diff --git a/uk/ac/sanger/artemis/chado/ChadoTransaction.java b/uk/ac/sanger/artemis/chado/ChadoTransaction.java
index 041287e8629a98cf145408c5ea048d97526737ca..7b365bc7ecbaa5a61813acbfd539eb7ee7ff90ab 100644
--- a/uk/ac/sanger/artemis/chado/ChadoTransaction.java
+++ b/uk/ac/sanger/artemis/chado/ChadoTransaction.java
@@ -55,6 +55,8 @@ public class ChadoTransaction
private Timestamp lastmodified;
/** the feature object */
private Object feature_obj;
+ /** the feature key */
+ private String featureKey;
private GFFStreamFeature gff_feature;
@@ -71,12 +73,14 @@ public class ChadoTransaction
public ChadoTransaction(final int type,
final Object feature_obj,
final Timestamp lastmodified,
- final GFFStreamFeature gff_feature)
+ final GFFStreamFeature gff_feature,
+ final String featureKey)
{
this.type = type;
this.lastmodified = lastmodified;
this.feature_obj = feature_obj;
this.gff_feature = gff_feature;
+ this.featureKey = featureKey;
}
@@ -162,4 +166,10 @@ public class ChadoTransaction
this.gff_feature = gff_feature;
}
+
+ public String getFeatureKey()
+ {
+ return featureKey;
+ }
+
}
diff --git a/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java b/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java
index dbaebbe81987cc2c8ee36c9532deb90df60758ed..458c9782a2fbdb8da67a8b72a6784721a28b60c2 100644
--- a/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java
+++ b/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java
@@ -136,49 +136,6 @@ public class ChadoTransactionManager
{
int start = event.getPosition();
int length = event.getSubSequence().length();
-
- FeatureVector features = entryGroup.getAllFeatures();
-
- for(int i=0; i<features.size(); i++)
- {
- Feature feature = features.elementAt(i);
-
- if(feature.getLocation().getFirstBase() >= start)
- {
- GFFStreamFeature gffFeature = (GFFStreamFeature)feature.getEmblFeature();
- FeatureSegmentVector segments = feature.getSegments();
-
- for(int j=0; j<segments.size(); j++)
- {
- FeatureSegment segment = segments.elementAt(j);
- String seg_id = gffFeature.getSegmentID( segment.getRawRange() );
- Range range_new;
- try
- {
- if(event.getType() == SequenceChangeEvent.DELETION)
- range_new = new Range(feature.getLocation().getFirstBase()-length,
- feature.getLocation().getLastBase()-length);
- else
- range_new = new Range(feature.getLocation().getFirstBase()+length,
- feature.getLocation().getLastBase()+length);
-
- // featureloc update
- FeatureLoc featureloc = getFeatureLoc(gffFeature, seg_id, range_new);
- ChadoTransaction tsn = new ChadoTransaction(ChadoTransaction.UPDATE,
- featureloc,
- gffFeature.getLastModified(), gffFeature);
-
- sql.add(tsn);
-
- }
- catch(OutOfRangeException e)
- {
- e.printStackTrace();
- }
-
- }
- }
- }
//
// update residues in srcfeature
@@ -187,6 +144,7 @@ public class ChadoTransactionManager
FeatureForUpdatingResidues chadoFeature = new FeatureForUpdatingResidues();
chadoFeature.setStartBase(start-1);
+ chadoFeature.setLength(length);
int newSequenceLength = entryGroup.getSequenceEntry().getEMBLEntry().getSequence().length();
@@ -207,7 +165,7 @@ public class ChadoTransactionManager
entryGroup.getSequenceEntry().getEMBLEntry().getSequence().length()));
ChadoTransaction tsn =
- new ChadoTransaction(ChadoTransaction.UPDATE, chadoFeature, null, null);
+ new ChadoTransaction(ChadoTransaction.UPDATE, chadoFeature, null, null, null);
sql.add(tsn);
}
else
@@ -259,7 +217,7 @@ public class ChadoTransactionManager
ideleted = ((Integer)deleted.elementAt(i)).intValue();
Range range_old = (Range)rv_old.elementAt(ideleted);
String seg_id = feature.getSegmentID(range_old);
- deleteFeature(seg_id);
+ deleteFeature(seg_id, feature.getKey().getKeyString());
feature.getSegmentRangeStore().remove(seg_id);
}
@@ -392,7 +350,8 @@ public class ChadoTransactionManager
tsn = new ChadoTransaction(ChadoTransaction.UPDATE,
featureloc,
- feature.getLastModified(), feature);
+ feature.getLastModified(), feature,
+ feature.getKey().getKeyString());
sql.add(tsn);
}
@@ -467,20 +426,20 @@ public class ChadoTransactionManager
(String)(qualifier_uniquename.getValues()).elementAt(0);
Splash.logger4j.debug("FEATURE_DELETED "+feature_uniquename);
+ GFFStreamFeature gff_feature =
+ (GFFStreamFeature)event.getFeature().getEmblFeature();
if(event.getFeature().getSegments().size() > 1)
{
- GFFStreamFeature gff_feature =
- (GFFStreamFeature)event.getFeature().getEmblFeature();
RangeVector ranges = gff_feature.getLocation().getRanges();
for(int i=0; i<ranges.size(); i++)
{
Range range = (Range)ranges.get(i);
feature_uniquename = gff_feature.getSegmentID(range);
- deleteFeature(feature_uniquename);
+ deleteFeature(feature_uniquename, gff_feature.getKey().getKeyString());
}
}
else
- deleteFeature(feature_uniquename);
+ deleteFeature(feature_uniquename, gff_feature.getKey().getKeyString());
}
catch(InvalidRelationException e)
{
@@ -538,7 +497,8 @@ public class ChadoTransactionManager
tsn = new ChadoTransaction(ChadoTransaction.UPDATE,
feature_relationship,
- feature.getLastModified(), feature);
+ feature.getLastModified(), feature,
+ feature.getKey().getKeyString());
sql.add(tsn);
}
}
@@ -665,7 +625,7 @@ public class ChadoTransactionManager
ChadoTransaction tsn = new ChadoTransaction(ChadoTransaction.INSERT,
chado_feature,
- null, (GFFStreamFeature)null);
+ null, (GFFStreamFeature)null, null);
sql.add(tsn);
}
@@ -775,7 +735,7 @@ public class ChadoTransactionManager
ChadoTransaction tsn = new ChadoTransaction(ChadoTransaction.INSERT,
chado_feature,
- null, (GFFStreamFeature)null);
+ null, (GFFStreamFeature)null, null);
sql.add(tsn);
}
@@ -783,7 +743,7 @@ public class ChadoTransactionManager
/**
* Set the transaction for deleting a feature.
*/
- private void deleteFeature(final String uniquename)
+ private void deleteFeature(final String uniquename, final String featureType)
{
org.gmod.schema.sequence.Feature chado_feature =
new org.gmod.schema.sequence.Feature();
@@ -791,7 +751,7 @@ public class ChadoTransactionManager
ChadoTransaction tsn = new ChadoTransaction(ChadoTransaction.DELETE,
chado_feature,
- null, (GFFStreamFeature)null);
+ null, (GFFStreamFeature)null, featureType);
sql.add(tsn);
}
@@ -950,7 +910,7 @@ public class ChadoTransactionManager
tsn = new ChadoTransaction(ChadoTransaction.UPDATE,
chado_feature,
- feature.getLastModified(), feature);
+ feature.getLastModified(), feature, null);
sql.add(tsn);
}
@@ -1122,7 +1082,7 @@ public class ChadoTransactionManager
lcvterm_id, rank);
tsn = new ChadoTransaction(type,
featureprop,
- feature.getLastModified(), feature);
+ feature.getLastModified(), feature, feature.getKey().getKeyString());
tsn.setUniquename(uniquename);
sql.add(tsn);
@@ -1135,7 +1095,7 @@ public class ChadoTransactionManager
tsn = new ChadoTransaction(type,
featureprop,
- feature.getLastModified(), feature);
+ feature.getLastModified(), feature, feature.getKey().getKeyString());
sql.add(tsn);
}
}
@@ -1187,7 +1147,7 @@ public class ChadoTransactionManager
(String)old_qualifier.getValues().get(0));
ChadoTransaction tsn = new ChadoTransaction(ChadoTransaction.UPDATE,
chado_feature,
- feature.getLastModified(), feature);
+ feature.getLastModified(), feature, feature.getKey().getKeyString());
tsn.setOldUniquename( (String)old_qualifier.getValues().get(0) );
sql.add(tsn);
@@ -1216,7 +1176,8 @@ public class ChadoTransactionManager
tsn = new ChadoTransaction(ChadoTransaction.DELETE,
old_dbxref,
- feature.getLastModified(), feature);
+ feature.getLastModified(), feature,
+ feature.getKey().getKeyString());
sql.add(tsn);
}
else if(qualifier_name.equals("codon_start"))
@@ -1228,7 +1189,8 @@ public class ChadoTransactionManager
tsn = new ChadoTransaction(ChadoTransaction.UPDATE,
featureloc,
- feature.getLastModified(), feature);
+ feature.getLastModified(), feature,
+ feature.getKey().getKeyString());
sql.add(tsn);
}
else if(isCvTag(qualifier_name))
@@ -1266,7 +1228,8 @@ public class ChadoTransactionManager
uniquename);
tsn = new ChadoTransaction(ChadoTransaction.DELETE,
feature_cvterm,
- feature.getLastModified(), feature);
+ feature.getLastModified(), feature,
+ feature.getKey().getKeyString());
sql.add(tsn);
}
else if(isSynonymTag(qualifier_name))
@@ -1279,7 +1242,8 @@ public class ChadoTransactionManager
tsn = new ChadoTransaction(ChadoTransaction.DELETE,
feature_synonym,
- feature.getLastModified(), feature);
+ feature.getLastModified(), feature,
+ feature.getKey().getKeyString());
sql.add(tsn);
}
@@ -1307,7 +1271,8 @@ public class ChadoTransactionManager
tsn = new ChadoTransaction(ChadoTransaction.INSERT,
new_dbxref,
- feature.getLastModified(), feature);
+ feature.getLastModified(), feature,
+ feature.getKey().getKeyString());
}
else if(qualifier_name.equals("codon_start"))
{
@@ -1317,7 +1282,8 @@ public class ChadoTransactionManager
tsn = new ChadoTransaction(ChadoTransaction.UPDATE,
featureloc,
- feature.getLastModified(), feature);
+ feature.getLastModified(), feature,
+ feature.getKey().getKeyString());
//sql.add(tsn);
}
else if(isCvTag(qualifier_name))
@@ -1328,7 +1294,8 @@ public class ChadoTransactionManager
qualifier_string, uniquename);
tsn = new ChadoTransaction(ChadoTransaction.INSERT,
feature_cvterm,
- feature.getLastModified(), feature);
+ feature.getLastModified(), feature,
+ feature.getKey().getKeyString());
}
else if(isSynonymTag(qualifier_name))
{
@@ -1340,7 +1307,8 @@ public class ChadoTransactionManager
tsn = new ChadoTransaction(ChadoTransaction.INSERT,
feature_synonym,
- feature.getLastModified(), feature);
+ feature.getLastModified(), feature,
+ feature.getKey().getKeyString());
}
sql.add(tsn);
}
diff --git a/uk/ac/sanger/artemis/chado/IBatisDAO.java b/uk/ac/sanger/artemis/chado/IBatisDAO.java
index 4eafc56416b7189fdcc1629a73ef0a13c3de882e..6e6f7c2b1d4cb100f2bd367a8f1fdb7191ceb844 100644
--- a/uk/ac/sanger/artemis/chado/IBatisDAO.java
+++ b/uk/ac/sanger/artemis/chado/IBatisDAO.java
@@ -93,15 +93,28 @@ public class IBatisDAO extends GmodDAO
org.gmod.schema.sequence.Feature feature =
new org.gmod.schema.sequence.Feature();
feature.setFeatureId(id);
- return getLazyFeature(feature);
+ return (Feature)sqlMap.queryForObject("getLazyFeature", feature);
+ }
+
+ public List getFeaturesByUniqueName(String uniquename)
+ {
+ org.gmod.schema.sequence.Feature feature =
+ new org.gmod.schema.sequence.Feature();
+ feature.setUniqueName(uniquename);
+ return sqlMap.queryForList("getLazyFeature", feature);
}
- public Feature getFeatureByUniqueName(String uniquename)
+ public Feature getFeatureByUniqueName(String uniquename, String featureType)
{
org.gmod.schema.sequence.Feature feature =
new org.gmod.schema.sequence.Feature();
feature.setUniqueName(uniquename);
- return getLazyFeature(feature);
+
+ CvTerm cvTerm = new CvTerm();
+ cvTerm.setName(featureType);
+ feature.setCvTerm(cvTerm);
+
+ return (Feature)sqlMap.queryForObject("getLazyFeature", feature);
}
@@ -362,21 +375,7 @@ public class IBatisDAO extends GmodDAO
{
return null;
}
-
- //////
- //////
-
-
- /**
- * Get the properties of a feature.
- * @param uniquename the unique name of the feature
- * @return the <code>List</code> of <code>Feature</code>
- */
- private Feature getLazyFeature(
- final org.gmod.schema.sequence.Feature feature)
- {
- return (Feature)sqlMap.queryForObject("getLazyFeature", feature);
- }
+
//////
////// SchemaDaoI
@@ -494,7 +493,10 @@ public class IBatisDAO extends GmodDAO
else if(o instanceof Feature)
{
if(o instanceof FeatureForUpdatingResidues)
+ {
+ sqlMap.update("updateFeatureLocByChangingSequence", o);
sqlMap.update("updateFeatureResidues", o);
+ }
else
sqlMap.update("updateFeature", o);
}
@@ -605,9 +607,11 @@ public class IBatisDAO extends GmodDAO
feature_dbxref.setDbXRef(dbXRef);
// get the feature id's
- Feature feature = (Feature)getFeatureByUniqueName(
+ List features = getFeaturesByUniqueName(
feature_dbxref.getFeature().getUniqueName());
- feature_dbxref.getFeature().setFeatureId( feature.getFeatureId() );
+
+ feature_dbxref.getFeature().setFeatureId(
+ ((Feature)features.get(0)).getFeatureId() );
sqlMap.insert("insertFeatureDbXRef", feature_dbxref);
}
@@ -693,7 +697,16 @@ public class IBatisDAO extends GmodDAO
protected Integer getDbId(Db db)
{
- return (Integer)sqlMap.queryForObject("getDbId", db);
+ Integer dbId = (Integer)sqlMap.queryForObject("getDbId", db);
+
+ if(dbId == null)
+ {
+ List dbIds = sqlMap.queryForList("getDbIdIgnoreCase", db);
+ if(dbIds.size() > 0)
+ dbId = (Integer)dbIds.get(0);
+ }
+
+ return dbId;
}
protected Integer getDbXRefId(DbXRef dbXRef)
diff --git a/uk/ac/sanger/artemis/chado/JdbcDAO.java b/uk/ac/sanger/artemis/chado/JdbcDAO.java
index 5d37e69e172ab5b5e58141eb22d348aad12bb03b..b17e8cc29cd3c07ce241d8ea041db642dffd94d3 100644
--- a/uk/ac/sanger/artemis/chado/JdbcDAO.java
+++ b/uk/ac/sanger/artemis/chado/JdbcDAO.java
@@ -109,14 +109,30 @@ public class JdbcDAO extends GmodDAO
* @param name the systematic id
* @return the Feature, or null
*/
- public Feature getFeatureByUniqueName(String uniquename)
+ public Feature getFeatureByUniqueName(final String uniquename, final String featureType)
{
Feature feature = new Feature();
feature.setUniqueName(uniquename);
feature.setFeatureId(-1);
+
+ CvTerm cvTerm = new CvTerm();
+ cvTerm.setName(featureType);
+ feature.setCvTerm(cvTerm);
+
return getLazyFeature(feature);
}
+ /**
+ * Return a features with this systematic id
+ *
+ * @param name the systematic id
+ * @return the Feature, or null
+ */
+ public List getFeaturesByUniqueName(String uniquename)
+ {
+ return getFeatureQuery(uniquename, -1, -1, null);
+ }
+
/**
* Return a list of features with any current (ie non-obsolete) name or synonym
*
@@ -131,7 +147,7 @@ public class JdbcDAO extends GmodDAO
// getFeatureSynonymsByName() needs implementing
//List feature_synonym_list = getFeatureSynonymsByName();
- return getFeatureQuery(name, -1, -1);
+ return getFeatureQuery(name, -1, -1, null);
}
/**
@@ -172,7 +188,7 @@ public class JdbcDAO extends GmodDAO
public List getFeaturesByLocatedOnFeature(final Feature feature)
{
return getFeatureQuery(null,
- feature.getFeatureLoc().getFeatureBySrcFeatureId().getFeatureId(), -1);
+ feature.getFeatureLoc().getFeatureBySrcFeatureId().getFeatureId(), -1, null);
}
/**
@@ -727,7 +743,8 @@ public class JdbcDAO extends GmodDAO
private Feature getLazyFeature(final Feature feature)
{
List list = getFeatureQuery(feature.getUniqueName(),
- -1, feature.getFeatureId());
+ -1, feature.getFeatureId(),
+ feature.getCvTerm());
if(list == null || list.size() < 1)
return null;
@@ -742,7 +759,8 @@ public class JdbcDAO extends GmodDAO
*/
private List getFeatureQuery(final String uniquename,
final int parentFeatureID,
- final int feature_id)
+ final int feature_id,
+ final CvTerm cvTerm)
{
final List list = new Vector();
try
@@ -759,8 +777,12 @@ public class JdbcDAO extends GmodDAO
+ "fr.subject_id=" + "f.feature_id" + " LEFT JOIN featureprop fp ON "
+ "fp.feature_id=" + "f.feature_id" + " LEFT JOIN featureloc fl ON "
+ "f.feature_id=" + "fl.feature_id"
- + " LEFT JOIN organism ON organism.organism_id=f.organism_id"
- + " WHERE ";
+ + " LEFT JOIN organism ON organism.organism_id=f.organism_id ";
+
+ if(cvTerm != null && cvTerm.getName() != null)
+ sql = sql + "LEFT JOIN cvterm ON f.type_id=cvterm.cvterm_id ";
+
+ sql = sql + " WHERE ";
if(uniquename != null)
sql = sql + "uniquename LIKE '" + uniquename + "'";
@@ -771,7 +793,10 @@ public class JdbcDAO extends GmodDAO
if(feature_id > -1)
sql = sql + "f.feature_id = " + feature_id;
- sql = sql // + " AND (fl.rank=fr.rank OR fr.rank IS NULL)"
+ if(cvTerm != null && cvTerm.getName() != null)
+ sql = sql + " AND cvterm.name="+cvTerm.getName();
+
+ sql = sql
+ " ORDER BY f.type_id, uniquename";
appendToLogFile(sql, sqlLog);
@@ -1322,23 +1347,38 @@ public class JdbcDAO extends GmodDAO
*/
private void updateFeatureResidues(FeatureForUpdatingResidues feature)
{
- String sql = " UPDATE feature SET "+
- "residues=substring(residues from 1 for "+ feature.getStartBase() + " || ";
+ String sql1 =
+ "UPDATE featureloc SET ";
+
+ if(feature.getNewSubSequence() != null)
+ sql1 = sql1 + "fmin=fmin+" + feature.getLength() +
+ " , fmax=fmax+" + feature.getLength();
+ else
+ sql1 = sql1 + "fmin=fmin-" + feature.getLength() +
+ " , fmax=fmax-" + feature.getLength();
+
+ sql1 = sql1 + " WHERE fmin >= " + feature.getStartBase() +
+ " AND srcfeature_id="+feature.getFeatureId();
+ appendToLogFile(sql1, sqlLog);
+
+ String sql2 = " UPDATE feature SET "+
+ "residues=substring(residues from 1 for "+ feature.getStartBase() + ") || ";
if(feature.getNewSubSequence() != null)
- sql = sql + feature.getNewSubSequence() + " || ";
+ sql2 = sql2 + "'" + feature.getNewSubSequence() + "' || ";
- sql = sql + "substring(residues from "+ feature.getEndBase() +
+ sql2 = sql2 + "substring(residues from "+ feature.getEndBase() +
" for "+ feature.getSeqLen() + "), "+
"seqlen=" + feature.getSeqLen() +
" WHERE feature_id="+feature.getFeatureId();
- appendToLogFile(sql, sqlLog);
+ appendToLogFile(sql2, sqlLog);
try
{
Statement st = conn.createStatement();
- st.executeUpdate(sql);
+ st.executeUpdate(sql1);
+ st.executeUpdate(sql2);
}
catch(SQLException sqle)
{
diff --git a/uk/ac/sanger/artemis/util/DatabaseDocument.java b/uk/ac/sanger/artemis/util/DatabaseDocument.java
index af8f764168f4e0551a690a528ee29529e83c7b87..ba7e4311415a37eb064d093f5540551d07877d37 100644
--- a/uk/ac/sanger/artemis/util/DatabaseDocument.java
+++ b/uk/ac/sanger/artemis/util/DatabaseDocument.java
@@ -680,7 +680,7 @@ public class DatabaseDocument extends Document
reset((String)getLocation(), (String)schema_search.get(0));
dao = getDAO();
Feature feature =
- (Feature)dao.getFeatureByUniqueName(search_gene);
+ (Feature)(dao.getFeaturesByUniqueName(search_gene).get(0));
ChadoCanonicalGene chado_gene = new ChadoCanonicalGene();
id_store.put(Integer.toString(feature.getFeatureId()), feature.getUniqueName());
@@ -1596,6 +1596,8 @@ public class DatabaseDocument extends Document
{
GmodDAO dao = getDAO();
+ if(dao instanceof IBatisDAO)
+ ((IBatisDAO) dao).startTransaction();
boolean unchanged;
//
@@ -1613,23 +1615,23 @@ public class DatabaseDocument extends Document
if(uniquename == null)
continue;
+
if(names_checked.contains(uniquename))
continue;
-
+
names_checked.add(uniquename);
+ String keyName = tsn.getFeatureKey();
unchanged = checkFeatureTimestamp(schema,
uniquename,
- tsn.getLastModified(), dao);
+ tsn.getLastModified(), dao,
+ keyName, tsn.getFeatureObject());
if(!unchanged)
return 0;
}
try
{
- if(dao instanceof IBatisDAO)
- ((IBatisDAO) dao).startTransaction();
-
//
// commit to database
for(i = 0; i < sql.size(); i++)
@@ -1651,7 +1653,7 @@ public class DatabaseDocument extends Document
uniquename = feature.getUniqueName();
Feature old_feature
- = dao.getFeatureByUniqueName(uniquename);
+ = dao.getFeatureByUniqueName(uniquename, tsn.getFeatureKey());
if(old_feature != null)
feature.setFeatureId( old_feature.getFeatureId() );
@@ -1711,7 +1713,7 @@ public class DatabaseDocument extends Document
names_checked.add(uniquename);
- Feature feature = dao.getFeatureByUniqueName(uniquename);
+ Feature feature = dao.getFeatureByUniqueName(uniquename, tsn.getFeatureKey());
if(feature != null)
{
feature.setTimeLastModified(ts);
@@ -1763,11 +1765,19 @@ public class DatabaseDocument extends Document
public boolean checkFeatureTimestamp(final String schema,
final String uniquename,
final Timestamp timestamp,
- final GmodDAO dao)
+ final GmodDAO dao,
+ final String keyName,
+ final Object featureObject)
{
- Feature feature = dao.getFeatureByUniqueName(uniquename);
+ Feature feature = dao.getFeatureByUniqueName(uniquename, keyName);
if(feature == null)
return true;
+
+ if(featureObject instanceof FeatureProp)
+ ((FeatureProp)featureObject).setFeature(feature);
+ else if(featureObject instanceof FeatureLoc)
+ ((FeatureLoc)featureObject).setFeatureByFeatureId(feature);
+
Timestamp now = feature.getTimeLastModified();
if(now != null && timestamp != null)
@@ -1796,6 +1806,7 @@ public class DatabaseDocument extends Document
return true;
}
+
public static void main(String args[])
{
try
@@ -1814,7 +1825,7 @@ public class DatabaseDocument extends Document
List schemas = new Vector();
schemas.add(args[1]);
List featureList = new Vector();
- featureList.add(dao.getFeatureByUniqueName(args[0]));
+ featureList.add(dao.getFeatureByUniqueName(args[0], "polypeptide"));
System.out.println("FINISHED getFeature()");
for(int i = 0; i < featureList.size(); i++)
{