@@ -0,0 +1,2156 @@
+/*%0A * Copyright (C) 2003 EBI, GRL%0A * %0A * This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by%0A * the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version.%0A * %0A * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or%0A * FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.%0A * %0A * You should have received a copy of the GNU Lesser General Public License along with this library; if not, write to the Free Software Foundation,%0A * Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA%0A */%0Apackage org.ensembl.healthcheck.testcase.generic;%0A%0Aimport java.util.Map;%0A%0Aimport org.ensembl.healthcheck.DatabaseRegistryEntry;%0A%0A/**%0A * Compare the RepeatTypes in the current database with those from the equivalent%0A * database on the secondary server.%0A */%0A%0Apublic class ComparePreviousVersionRepeatTypes extends ComparePreviousVersionBase %7B%0A%0A%09/**%0A%09 * Create a new XrefTypes testcase.%0A%09 */%0A%09public ComparePreviousVersionRepeatTypes() %7B%0A%0A%09%09addToGroup(%22post_genebuild%22);%0A%09%09addToGroup(%22release%22);%0A%09%09setDescription(%22Compare the types of repeat features in the current database with those from the equivalent database on the secondary server%22);%0A%0A%09%7D%0A%0A%09// ----------------------------------------------------------------------%0A%0A%09protected Map getCounts(DatabaseRegistryEntry dbre) %7B%0A%0A%09%09return getCountsBySQL(dbre, %22SELECT DISTINCT(rc.repeat_type), COUNT(*) FROM repeat_feature rf, repeat_consensus rc WHERE rf.repeat_consensus_id=rc.repeat_consensus_id GROUP BY rc.repeat_type%22);%0A%0A%09%7D%0A%0A%09// ------------------------------------------------------------------------%0A%0A%09protected String entityDescription() %7B%0A%0A%09%09return %22Repeats of repeat consensus type%22;%0A%0A%09%7D%0A%0A%09// ------------------------------------------------------------------------%0A%0A%09protected double threshold() %7B%0A%0A%09%09return 0.75;%0A%0A%09%7D%0A%0A%09// ------------------------------------------------------------------------%0A%0A%7D // ComparePreviousVersionRepeatTypes%0A

Check types of repeat features against previous release.