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

Image Modified

IGB Context Menu

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Context Menu API Overview

Image Added

Image Removed

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.contextmenu.menuapi.model;
import static comjava.google.common.base.Preconditions.checkNotNullutil.Set;
import static comjava.googleutil.common.base.Preconditions.checkState;
import com.google.common.base.Strings;
import com.google.common.collect.ImmutableSet;
import java.util.Optional;
import java.util.Set;
import java.util.function.Function;
/**
 *
 * @author dcnorris
 */
public class ContextMenuItem {
    private final String menuLabelfunction.Function;

public class ContextMenuItem extends MenuItem {
    private ContextMenuSection menuSection = ContextMenuSection.APP;
    public ContextMenuItem(String menuLabel, Set<MenuItem> subMenuItems) {
        super(menuLabel, subMenuItems);
    private}
 MenuIcon menuIcon;
  public ContextMenuItem(String privatemenuLabel, Function<Void, Void> action;) {
    private Set<ContextMenuItem> subMenuItems;
  super(menuLabel, action);
 private int weight = 0;}
    public void ContextMenuItemsetMenuSection(String menuLabel, Set<ContextMenuItem> subMenuItemsContextMenuSection menuSection) {
        this.menuSection = checkNotNull(menuLabel)menuSection;
    }
    checkNotNullpublic ContextMenuSection getMenuSection(subMenuItems); {
        checkState(!Strings.isNullOrEmpty(menuLabel))return menuSection;
        checkState(!subMenuItems.isEmpty());
        this.menuLabel = menuLabel;
        this.subMenuItems = ImmutableSet.copyOf(subMenuItems);
    }}
}

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;
    private static final Logger logger = LoggerFactory.getLogger(MenuIcon.class);
    public ContextMenuItemMenuIcon(String menuLabel, Function<Void, Void> actionInputStream resourceAsStream) {
        try checkNotNull(menuLabel);
  {
      checkState(!Strings.isNullOrEmpty(menuLabel));
      encodedImage  checkNotNull(action= BaseEncoding.base64().encode(IOUtils.toByteArray(resourceAsStream));
        } catch this.menuLabel = menuLabel;
(Exception ex) {
            this.action = actionlogger.error(ex.getMessage(), ex);
        subMenuItems = ImmutableSet.of();}
    }
    public Stringbyte[] getMenuLabelgetEncodedImage() {
        return menuLabelBaseEncoding.base64().decode(encodedImage);
    }
}

    public Function<Void, Void> getAction()

ContextMenuSection

Code Block

theme	Midnight

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

public enum ContextMenuSection {
    INFORMATION,
    return action;SEQUENCE,
    }APP,
    public Set<ContextMenuItem> getSubMenuItems() {
        return subMenuItems;
    }
    public void setWeight(int weight) {
        this.weight = weight;
    }
    public void setMenuIcon(MenuIcon menuIcon) {
        this.menuIcon = menuIcon;
    }
    public Optional<MenuIcon> getMenuIcon() {
        return Optional.ofNullable(menuIcon);
    }
}

MenuIcon

Code Block

theme	Midnight

packageUI_ACTION;
}

Context Menu Sections

Image Added

Context Menu Quickstart Code

ContextMenuExtension

Code Block

theme	Midnight

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.contextmenu.menuapi.model.ContextMenuSection;
import comorg.googlelorainelab.commonigb.io.BaseEncoding;
import java.io.InputStreammenu.api.model.MenuIcon;
import org.apache.commons.io.IOUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
@Component(immediate *
 * @author dcnorris
 */= true)
public class MenuIconContextMenuExtension {
implements    private String encodedImage;AnnotationContextMenuProvider {
    private static final Logger loggerLOG = LoggerFactory.getLogger(MenuIconContextMenuExtension.class);
    publicprivate MenuIcon(InputStream resourceAsStream) {
   static final String ICONPATH = "terminal.png";
     try {@Override
    public Optional<List<ContextMenuItem>> buildMenuItem(AnnotationContextEvent event) {
    encodedImage = BaseEncoding.base64().encode(IOUtils.toByteArray(resourceAsStream));
  ContextMenuItem contextMenuItem = new ContextMenuItem("Log Selection }ids", catch (ExceptionVoid ext) -> {
            loggerevent.errorgetSelectedItems(ex).getMessagestream(), ex.map(selectedSym -> selectedSym.getID()).forEach(LOG::info);
         }
   return }t;
      public byte[] getEncodedImage(}) {;
        return BaseEncoding.base64try (InputStream resourceAsStream = ContextMenuExtension.class.getClassLoader().decodegetResourceAsStream(encodedImageICONPATH));
    }
}

MenuSection

Code Block

theme	Midnight

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

Context Menu Sections

Image Removed

Context Menu Quickstart Code

ContextMenuExtension

Code Block

theme	Midnight

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) -> {
   {
            contextMenuItem.setMenuIcon(new MenuIcon(resourceAsStream));
        } catch (Exception ex) {
            LOG.error(ex.getMessage(), ex);
        }
        contextMenuItem.setMenuSection(ContextMenuSection.INFORMATION);
        return Optional.ofNullable(Arrays.asList(contextMenuItem));
    }
}

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"
         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>org.lorainelab.igb</groupId>
        <artifactId>igb-project</artifactId>
        <version>9.0.0</version>
    </parent>
    <groupId>org.lorainelab.igb</groupId>
    <artifactId>org.lorainelab.igb.menu.api.quickstart</artifactId>
    <version>1.0.0</version>
    <packaging>bundle</packaging>
    <name>Context Menu Extension Quickstart</name>
    
    <dependencies>
        <dependency>
            <groupId>biz.aQute.bnd</groupId>
            <artifactId>bndlib</artifactId>
            <scope>provided</scope>
        </dependency>
        <dependency>
          event.getSelectedItems().stream().map(selectedSym -> selectedSym.getID()).forEach(logger::info);<groupId>org.lorainelab.igb</groupId>
            return t;
<artifactId>genometry</artifactId>
            });
<scope>provided</scope>
        </dependency>  try
 (InputStream resourceAsStream = ContextMenuExtension.class.getClassLoader().getResourceAsStream(ICONPATH)) {
   <!--Start of logging dependencies-->
      contextMenuItem.setMenuIcon(new MenuIcon(resourceAsStream));  <dependency>
        } catch (Exception ex) { <groupId>org.slf4j</groupId>
            logger.error(ex.getMessage(), ex);
<artifactId>slf4j-api</artifactId>
            }<scope>provided</scope>
        return Optional.ofNullable(contextMenuItem);</dependency>
    }
    @Override
    public MenuSection getMenuSection() {
<!--End of logging dependencies-->
          <dependency>
  return MenuSection.INFORMATION;
    }
}

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>org.lorainelab.igb</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>org.lorainelab.igb.menu.api</artifactId>
            <scope>provided</scope>
        </dependency>
    </dependencies>
    <build>
        <plugins>
            <groupId>com.affymetrix</groupId><plugin>
        <artifactId>igb-project</artifactId>
        <version>9<groupId>org.0apache.0<felix</version>groupId>
        <relativePath>../../pom.xml</relativePath>        <artifactId>maven-bundle-plugin</artifactId>
    </parent>
    <groupId>org.lorainelab.igb</groupId>
    <artifactId>context-menu-api</artifactId>
    <packaging>bundle<<extensions>true</packaging>extensions>
      <name>Context Menu API</name>
    
    <dependencies><executions>
        <dependency>
            <groupId>biz.aQute.bnd</groupId>
<execution>
              <artifactId>bndlib</artifactId>
          <id>build plugin <scope>provided<repository</scope>id>
        </dependency>
        <dependency>
        <goals>
    <groupId>com.affymetrix</groupId>
            <artifactId>genometry</artifactId>
            <scope>provided</scope>
     <goal>
   </dependency>  
        <dependency>
            <groupId>com.affymetrix</groupId>
       index
     <artifactId>igb-services</artifactId>
            <scope>provided</scope>
        </dependency>   </goal>   
        <dependency>
            <groupId>com.google.guava</groupId>
            <artifactId>guava</artifactId>
            <scope>provided<</scope>goals>
           </dependency>
        <!--Start of logging dependencies-->
  <phase>package</phase>
      <dependency>
            <groupId>org.slf4j</groupId>
      <configuration>
      <artifactId>slf4j-api</artifactId>
              <scope>provided</scope>
        <obrRepository>${project.build.directory}</dependency>
obrRepository>    
     <!--End of logging dependencies-->
        <dependency>
            <groupId>com.affymetrix</groupId>
<mavenRepository>${project.build.directory}</mavenRepository>               <artifactId>affymetrix-common</artifactId>
       
     <scope>provided</scope>           
        </dependency>configuration>
        <dependency>
            <groupId>commons-io<</groupId>execution>
             <artifactId>commons-io</artifactId>
   </executions>
         <scope>provided</scope>       <configuration>
        </dependency>
    </dependencies>
    <build>
    <instructions>
    <plugins>
            <plugin>
       <Bundle-SymbolicName>${project.artifactId}</Bundle-SymbolicName>
         <artifactId>maven-clean-plugin</artifactId>
               <Import-Package>*</plugin>Import-Package>
              <plugin>
          <Export-Package/>
        <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-dependency-plugin</artifactId>
 <Service-Component>*</Service-Component>
           </plugin>          
     <Bundle-Description>${bundleDescription}</Bundle-Description>
       <plugin>
                <groupId>org.apache.felix</groupId></instructions>
                <artifactId>maven-bundle-plugin</artifactId>
</configuration>
            </plugin>     <extensions>true</extensions>
                <configuration><plugin>
                <groupId>org.lorainelab</groupId>
    <instructions>
             <artifactId>bundle-markdown-encoder</artifactId>
           <Bundle-SymbolicName>${project.artifactId}</Bundle-SymbolicName>
     <executions>
                   <Import-Package>*</Import-Package> <execution>
                        <Export-Package><goals>
                            ${project.groupId}.context.menu,<goal>encodeMarkdown</goal>
                        </goals>
      ${project.groupId}.context.menu.model
              </execution> 
         </Export-Package>
       </executions>
                 <Service-Component>*</Service-Component><configuration>
                    </instructions><manifestFile>${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.

...

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

...

Page tree

Versions Compared

Old Version 16

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

MenuSection

Context Menu Sections

Context Menu Quickstart Code

ContextMenuExtension

pom.xml

pom.xml

(Optional) Add README.md

Page tree

Page History

Versions Compared

Old Version 16

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

MenuSection

Context Menu Sections

Context Menu Quickstart Code

ContextMenuExtension

pom.xml

pom.xml

(Optional) Add README.md