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Aug 25, 2013

  1. remove 'our method' syntax, which breaks JVM tests; Range.t passes

    authored August 24, 2013

Sep 04, 2012

  1. some last minute clenaup

    authored September 03, 2012
  2. various fixes to Ranges including some test brainos; now passing Rang…

    …e tests
    authored September 03, 2012
  3. commenting out all passing tests and focusing on the crapped out ones…

    …, whittled down to 26 failing
    authored September 03, 2012
  4. get range tests running again (even if they fail)

    authored September 03, 2012

Apr 13, 2012

  1. get Range compiling again with rakudo

    authored April 12, 2012

Apr 15, 2011

  1. Philip Mabon

    Action and Grammar now only parse one fasta record at a time instead …

    …of multiple. Allows for 'lazy' grammars. Cleaned up FastaIO and SeqIO abit to reflect the new changes with using Role::IO.pm role however still needs a redesign
    authored April 14, 2011

Apr 07, 2011

  1. Philip Mabon

    implemented is_valid method in TypeManager. No test for it

    authored April 06, 2011

Apr 06, 2011

  1. Philip Mabon

    Implemented as_text, target_id and display_text.

    authored April 06, 2011
  2. Philip Mabon

    Implemented hash_tree and get_values. Added more tests.

    authored April 06, 2011
  3. Philip Mabon

    Implemented and added test for hash_tree,comment and url

    authored April 06, 2011
  4. Philip Mabon

    Implemented hash_tree and display_text methods . Implemented and adde…

    …d tests for the following private attribute getter/setter methods : end,rp,rg,publisher,editors,encoded_ref,doi,consortium and gb_reference
    authored April 06, 2011
  5. Philip Mabon

    implemented hash_tree and added a test

    authored April 06, 2011
  6. Philip Mabon

    Added test for every method in Comment.pm . Removed old p5 code for n…

    …ew method. Implemented hash_tree , type and alias method for text attribute
    authored April 05, 2011
  7. Philip Mabon

    Initial implementation of OntologyTerm and AnnotationFactory. Uncomme…

    …nted more test and most are passing.
    authored April 05, 2011

Apr 04, 2011

  1. Philip Mabon

    Implemented remove_Annotation and flatten_Annotations methods. Uncomm…

    …ented p6 code in TypeManager. Made %type attribute into a public one for now in TypeManager. Passing more tests.
    authored April 04, 2011
  2. Philip Mabon

    Added attribute tagname and methods for StructuredValue.pm. Passing m…

    …ore tests
    authored April 04, 2011
  3. Philip Mabon

    implemented get_all_Annotation method. Passing more tests

    authored April 04, 2011
  4. Philip Mabon

    renamed Collects.pm to AnnotationCollectionI so we can use the role. …

    …The role is mostly just a shell so we have a common interface for Collection objects. Added attribute and method tagname to Collection.pm with also another multi method add_Annotation. Passing more tests as well.
    authored April 03, 2011
  5. Philip Mabon

    implemented get_all_values method and uncommented the test for it.

    authored April 03, 2011

Apr 03, 2011

  1. Philip Mabon

    Initial implementation of SructuredValue.pm. Only have bare bones don…

    …e at the moment. Passing more tests
    authored April 03, 2011

Apr 02, 2011

  1. Philip Mabon

    for some reason I need a newline before and after the 'use' statement…

    …s otherwise it will not compile.
    authored April 02, 2011
  2. Philip Mabon

    Changed AnnotationI so that it can be parent of other Annotation clas…

    …ses. Added Bio::AnnotationI interface to all Annotation subclasses. Added a multi method add_Annotation for Collection.pm as well. Passing more tests.
    authored April 02, 2011
  3. Philip Mabon

    Added new initial implementation of Target.pm. method get_all_annotat…

    …ion_keys is done. Added tagname method and attribute for Comment. Passing more tests and fixed some formatting of test file.
    authored April 02, 2011
  4. Philip Mabon

    deleted a closing brace on accident

    authored April 02, 2011
  5. Philip Mabon

    Added data structure to store annotation for Collection.pm. Implement…

    …ed get_Annotations method. Added tagname method and attribute for DBLink.pm. Uncommented more tests
    authored April 02, 2011

Apr 01, 2011

  1. Philip Mabon

    Made method database a multi because Reference is a sub class and nee…

    …d to override it. Initial implementation of Comment and Reference Annotation classes. Just enough to get test passing. Added more tests
    authored April 01, 2011
  2. Philip Mabon

    Added basic implementation for Collection.pm and TypeManage.pm. Added…

    … basic tests as well.
    authored April 01, 2011
  3. Philip Mabon

    initial version of Annotation::DBLink done with tests to go along

    authored April 01, 2011
  4. Philip Mabon

    Initial implementation of Annotation::SimpleValue.pm with correspondi…

    …ng test file.
    authored April 01, 2011
  5. Philip Mabon

    Now can use either 'desc' or 'description' methods to set private att…

    …ribute 'description'. Added a test.
    authored April 01, 2011
  6. Philip Mabon

    Made $!id a private attribute and created getter/setter with method n…

    …ame: id and display_id. Allowed in constructor both 'id' and 'display_id' to both initalize $!id. Same with 'desc' and 'description'
    authored April 01, 2011
  7. Philip Mabon

    Passing two more tests. Implemented initial version of guess_alphabet…

    … and created getter/setter for seq attribute
    authored April 01, 2011
  8. Philip Mabon

    Subseq can now accept Bio::Role::Location type object/role for subseq…

    … method. Fixed a bug where $min and $max would be initialized as match object and not integer. This causes issue where type constraints in method signature in Subseq. Passing the last test for PrimarySeq.t
    authored April 01, 2011
  9. Philip Mabon

    Trunc is a multi method now where it now accepts a Location object. P…

    …assing a few more test
    authored April 01, 2011
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