[Gmod-apollo-cmts] CVS: apollo/src/java/apollo/dataadapter/chado/jdbc JdbcChadoAdapter.java,1.105,1.106

[Mark G. <mg...@us...>]

Update of /cvsroot/gmod/apollo/src/java/apollo/dataadapter/chado/jdbc
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv14052/src/java/apollo/dataadapter/chado/jdbc

Modified Files:
	JdbcChadoAdapter.java 
Log Message:
loading a dataset from bdgp was incredibly slow in apollo - it was
taking 4 minutes! - turns out this dataset had a huge amount of
features in one tier ~7000 - in drawableFeatureSet.addFeatureDrawable
findDrawable was being called - for eveyry feature added - and
findDrawable iterates through every drawable in the set to make sure
its not already there - for large sets this is extremely costly. i
added this a few months ago to deal with splits adding the same
feature twice - this is not the way to address this issue (at the time
i thought it a nice check to have - little did i know the bottleneck i
added) - so i took out the offending code and the 4 minute load went
down to 26 seconds - steve searle noticed this problem as well and
took out for in the non-editing case - but really it needs to be taken
out for all cases as one might be editing on very large datasets as is
currently the case.

also put in non-analysis check for gene query.



Index: JdbcChadoAdapter.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/dataadapter/chado/jdbc/JdbcChadoAdapter.java,v
retrieving revision 1.105
retrieving revision 1.106
diff -C2 -d -r1.105 -r1.106
*** JdbcChadoAdapter.java	29 Aug 2005 21:48:43 -0000	1.105
--- JdbcChadoAdapter.java	30 Aug 2005 00:02:05 -0000	1.106
***************
*** 928,931 ****
--- 928,932 ----
        "AND trans2gene." + objFeatCol + " = gene.feature_id  " +
        "AND gene.type_id = " + getFeatureCVTermId("gene") + " " +
+       "AND gene.is_analysis = 'f' " +
        featLocWhereClause +
        "ORDER BY gene.feature_id, trans.feature_id, exonloc." + fminCol + "  ";