[Gmod-apollo-cmts] CVS: apollo/src/java/apollo/dataadapter/chado/jdbc TigrChadoInstance.java, 1.15, 1.16

[Jonathan C. <jcr...@us...>]

Update of /cvsroot/gmod/apollo/src/java/apollo/dataadapter/chado/jdbc
In directory sc8-pr-cvs2.sourceforge.net:/tmp/cvs-serv15429

Modified Files:
	TigrChadoInstance.java 
Log Message:
Accounting for small change in addSearchHits method.  Also 
modified to retrieve gene properties, synonyms, and dbxrefs.


Index: TigrChadoInstance.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/dataadapter/chado/jdbc/TigrChadoInstance.java,v
retrieving revision 1.15
retrieving revision 1.16
diff -C2 -d -r1.15 -r1.16
*** TigrChadoInstance.java	27 Jan 2007 15:56:33 -0000	1.15
--- TigrChadoInstance.java	8 Feb 2007 20:54:21 -0000	1.16
***************
*** 182,187 ****
      // ------------------------------------------------
      logger.debug("retrieving 1-level annotations");
      // list of 1-level annotations is configured in chado-config.xml
!     getAnnotations(conn,seq,annotations,featLocImp,false,false,false,adapter);
      logger.debug("done retrieving 1-level annotations");
  
--- 182,192 ----
      // ------------------------------------------------
      logger.debug("retrieving 1-level annotations");
+ 
+     boolean getFeatProps = true;
+     boolean getSynonyms = true;
+     boolean getDbXRefs = true;
+ 
      // list of 1-level annotations is configured in chado-config.xml
!     getAnnotations(conn,seq,annotations,featLocImp,getFeatProps,getSynonyms,getDbXRefs,adapter);
      logger.debug("done retrieving 1-level annotations");
  
***************
*** 227,231 ****
      boolean makeSeqsLazy = true;
      getChadoAdapter().addSearchHits(conn, hitProgs, setTargetSeqs, getTgtSeqSep,
! 				    makeSeqsLazy, getTargetSeqDescriptions,"defline",joinWithFeatureProp,seq, 
  				    results,primaryScoreColumn,getAlignSeqs,featLocImp);
      adapter.fireProgressEvent(new ProgressEvent(this,hero,"Retrieved " + progNameList + " results"));
--- 232,236 ----
      boolean makeSeqsLazy = true;
      getChadoAdapter().addSearchHits(conn, hitProgs, setTargetSeqs, getTgtSeqSep,
! 				    makeSeqsLazy, getTargetSeqDescriptions,joinWithFeatureProp,seq, 
  				    results,primaryScoreColumn,getAlignSeqs,featLocImp);
      adapter.fireProgressEvent(new ProgressEvent(this,hero,"Retrieved " + progNameList + " results"));