diff --git a/uk/ac/sanger/artemis/chado/GmodDAO.java b/uk/ac/sanger/artemis/chado/GmodDAO.java index ba10e0aaa4f722c2c8b50ff37d65ab85dcfc881c..0994d850431f26078a103fb27c5281054417a3bd 100644 --- a/uk/ac/sanger/artemis/chado/GmodDAO.java +++ b/uk/ac/sanger/artemis/chado/GmodDAO.java @@ -51,6 +51,7 @@ public abstract class GmodDAO { private static org.apache.log4j.Logger logger4j = org.apache.log4j.Logger.getLogger(GmodDAO.class); + public abstract List getOrganismsContainingSrcFeatures(); public abstract List getSimilarityMatchesByFeatureIds(final List featureIds); public abstract List getSimilarityMatches(final Integer srcFeatureId); @@ -267,10 +268,7 @@ public abstract class GmodDAO * @param commonName the short name to look up * @return the corresponding organism, or null */ - public Organism getOrganismByCommonName(String commonName) - { - return null; - } + public abstract Organism getOrganismByCommonName(String commonName); /** * Get a list of the common name of all the organisms. diff --git a/uk/ac/sanger/artemis/chado/IBatisDAO.java b/uk/ac/sanger/artemis/chado/IBatisDAO.java index 2e9f1c99d4963e46df109b19028acdca075abefd..8c5edbd5ee0b925bf39622ec8be2399b063ba698 100644 --- a/uk/ac/sanger/artemis/chado/IBatisDAO.java +++ b/uk/ac/sanger/artemis/chado/IBatisDAO.java @@ -692,6 +692,13 @@ public class IBatisDAO extends GmodDAO return sqlMap.queryForList("getOrganism", null); } + public Organism getOrganismByCommonName(String commonName) + { + Organism o = new Organism(); + o.setCommonName(commonName); + return (Organism)sqlMap.queryForObject("getOrganism", o); + } + ////// ////// PubDaoI ////// diff --git a/uk/ac/sanger/artemis/chado/JdbcDAO.java b/uk/ac/sanger/artemis/chado/JdbcDAO.java index a4b0b7975c5c0406c9cb3fc963bb7d360a83ed83..e5f4a951bf21724c0c3d6ff371f385d305276f9c 100644 --- a/uk/ac/sanger/artemis/chado/JdbcDAO.java +++ b/uk/ac/sanger/artemis/chado/JdbcDAO.java @@ -2290,4 +2290,9 @@ public class JdbcDAO extends GmodDAO { } + + public Organism getOrganismByCommonName(String commonName) + { + return null; + } }