Progress:

• Initially I was trying to check how the app functions when we install it in IGB.
• When I tried to install the app, nothing was changing in the "VIEW" menu of IGB as written in the code.
• I realized that the bundle activator tag and everything in the POM is changed multiple times in order make it a standalone repo.
• Then as per the discussion, in order to remove activate method and to use @component annotation, I uncommented the @component line which was already there.
• After that I started checking previous commits.
• The TranscriptIsoform app code initially was using "IgbMenuItemProvider". At that time the code had @activate method as well as @component annotation.(I don't know if that was in a working state as IgbMenuItemProvider is not longer supported and I was unable to build that code.)
  https://bitbucket.org/pkulka10/developmentplugins/commits/e2b1c688e48d5e40e1e8e8665791605fcc2a4ed5#chg-TranscriptIsoform/src/main/java/com/gene/transcriptisoform/TranscriptIsoFormMenuProvider.java
• Later it was changed to implement "MenuBarEntryProvider" in following commit:
  https://bitbucket.org/pkulka10/developmentplugins/commits/f74e0b2065ae033950cdbffbf46e1d32749f255d
• After above commit, the component part was commented and the activate method along with Optional<List<MenuItem>> getMenuItems() method from "MenuBarEntryProvider" was used to display menuItem with submenu items (menu items which appear after the app installation) in order to introduce app's functionality. Optional<List<MenuItem>> getMenuItems() is just written but the code inside it is commented and is not affecting the IGB Menu manipulation.
• To remove activate method I will have to use Optional<List<MenuItem>> getMenuItems() method properly like other available apps to add a Menu Item dynamically in IGB.
• Then I checked the IGB code as well as other available app's code to make sure if any code uses IGB MenuBarEntryProvider methods to load the menu items with submenu dynamically.
• I found that the repos which I had referred only adds one menu item and not a menu with submenu.
• I tried a few ways to add submenu items using MenuBarEntryProvider but I am not sure how the function given below works:
  MenuItem(String menuLabel, Set<MenuItem> subMenuItems)
  as this should be used to add submenu items in IGB menu item.
• I passed a Set of MenuItems to create submenu but the submenu is not getting rendered on the screen. Only one menuItem without submenu is being displayed even after doing so.
• Also, I wanted to mention that if we are using MenuBarEntryProvider to add submenu dynamically then we don't have enough options to add different type of submenu. The submenu item types which are needed: normal menuItem(available), CheckBoxMenuItem(available) and a group of radioButtonMenuItems(unavailable).
  I have assigned available/unavailable tag next to the types which are provide/not provided in "org.lorainelab.igb.menu.api.model" package.

Prof. [~aloraine], please correct me if I am wrong.
I have tried a few ways to add submenu but I am a bit confused about things mentioned below:

• When we create a set of MenuItem to add as a submenu and when it is passed to a function MenuItem(String menuLabel, Set<MenuItem> subMenuItems) of MenuItem, this Set is assigned to a private "subMenuItems" property of the class and in order to add to to the actual menu in IGB it should be accessed with the help of Set<MenuItem> getSubMenuItems() function of the class.
  -When I tried searching for the call to "getSubMenuItems" function mentioned above in the IGB codebase, I only found it in the "SeqMapView" class file which is used to add submenu items in the "popup menu" which I think is called upon the selection of Syms. In that code it iterates over the list Set of MenuItems receives with the help of Set<MenuItem> getSubMenuItems() function of MenuItem class.
• According to me, there should be a code in IGB which is triggered when we add the new MenuItem in IGB Menu which iterates over the list Set of MenuItems receives with the help of Set<MenuItem> getSubMenuItems() function of MenuItem class as well. I couldn't find a piece of code which manipulates IGB menu by calling "getSubMenuItems" Set which provides a list of MenuItems that should be added in submenu.
• We might need to change a few things on IGB side for that.
  Also, I referred the plugins which are available in IGB code as well as the apps which are available and found that no other app is trying to add a submenu in IGB dynamically.
  Dr. Loraine, if you know any old app which tries to add menu with a submenu in IGB at run time then please let me know the name of that app.
  It would be great if you could suggest something in this situation.

• To check out the difference between (1) IgbMenuItemProvider and (2) MenuBarEntryProvider refer:
  (1) https://bitbucket.org/lorainelab/integrated-genome-browser/src/igb_8_4/core/igb-services-api/src/main/java/com/lorainelab/igb/services/window/menus/IgbMenuItemProvider.java
  (2) https://bitbucket.org/lorainelab/integrated-genome-browser/src/igb-9.0.0-pre-rollback/core/menu-api/src/main/java/org/lorainelab/igb/menu/api/MenuBarEntryProvider.java

• Also, I was working on IGB 8.2 to check the functionality of the older version of this app.
• I checked out to "igb_8_2" branch, then I changed a few things in the pom to make the plugin work. The old plugin had packaging type JAR.
• I changed it to bundle in order to generate repository.xml
• POM changes:

  <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>8.2</version>
          <relativePath>../../pom.xml</relativePath>
      </parent>
  
      <groupId>com.affymetrix</groupId>
      <artifactId>transcriptIsoForm</artifactId>
      <version>0.0.1</version>
      
      <packaging>bundle</packaging>
  
      <name>transcriptIsoForm</name>
      
      <dependencies>        
          <dependency>
              <groupId>org.apache.felix</groupId>
              <artifactId>org.apache.felix.main</artifactId>
              <scope>provided</scope>
          </dependency>    
          <dependency>
              <groupId>com.affymetrix</groupId>
              <artifactId>igb</artifactId>
              <scope>provided</scope>
          </dependency>
          <dependency>
              <groupId>net.sf</groupId>
              <artifactId>sam-ext</artifactId>
              <scope>provided</scope>
          </dependency>
          <dependency>
              <groupId>com.affymetrix</groupId>
              <artifactId>genoviz</artifactId>
              <scope>provided</scope>
          </dependency>
          <dependency>
              <groupId>com.affymetrix</groupId>
              <artifactId>igb-service</artifactId>
              <scope>provided</scope>
          </dependency>
          <dependency>
              <groupId>com.affymetrix</groupId>
              <artifactId>igbSwingExt</artifactId>
              <scope>provided</scope>
          </dependency>
          <dependency>
              <groupId>net.sf</groupId>
              <artifactId>igb-picard</artifactId>
              <scope>provided</scope>
          </dependency>
          <dependency>
              <groupId>com.affymetrix</groupId>
              <artifactId>genometryImpl</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>
                      <execution>
                          <id>build obr plugin repository</id>
                          <goals>
                              <goal>
                                  bundle
                              </goal>                     
                          </goals>
  			<configuration>
                              <instructions>
  				<Include-Resource>${project.build.directory}/repository.xml, {maven-resources}</Include-Resource>
                              </instructions>
                          </configuration>
                      </execution>
                  </executions>
                  <configuration>
                      <instructions>
                          <Bundle-SymbolicName>${project.artifactId}</Bundle-SymbolicName>
                          <Export-Package/>
                          <Bundle-Activator>com.gene.transcriptisoform.Activator</Bundle-Activator>
                          <Bundle-ActivationPolicy>lazy</Bundle-ActivationPolicy>
                          <Bundle-Description>${bundleDescription}</Bundle-Description>
                          <Service-Component>*</Service-Component>
                      </instructions>
                  </configuration>
              </plugin>
              
              <plugin>
                  <groupId>org.lorainelab</groupId>
                  <artifactId>bundle-markdown-encoder</artifactId>
                  <version>1.0.0</version>
                  <executions>
                      <execution>
                          <goals>
                              <goal>encodeMarkdown</goal>
                          </goals>
                      </execution> 
                  </executions>
              </plugin>                
          </plugins>
      </build>
  </project>
  

• The plugin was installed successfully after making these changes. Attaching a screenshot of the menu to the ticket for future reference.
• Then as discussed, I tried to figure out the functionality of the app by selecting RefSeq track. I thought a graph will be shown but nothing appeared on the screen. Even when I changed the brightness and thickness options from the "View" menu.
• The older code is using Activator class and for displaying menu with submenus it is using "com.affymetrix.genoviz.swing.AMenuItem".

Progress:

• I tried to replicate the old functionality by pasting "Activator" class in the old code directly to the newer one just to make sure the menu is getting rendered properly.
• Then I changed small sections of it, to make it like the newer one by removing ServiceRegistrar and with the reference of NCBIPrimer older and newer version as event NCBI app used to have an "Activator" class.
• I am still facing a few issues with it which I am going to work on today.

Progress:

• I am able to add the submenu and submenu to the submenus.
• We have also added the actionListeners to these menu items today.
• We are not sure how these options work.
  Prof. [~aloraine], do you have any idea about it?
  I have shared the IGB 8.2 code with you just now which has a working old version of the app inside developmentPlugins directory.
  Could you please install it and let us know what exactly those submenu items do?
  It would be great if you mention the steps to check the functionality.
  cc: Shamika Gajanan Kulkarni

Thanks for the zip file! It was fun to run an older version of IGB.

Workflow to demo Transcript Isoform App

• Open Arabidopsis thaliana genome
• Under Data Access panel, open an RNA-Seq data set. For examle, if you are running this older version of IGB, open Pollen > RNA-Seq > SM > Reads > Pollen, Alignments.
• Zoom in on a gene that has some introns. Click Load Data to load some read alignments into the browser. If you are using this older version of IGB, use the Advanced Search tab Keyword Search to find genes that have "pollen" in the description. This will ensure you find some genes that are actually expressed in pollen.
• Select a reference track: Choose View > Transcript Isoform > Select Reference Tiers.
• What should happen next is that a "chevron" (looks like a "v") should appear above introns in the reference tier wherever there are "gapped" reads that span the intron.

This chevron graphic is meant to visually summarize the number of read alignments that support each intron shown in the reference tier.

Question:

• How did you get Jira to insert the pom.xml code?

See attached image for Transcript Isoform running in IGB 8.2.0.

Pro. [~aloraine]
To insert POM I enclosed the code inside
{code:xml}<insert you code here>{code}

I thought it would be convenient to check the code in the comment that way as it is shown in a different window which preserved the formatting.
Like xml there are different tags which we can use which can be explored using the link present below:
https://confluence.atlassian.com/doc/code-block-macro-139390.html

Changes are present at:
https://bitbucket.org/pkulka10/experimental-apps-for-igb/commits/51a3f4f09268f72eaf395f9ff36b9bff16cc8171

Please follow the steps "Workflow to demo Transcript Isoform App" as mentioned in the previous comment.
Also, I was trying to run it one last time with latest master's mac installer using the same workflow but IGB's quickload was throwing some exception which is attached as an image to the ticket.
I think it is happening because of large amount of data.

Yes, the user may need to zoom in to a region and only then select the reference tier. This is obviously not the best design. We will need to better understand how to throttle loading of the alignments.

However, it looks like you have got it working - a good first draft.

Can you do this one next - after the PR is merged?

https://jira.transvar.org/browse/IGBF-2373

Sure. I will do that asap

PR submitted.
code changes can be found at:
https://bitbucket.org/lorainelab/experimental-apps-for-igb/pull-requests/12/igbf-2123-refactor-transcriptisoform-app/diff

PR merged.

• commit: IGBF-2123 : Refactor TranscriptIsoform App

is now on master branch.

cc: Prutha Kulkarni

Note this cannot be tested until the bitbucket pipelines are configured properly at the team repository at https://bitbucket.org/lorainelab/transcriptisoform. Hence IGBF-2373 is a blocker for testing.

Tested on the latest dev version of IGB on macOS.

• The expected behavior described in this comment occurs.
• Toggling between the View > Transcript Isoform > Show density options results in visually different 'chevrons' in the intergenic reference tiers. I am not sure of the significance of these differences or what they are expected to be, but the functionality of the app from the new repo seems to resemble that of the same app from the experimental apps repo.
• I noticed that the build at the new repo fails, but since IGBF-2373 has been resolved, it may be good to try the build again.
• Some intergenic regions have multiple overlapping 'chevrons' on the reference tiers. Is this expected? I have attached a screenshot (overlapping_chevrons.png) - the same behavior seems to be present when running the app from the experimental repo.

The app seems to be functioning as expected. Moving to done.