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  1. Jalview
  2. JAL-1601

Migrate the JABA 2 JPred client to directly call JPred as a REST service

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      Description

      The new style JPred consensus annotation is based on the JABA Jpred service. The client code needs to be refactored to:
      1. call the JPred server directly.
      2. also support per-sequence JPred prediction runs.

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          Improvement - An improvement or enhancement to an existing feature or task. JAL-1379 JABA 2 Jpred client

          • Major - Major loss of function.
          • Closed
          related with

          Improvement - An improvement or enhancement to an existing feature or task. JAL-1391 extend per-sequence JWS2 annotator to support selected range on visible sequence annotation

          • Major - Major loss of function.
          • Open

          Improvement - An improvement or enhancement to an existing feature or task. JAL-2103 Allow access to full alignment from JPred4 sequence profile search

          • Critical - Crashes, loss of data, severe memory leak.
          • In Progress
          mentioned on

          GitLab Commit - JAL-1601 Add jslibs for hmmer and jpred

          GitLab Commit - JAL-1601 Add sec str pred provider and client interfaces

          GitLab Commit - JAL-1601 Change getSubJobs return type

          GitLab Commit - JAL-1601 Create action and task for sec. str. pred. jobs

          GitLab Commit - JAL-1601 Create alignment copying method in AlignmentUtils

          GitLab Commit - JAL-1601 Create SecStructPredTask class

          GitLab Commit - JAL-1601 Expand secondary structure prediction tests

          GitLab Commit - JAL-1601 Fix broken Alignment Annotation test

          GitLab Commit - JAL-1601 fix phmmer client js library

          GitLab Commit - JAL-1601 Implement JPred4 client and discoverer

          GitLab Commit - JAL-1601 Implement JPred4 WS client and discoverer

          GitLab Commit - JAL-1601 Implement sec str pred for single sequences

          GitLab Commit - JAL-1601 Load and display JPred4 service in AlignFrame

          GitLab Commit - JAL-1601 Move job class as inner task class

          GitLab Commit - JAL-1601 Patch JPred4 service tests.

          GitLab Commit - JAL-1601 Propagate hidden columns to the output alignment

          GitLab Commit - JAL-1601 Propagate representative sequence to the final output alignment

          GitLab Commit - JAL-1601 Rename task class to SecStructPredMsaTask

          GitLab Commit - JAL-1601 Reuse existing "getNonEmptySequenceSet" method

          GitLab Commit - JAL-1601 Set job status to server error if collecting results throws an uncaught exception

          GitLab Commit - JAL-1601 Test alignment submitted to service

          GitLab Commit - JAL-1601 Test getVisibleCongigMapFor

          GitLab Commit - JAL-1601 Update javadoc of getAlignmentAndHiddenColumns

          GitLab Commit - Merge branch 'bug/JAL-4313-make-visible-annot-fix' into JAL-1601-direct-jpred4-rest-service

          GitLab Commit - Merge branch 'bug/JAL-4313-make-visible-annot-fix' into JAL-1601-direct-jpred4-rest-service

          GitLab Commit - Merge branch 'JAL-1601-direct-jpred4' into 'development/Release_2_12'

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              Assignee:
              mmwarowny Mateusz Warowny
              Reporter:
              jprocter James Procter
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                Dates

                Created:
                Updated: