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Commits on Feb 16, 2017
  1. Update README.textile: New release tag v3.3.3

    groupschoof committed Feb 16, 2017
    Updated tag in "Get AHRD" instructions so people get changes of latest commits.
    Changed goa_uniprot_all file suffix from "gpa" to "gaf", because this is what the DEFAULT_REFERENCE_GO_REGEX actually matches.
    Updated the "last visit" time stamp for the UNIPROT section on the EBI FTP Server.
    Fixed Typo.
Commits on Sep 24, 2016
  1. Updated documentation to explain blacklisting and filtering when comp…

    groupschoof committed Sep 24, 2016
    …uting performance scores.
Commits on Sep 23, 2016
Commits on Sep 14, 2016
Commits on Sep 2, 2016
  1. Fixed issue #10

    asishallab committed Sep 2, 2016
    Proposed fix is not as flexible as the one implemented here.
    Problem was caused by non *nix like line breaks like '\r'.
    Now using regex (\r|\n)+ to split String into lines.
Commits on Aug 30, 2016
  1. Typo and eclipse-.gitignore

    FlorianBoecker committed Aug 30, 2016
    Fixed typo in fasta header line mismatch message
    (ahrd.model.BlastResult.parseBlastDatabase)
    
    Added eclipse specific entries to .gitignore file
    (.externalToolBuilders/ and .project)
Commits on Aug 19, 2016
  1. Merged remote README

    asishallab committed Aug 19, 2016
  2. Changed token balcklist to strict word-matching. Some tokens were dis…

    asishallab committed Aug 19, 2016
    …carded, that actually make sense.
Commits on Aug 18, 2016
  1. Implemented option to filter the reference descriptions as is done wi…

    asishallab committed Aug 18, 2016
    …th candidate descriptions of normal BlastResults. That involves: Blacklisting, Filtering, and Blacklisting of Tokens.
Commits on Aug 12, 2016
  1. Deleted symbolic link to example input file for generation of extende…

    asishallab committed Aug 12, 2016
    …d GO annotation tables.
  2. Merged remote master

    asishallab committed Aug 12, 2016
  3. Removing option to generate extended GO Annotation tables

    asishallab committed Aug 12, 2016
    It was buggy. At least using the default EBI Gene-Ontology MySQL instance.
    The problem was that queries did not accept all Terms submitted (if too many)
    and then did not return parent terms for all original queries. Hence we deprecate
    this function. Possibly works with local installations. But better would be
    to use the OBO OWL files with adequate Java libraries to parse these.
Commits on Jul 28, 2016
  1. Merge pull request #8 from wmnwmn/master

    groupschoof committed Jul 28, 2016
    Remove several special chars from comments which prevented building b…
Commits on Jul 22, 2016
  1. Remove several special chars from comments which prevented building b…

    Will Nelson
    Will Nelson committed Jul 22, 2016
    …y ant on
    
    my platform (issue#6). in BlastResult the chars printed as "..." for function arguments.
    In EvaluationScoreCalculator they were exponents "2" and I changed them to "^2".
Commits on Jul 17, 2016
  1. Fixed bug when trying to select GO Term Parents of deprecated or non …

    asishallab committed Jul 17, 2016
    …existing GO Term Accessions.
Commits on Jul 16, 2016
Commits on Jul 14, 2016
  1. Corrected link in TOC to chapter about new param

    groupschoof committed Jul 14, 2016
    The parameter is "prefer_reference_with_go_annos"
  2. Merge pull request #7 from asishallab/patch-3

    groupschoof committed Jul 14, 2016
    Added documentation about the NEW parameter prefer_reference_with_go_…
  3. Started implementing new AHRD function to preferably use candidate re…

    asishallab committed Jul 14, 2016
    …ferences with GO Term Annotations
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