[Saint-annotate-user] SF.net SVN: saint-annotate:[10] trunk

[<all...@us...>]

Revision: 10
          http://saint-annotate.svn.sourceforge.net/saint-annotate/?rev=10&view=rev
Author:   allysonlister
Date:     2009-07-23 14:59:08 +0000 (Thu, 23 Jul 2009)

Log Message:
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UniProtRecord now has a method for displaying just the description and not the description + accession. The ResultsRecord.mergeRecords() method now merges EntityTypes properly. Saint will now wuery using a stored UniProt accession that is already present in the model as well as with id/name. This will need to be updated shortly to store more than one UniProt accession. Added the ability to choose from the recommended name as well as the gene name for your species name. Can now search on all gene annotations rather than just the name. Now displays the submitted name for the UniProt URIs if the recommended name is not present. Will search additionally within the protein name if there were no uniprot hits at all on the gene annotations. performs simple query string parsing if there were no results at all (removal of final I and A, and tokenising on "_").

Modified Paths:
--------------
    trunk/pom.xml
    trunk/saint.iws
    trunk/src/main/java/uk/ac/cisban/saint/client/AnnotationDetail.java
    trunk/src/main/java/uk/ac/cisban/saint/client/Annotator.java
    trunk/src/main/java/uk/ac/cisban/saint/client/MasterQueryService.java
    trunk/src/main/java/uk/ac/cisban/saint/client/MasterQueryServiceAsync.java
    trunk/src/main/java/uk/ac/cisban/saint/client/structure/ResultsRecord.java
    trunk/src/main/java/uk/ac/cisban/saint/client/structure/SbmlAnnotGroup.java
    trunk/src/main/java/uk/ac/cisban/saint/client/structure/records/UniprotRecord.java
    trunk/src/main/java/uk/ac/cisban/saint/parsing/sbml/SbmlManipulator.java
    trunk/src/main/java/uk/ac/cisban/saint/parsing/uniprot/UniProtHelper.java
    trunk/src/main/java/uk/ac/cisban/saint/querying/uniprot/UniProtQuerier.java
    trunk/src/main/java/uk/ac/cisban/saint/server/MasterQueryServiceImpl.java
    trunk/src/test/java/uk/ac/cisban/saint/server/SaintUniProtQueryServiceImplTest.java

Added Paths:
-----------
    trunk/src/main/java/uk/ac/cisban/saint/parsing/QueryParser.java
    trunk/src/test/java/uk/ac/cisban/saint/client/structure/ResultsRecordTest.java
    trunk/src/test/java/uk/ac/cisban/saint/parsing/QueryParserTest.java

Property Changed:
----------------
    trunk/


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