent

ContextMenuItem

MenuIcon

MenuIcon

Context Menu Sections

Context Menu Quickstart Code

ContextMenuExtension

pom.xml

(Optional) Add README.md

Building the Example

Results

Page tree

Page History

Versions Compared

Old Version 10

New Version Current

Key

Getting Started

What is a context menu?

Example Context Menu on OS X 10.9

Context Menu API Overview

Interface

Data Model

AnnotationContextEvent

ContextMenuItem

MenuIcon

MenuIcon

Context Menu Sections

Context Menu Quickstart Code

ContextMenuExtension

pom.xml

(Optional) Add README.md

Building the Example

Results