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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

What is a context menu?

Info
titleWikipedia

"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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Image Removed 

Interface

Code Block
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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
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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
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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 ContextMenuItemfunction.Function;

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

MenuIcon

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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;
  checkNotNull(menuLabel);
  private static final Logger logger = checkState(!Strings.isNullOrEmpty(menuLabel)LoggerFactory.getLogger(MenuIcon.class);
    public MenuIcon(InputStream   checkNotNull(action);resourceAsStream) {
        this.menuLabel = menuLabel;
    try {
    this.action = action;
        subMenuItemsencodedImage = ImmutableSet.of()BaseEncoding.base64().encode(IOUtils.toByteArray(resourceAsStream));
    }
    public} Stringcatch getMenuLabel(Exception ex) {
        return menuLabel;
    }
    public Function<Void, Void> getAction() {logger.error(ex.getMessage(), ex);
        return action;}
    }
    public Set<ContextMenuItem>byte[] getSubMenuItemsgetEncodedImage() {
        return subMenuItemsBaseEncoding.base64().decode(encodedImage);
    }
}
    public void setWeight(int weight)

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

public enum ContextMenuSection {
    INFORMATION,
    this.weight = weight;SEQUENCE,
    }APP,
    public void setMenuIcon(MenuIcon menuIcon) {
        this.menuIcon = menuIcon;
    }
    public Optional<MenuIcon> getMenuIcon() {
        return Optional.ofNullable(menuIcon);
    }
}

MenuIcon

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package org.lorainelab.igb.context.menu.model;
import com.google.common.io.BaseEncoding;
import java.io.InputStreamUI_ACTION;
}

Context Menu Sections

Image Added

Context Menu Quickstart Code

ContextMenuExtension

Code Block
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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.apachelorainelab.commonsigb.io.IOUtils;
import org.slf4j.Loggermenu.api.model.ContextMenuItem;
import org.slf4j.LoggerFactory;
/**
 *
 * @author dcnorris
 */
public class MenuIcon {
    private String encodedImage;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 loggerLOG = LoggerFactory.getLogger(MenuIconContextMenuExtension.class);
    private static final publicString MenuIcon(InputStream resourceAsStream) {ICONPATH = "terminal.png";
    @Override
    trypublic {
Optional<List<ContextMenuItem>> buildMenuItem(AnnotationContextEvent event) {
        ContextMenuItem encodedImagecontextMenuItem = new BaseEncoding.base64().encode(IOUtils.toByteArray(resourceAsStream));
        } catch (Exception ex)ContextMenuItem("Log Selection ids", (Void t) -> {
            loggerevent.errorgetSelectedItems(ex).getMessagestream(), ex);
   .map(selectedSym -> selectedSym.getID()).forEach(LOG::info);
         }
   return }t;
      public byte[] getEncodedImage() {
});
        try (InputStream resourceAsStream return= BaseEncodingContextMenuExtension.class.base64getClassLoader().decodegetResourceAsStream(encodedImageICONPATH)); {
      }
}

MenuSection

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package org.lorainelab.igb.context.menu;
/**
 *
 * @author dcnorris
 */
public enum MenuSection      contextMenuItem.setMenuIcon(new MenuIcon(resourceAsStream));
        } catch (Exception ex) {
    INFORMATION, SEQUENCE, APP, UI_ACTION;
}

Context Menu Sections

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Conext Menu Quickstart Code

ContextMenuExtension

Code Block
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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) -> {
          LOG.error(ex.getMessage(), ex);
        }
        contextMenuItem.setMenuSection(ContextMenuSection.INFORMATION);
        return Optional.ofNullable(Arrays.asList(contextMenuItem));
    }
}

pom.xml

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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>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>
         event.getSelectedItems().stream().map(selectedSym -> selectedSym.getID()).forEach(logger::info);
<dependency>
            <groupId>biz.aQute.bnd</groupId>
   return t;
        });<artifactId>bndlib</artifactId>
        try  (InputStream resourceAsStream = ContextMenuExtension.class.getClassLoader().getResourceAsStream(ICONPATH)) {
  <scope>provided</scope>
        </dependency>
       contextMenuItem.setMenuIcon(new MenuIcon(resourceAsStream)); <dependency>
        } catch (Exception ex) { <groupId>org.lorainelab.igb</groupId>
            logger.error(ex.getMessage(), ex);
<artifactId>genometry</artifactId>
            }<scope>provided</scope>
        </dependency> return Optional.ofNullable(contextMenuItem);

       }
 <!--Start of logging @Overridedependencies-->
    public  MenuSection getMenuSection() {<dependency>
        return MenuSection.INFORMATION;
    }
}

pom.xml

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<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
<groupId>org.slf4j</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>  <artifactId>slf4j-api</artifactId>
    <parent>
        <groupId>com.affymetrix<<scope>provided</groupId>scope>
        <artifactId>igb-project<</artifactId>dependency>
        <version>9.0.0</version>
<!--End of logging dependencies-->
          <relativePath>../../pom.xml</relativePath><dependency>
    </parent>
        <groupId>org.lorainelab.igb</groupId>
    <artifactId>context-menu-        <artifactId>org.lorainelab.igb.menu.api</artifactId>
      <packaging>bundle</packaging>
    <name>Context Menu API<<scope>provided</name>scope>
    
    <dependencies></dependency>
    </dependencies>
    <dependency><build>
        <plugins>
    <groupId>biz.aQute.bnd</groupId>
        <plugin>
    <artifactId>bndlib</artifactId>
            <scope>provided</scope><groupId>org.apache.felix</groupId>
        </dependency>
         <dependency><artifactId>maven-bundle-plugin</artifactId>
            <groupId>com.affymetrix</groupId>
    <extensions>true</extensions>
        <artifactId>genometry</artifactId>
        <executions>
    <scope>provided</scope>
        </dependency>  
      <execution>
  <dependency>
            <groupId>com.affymetrix</groupId>
          <id>build plugin <artifactId>igb-services<repository</artifactId>id>
            <scope>provided</scope>
        </dependency>    <goals>
    
        <dependency>
            <groupId>com.google.guava</groupId>
    <goal>
        <artifactId>guava</artifactId>
             <scope>provided</scope>
        </dependency>
   index
     <!--Start of logging dependencies-->
        <dependency>
            <groupId>org.slf4j</groupId>
</goal>            <artifactId>slf4j-api</artifactId>
            <scope>provided</scope>
        </dependency>
        <!--End of logging dependencies-->
        <dependency></goals>
            <groupId>com.affymetrix</groupId>
            <artifactId>affymetrix-common<<phase>package</artifactId>phase>
             <scope>provided</scope>           <configuration>
        </dependency>
        <dependency>
            <groupId>commons-io</groupId>
<obrRepository>${project.build.directory}</obrRepository>    
        <artifactId>commons-io</artifactId>
             <scope>provided</scope>       
<mavenRepository>${project.build.directory}</mavenRepository>          </dependency>
    </dependencies>
    <build>
    
    <plugins>
            <plugin>
        </configuration>
        <artifactId>maven-clean-plugin</artifactId>
            </plugin>execution>
             <plugin>   </executions>
                <groupId>org.apache.maven.plugins</groupId>
<configuration>
                 <artifactId>maven-dependency-plugin</artifactId>
   <instructions>
         </plugin>          
    <Bundle-SymbolicName>${project.artifactId}</Bundle-SymbolicName>
        <plugin>
                <groupId>org.apache.felix</groupId><Import-Package>*</Import-Package>
                <artifactId>maven-bundle-plugin</artifactId>
        <Export-Package/>
                 <extensions>true</extensions>
       <Service-Component>*</Service-Component>
                        <configuration><Bundle-Description>${bundleDescription}</Bundle-Description>
                    <instructions></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
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# 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       <Bundle-SymbolicName>${project.artifactId}</Bundle-SymbolicName>
                        <Import-Package>*</Import-Package>
                        <Export-Package>
               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) -> {
             ${project.groupId}.context.menu,
    event.getSelectedItems().stream().map(selectedSym -> selectedSym.getID()).forEach(logger::info);
                return t;
        ${project.groupId}.context.menu.model});
        try (InputStream resourceAsStream              </Export-Package>
     = ContextMenuExtension.class.getClassLoader().getResourceAsStream(ICONPATH)) {
            contextMenuItem.setMenuIcon(new MenuIcon(resourceAsStream));
      <Service-Component>*</Service-Component>
  } catch (Exception ex) {
            logger.error(ex.getMessage(),  </instructions>
ex);
        }
         </configuration>
return Optional.ofNullable(contextMenuItem);
    }
    @Override
    public </plugin>  MenuSection getMenuSection() {
        </plugins>return MenuSection.INFORMATION;
    </build>
</project>}
}
```

 

Building the Example

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