/**
* Check that any _rna_edit attribute represents a substitution rather than an insertion or
* deletion
*/
private boolean checkRnaEditAttributes(final DatabaseRegistryEntry dbre) {
boolean ok = true;
RowMapper<Attrib> mapper =
new RowMapper<Attrib>() {
public Attrib mapRow(ResultSet rs, int row) throws SQLException {
return new Attrib(rs.getString(1), rs.getLong(2), rs.getString(3));
}
};
String sql =
"select sr.name, sr.seq_region_id, sra.value "
+ "from seq_region sr join seq_region_attrib sra using (seq_region_id) "
+ "join attrib_type at using (attrib_type_id) where at.code =?";
List<Attrib> attributes = getSqlTemplate(dbre).queryForList(sql, mapper, "_rna_edit");
for (Attrib a : attributes) {
if (!a.isOk()) {
ReportManager.warning(this, dbre.getConnection(), a.toString());
ok = false;
}
}
if (!ok) {
ReportManager.problem(
this,
dbre.getConnection(),
"Detected sequence regions with incorrectly formatted _rna_edit attributes. Check warnings");
}
return ok;
}
@Override
public void activate(int fbufWidth, int fbufHeight) {
prog.bind();
uScreenSize.bind(fbufWidth, fbufHeight);
vertices.bind(GL20.GL_ARRAY_BUFFER);
aMatrix.bind(VERTEX_STRIDE, 0);
aTranslation.bind(VERTEX_STRIDE, 16);
aPosition.bind(VERTEX_STRIDE, 24);
if (aTexCoord != null) aTexCoord.bind(VERTEX_STRIDE, 32);
aColor.bind(VERTEX_STRIDE, 40);
elements.bind(GL20.GL_ELEMENT_ARRAY_BUFFER);
ctx.checkGLError("Shader.prepare bind");
}
