diff --git a/uk/ac/sanger/artemis/chado/ChadoDemo.java b/uk/ac/sanger/artemis/chado/ChadoDemo.java
index 18a3b961c0ae2e10c813f34fc9c3411c10a9395f..2c62eb138ff4034c69c2276d6f9f1b8a5248af62 100644
--- a/uk/ac/sanger/artemis/chado/ChadoDemo.java
+++ b/uk/ac/sanger/artemis/chado/ChadoDemo.java
@@ -25,13 +25,8 @@
package uk.ac.sanger.artemis.chado;
import org.gmod.schema.cv.CvTerm;
-import org.gmod.schema.general.DbXRef;
-import org.gmod.schema.pub.Pub;
-import org.gmod.schema.pub.PubDbXRef;
import org.gmod.schema.sequence.Feature;
import org.gmod.schema.sequence.FeatureCvTerm;
-import org.gmod.schema.sequence.FeatureCvTermDbXRef;
-import org.gmod.schema.sequence.FeatureCvTermProp;
import org.gmod.schema.sequence.FeatureDbXRef;
import org.gmod.schema.sequence.FeatureSynonym;
import org.gmod.schema.sequence.FeatureProp;
@@ -51,6 +46,7 @@ import java.util.Enumeration;
import java.util.Hashtable;
import java.util.Iterator;
import java.util.List;
+import java.util.Collection;
import java.util.Vector;
import javax.swing.JLabel;
@@ -118,6 +114,8 @@ public class ChadoDemo
*/
public ChadoDemo()
{
+ uk.ac.sanger.artemis.components.Splash.initLogger();
+
try
{
setLocation();
@@ -315,7 +313,8 @@ public class ChadoDemo
List attributes = (List)chado_feature.getFeatureProps();
List dbxrefs = dao.getFeatureDbXRefsByFeatureUniquename(uniquename);
List featureCvTerms = dao.getFeatureCvTermsByFeature(chado_feature);
- List featureCvTermDbXRefs = dao.getFeatureCvTermDbXRef(chado_feature);
+ List featureCvTermDbXRefs = dao.getFeatureCvTermDbXRefByFeature(chado_feature);
+ List featureCvTermPubs = dao.getFeatureCvTermPubByFeature(chado_feature);
if(dbxrefs.size() > 0)
{
@@ -329,7 +328,7 @@ public class ChadoDemo
attr_buff.append("\n");
}
- List synonyms = (List)chado_feature.getFeatureSynonyms();
+ Collection synonyms = chado_feature.getFeatureSynonyms();
// append synonyms
if(synonyms != null && synonyms.size() > 0)
@@ -337,10 +336,10 @@ public class ChadoDemo
FeatureSynonym alias;
System.out.println("\n\nNow get synonym & type_id.......\n\n");
-
- for(int i = 0; i < synonyms.size(); i++)
+ Iterator it = synonyms.iterator();
+ while(it.hasNext())
{
- alias = (FeatureSynonym) synonyms.get(i);
+ alias = (FeatureSynonym)it.next();
attr_buff.append("/");
attr_buff.append(alias.getSynonym().getCvTerm().getName() + "=");
attr_buff.append(alias.getSynonym().getName());
@@ -351,14 +350,17 @@ public class ChadoDemo
}
if(attributes != null)
- for(int i = 0; i < attributes.size(); i++)
+ {
+ Iterator it = attributes.iterator();
+ while(it.hasNext())
{
- FeatureProp featprop = (FeatureProp) attributes.get(i);
+ FeatureProp featprop = (FeatureProp)it.next();
attr_buff.append("/" + featprop.getCvTerm().getName() + "="
+ GFFStreamFeature.decode(featprop.getValue()) + "\n");
}
-
+ }
+
if(featureCvTerms != null)
{
for(int j=0; j<featureCvTerms.size(); j++)
@@ -367,7 +369,7 @@ public class ChadoDemo
FeatureCvTerm feature_cvterm = (FeatureCvTerm)featureCvTerms.get(j);
DatabaseDocument.appendControlledVocabulary(attr_buff, dao, feature_cvterm,
- featureCvTermDbXRefs, pubDbXRefs);
+ featureCvTermDbXRefs, featureCvTermPubs, pubDbXRefs);
attr_buff.append("\n");
}
@@ -412,11 +414,12 @@ public class ChadoDemo
feature = (Feature) featureList.get(i);
// assume only one featureloc
- List locs = (List)feature.getFeatureLocsForFeatureId();
+ Collection locs = feature.getFeatureLocsForFeatureId();
if(locs != null && locs.size() > 0)
{
- FeatureLoc loc = (FeatureLoc)locs.get(0);
+ Iterator it = locs.iterator();
+ FeatureLoc loc = (FeatureLoc)it.next();
int fmin = loc.getFmin().intValue() + 1;
int fmax = loc.getFmax().intValue();
rowData[i][4] = fmin + "..." + fmax;
diff --git a/uk/ac/sanger/artemis/chado/GmodDAO.java b/uk/ac/sanger/artemis/chado/GmodDAO.java
index b5ce43ab648910551c853e0ba36d87225fa74030..b0480f07155e525089da76fe625f92822387be39 100644
--- a/uk/ac/sanger/artemis/chado/GmodDAO.java
+++ b/uk/ac/sanger/artemis/chado/GmodDAO.java
@@ -45,7 +45,9 @@ public abstract class GmodDAO implements SequenceDaoI, SchemaDaoI, OrganismDaoI,
public abstract List getPubDbXRef();
- public abstract List getFeatureCvTermDbXRef(Feature feature);
+ public abstract List getFeatureCvTermDbXRefByFeature(Feature feature);
+
+ public abstract List getFeatureCvTermPubByFeature(Feature feature);
/**
* Return the list of all feature_synonyms as Feature.featureSynonyms
diff --git a/uk/ac/sanger/artemis/chado/IBatisDAO.java b/uk/ac/sanger/artemis/chado/IBatisDAO.java
index 2d7b15891a1e71fbf867aa77f4fe62b7fb54cab4..742ac5edf1a2dc20de29a8d3063da4d5ad06d40f 100644
--- a/uk/ac/sanger/artemis/chado/IBatisDAO.java
+++ b/uk/ac/sanger/artemis/chado/IBatisDAO.java
@@ -305,11 +305,16 @@ public class IBatisDAO extends GmodDAO
}
- public List getFeatureCvTermDbXRef(Feature feature)
+ public List getFeatureCvTermDbXRefByFeature(Feature feature)
{
return sqlMap.queryForList("getFeatureCvTermDbXRef", feature);
}
+ public List getFeatureCvTermPubByFeature(Feature feature)
+ {
+ return sqlMap.queryForList("getFeatureCvTermPub", feature);
+ }
+
public List getProducts()
{
return null;
diff --git a/uk/ac/sanger/artemis/chado/JdbcDAO.java b/uk/ac/sanger/artemis/chado/JdbcDAO.java
index a3ef5e23589c5f2a825e250f08acf029c66991df..f9c6e14c4c2001473c4ff6d71d44a9c53843f30c 100644
--- a/uk/ac/sanger/artemis/chado/JdbcDAO.java
+++ b/uk/ac/sanger/artemis/chado/JdbcDAO.java
@@ -41,6 +41,7 @@ import org.gmod.schema.sequence.FeatureLoc;
import org.gmod.schema.sequence.FeatureRelationship;
import org.gmod.schema.sequence.FeatureSynonym;
import org.gmod.schema.sequence.FeatureCvTermDbXRef;
+import org.gmod.schema.sequence.FeatureCvTermPub;
import org.gmod.schema.general.DbXRef;
import org.gmod.schema.organism.Organism;
import org.gmod.schema.cv.CvTerm;
@@ -231,6 +232,9 @@ public class JdbcDAO extends GmodDAO
CvTerm cvterm = new CvTerm();
cvterm.setCvTermId(rs.getInt("cvterm_id"));
cvterm.setName(rs.getString("cvterm_name"));
+ Cv cv = new Cv();
+ cv.setName(rs.getString("cv_name"));
+ cvterm.setCv(cv);
DbXRef dbxref = new DbXRef();
dbxref.setAccession(rs.getString("accession"));
@@ -254,6 +258,8 @@ public class JdbcDAO extends GmodDAO
int next_fc_rank = -1;
int next_feature_cvterm_id = -1;
int feature_cvterm_id = rs.getInt("feature_cvterm_id");
+ feature_cvterm.setFeatureCvTermId(feature_cvterm_id);
+
do
{
FeatureCvTermProp featureProp = new FeatureCvTermProp();
@@ -576,7 +582,7 @@ public class JdbcDAO extends GmodDAO
return null;
}
- public List getFeatureCvTermDbXRef(Feature feature)
+ public List getFeatureCvTermDbXRefByFeature(Feature feature)
{
String sql = "SELECT fcd.feature_cvterm_id, dbx.*, db.name "+
"FROM feature_cvterm_dbxref fcd "+
@@ -626,6 +632,48 @@ public class JdbcDAO extends GmodDAO
}
}
+ public List getFeatureCvTermPubByFeature(Feature feature)
+ {
+ String sql = "SELECT fcp.feature_cvterm_id, pub.* " +
+ "FROM feature_cvterm_pub fcp " +
+ "LEFT JOIN pub ON fcp.pub_id=pub.pub_id ";
+
+ if(feature != null && feature.getUniqueName() != null)
+ sql = sql+ " " +
+ "LEFT JOIN feature_cvterm fc ON fcp.feature_cvterm_id=fc.feature_cvterm_id "+
+ "WHERE feature_id=(SELECT feature_id FROM feature WHERE uniquename='"+
+ feature.getUniqueName()+"')";
+
+ appendToLogFile(sql, sqlLog);
+
+ try
+ {
+ Statement st = conn.createStatement();
+ ResultSet rs = st.executeQuery(sql);
+ List featureCvTermPubs = new Vector();
+ FeatureCvTermPub featureCvTermPub;
+ while(rs.next())
+ {
+ featureCvTermPub = new FeatureCvTermPub();
+ FeatureCvTerm featureCvTerm = new FeatureCvTerm();
+ featureCvTerm.setFeatureCvTermId( rs.getInt("feature_cvterm_id") );
+ featureCvTermPub.setFeatureCvTerm(featureCvTerm);
+
+ Pub pub = new Pub();
+ pub.setUniqueName(rs.getString("uniquename"));
+
+ featureCvTermPub.setPub(pub);
+ featureCvTermPubs.add(featureCvTermPub);
+ }
+
+ return featureCvTermPubs;
+ }
+ catch(SQLException sqle)
+ {
+ throw new RuntimeException(sqle);
+ }
+ }
+
public List getProducts()
{
return null;
@@ -748,6 +796,8 @@ public class JdbcDAO extends GmodDAO
feature.setFeatureProps(new Vector());
feature.addFeatureProp(featureprop);
}
+ else
+ feature.setFeatureProps(new Vector(0));
// feature relationship
FeatureRelationship feature_relationship = new FeatureRelationship();
@@ -769,6 +819,8 @@ public class JdbcDAO extends GmodDAO
feature.addFeatureRelationshipsForSubjectId(feature_relationship);
}
+ else
+ feature.setFeatureRelationshipsForSubjectId(new Vector(0));
if(!rs.isLast())
{
@@ -1051,7 +1103,8 @@ public class JdbcDAO extends GmodDAO
pubDbXRef = new PubDbXRef();
Pub pub = new Pub();
pub.setPubId(rs.getInt("pub_id"));
-
+ pubDbXRef.setPub(pub);
+
DbXRef dbXRef = new DbXRef();
dbXRef.setAccession(rs.getString("accession"));
dbXRef.setDescription(rs.getString("description"));