@@ -0,0 +1,2397 @@
+/*%0A Copyright (C) 2003 EBI, GRL%0A %0A This library is free software; you can redistribute it and/or%0A modify it under the terms of the GNU Lesser General Public%0A License as published by the Free Software Foundation; either%0A 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,%0A but WITHOUT ANY WARRANTY; without even the implied warranty of%0A MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU%0A Lesser General Public License for more details.%0A %0A You should have received a copy of the GNU Lesser General Public%0A License along with this library; if not, write to the Free Software%0A Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA%0A */%0Apackage org.ensembl.healthcheck.testcase.generic;%0A%0Aimport java.sql.Connection;%0Aimport java.util.ArrayList;%0Aimport java.util.List;%0A%0Aimport org.ensembl.healthcheck.DatabaseRegistryEntry;%0Aimport org.ensembl.healthcheck.DatabaseType;%0Aimport org.ensembl.healthcheck.ReportManager;%0Aimport org.ensembl.healthcheck.testcase.SingleDatabaseTestCase;%0A%0A/**%0A * Check that transcript frameshift attributes have been calculated.%0A */%0A%0Apublic class FrameshiftAttributes extends SingleDatabaseTestCase %7B%0A%0A%09/**%0A%09 * Create a new FrameshiftAttributes testcase.%0A%09 */%0A%09public FrameshiftAttributes() %7B%0A%0A%09%09addToGroup(%22post_genebuild%22);%0A%09%09addToGroup(%22release%22);%0A%09%09setDescription(%22Check that transcript frameshift attributes have been calculated.%22);%0A%0A%09%7D%0A%0A%09/**%0A%09 * Only applies to core dbs.%0A%09 */%0A%09public void types() %7B%0A%0A%09%09List types = new ArrayList();%0A%0A%09%09types.add(DatabaseType.CORE);%0A%0A%09%09setAppliesToTypes(types);%0A%0A%09%7D%0A%0A%09/**%0A%09 * Run the test.%0A%09 * %0A%09 * @param dbre%0A%09 *          The database to use.%0A%09 * @return true if the test pased.%0A%09 * %0A%09 */%0A%09public boolean run(DatabaseRegistryEntry dbre) %7B%0A%0A%09%09boolean result = true;%0A%0A%09%09Connection con = dbre.getConnection();%0A%0A%09%09int rows = getRowCount(con,%0A%09%09%09%09%22SELECT COUNT(*) FROM attrib_type at, transcript_attrib ta WHERE at.attrib_type_id=ta.attrib_type_id AND at.code='Frameshift'%22);%0A%0A%09%09if (rows == 0) %7B%0A%0A%09%09%09ReportManager.problem(this, con, %22No transcript frameshift attributes found%22);%0A%09%09%09result = false;%0A%0A%09%09%7D else %7B%0A%0A%09%09%09ReportManager.correct(this, con, rows + %22 transcript frameshift attributes found%22);%0A%0A%09%09%7D%0A%0A%09%09return result;%0A%0A%09%7D // run%0A%0A%09// ----------------------------------------------------------------------%0A%0A%7D // ESTStableID%0A

Check that transcript frameshift attributes have been calculated for core databases.