From a78c82836ee4a0eedad21519abca317fcc44aaf8 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Wed, 5 Jul 2006 12:32:28 +0000
Subject: [PATCH] implement multiple locations for chado features
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@4518 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
uk/ac/sanger/artemis/chado/ChadoDemo.java | 8 +-
uk/ac/sanger/artemis/chado/ChadoFeature.java | 80 +++++++++++++++++++-
uk/ac/sanger/artemis/chado/IBatisDAO.java | 2 +-
3 files changed, 84 insertions(+), 6 deletions(-)
diff --git a/uk/ac/sanger/artemis/chado/ChadoDemo.java b/uk/ac/sanger/artemis/chado/ChadoDemo.java
index 17d49dc42..f533a4f8d 100644
--- a/uk/ac/sanger/artemis/chado/ChadoDemo.java
+++ b/uk/ac/sanger/artemis/chado/ChadoDemo.java
@@ -358,8 +358,10 @@ public class ChadoDemo
{
feature = (ChadoFeature) featureList.get(i);
- int fmin = feature.getFeatureloc().getFmin() + 1;
- int fmax = feature.getFeatureloc().getFmax();
+ // assume only one featureloc
+ ChadoFeatureLoc loc = (ChadoFeatureLoc)feature.getFeaturelocsForFeatureId().get(0);
+ int fmin = loc.getFmin() + 1;
+ int fmax = loc.getFmax();
rowData[i][0] = feature.getOrganism().getAbbreviation();
rowData[i][1] = feature.getUniquename();
@@ -367,7 +369,7 @@ public class ChadoDemo
//rowData[i][2] = (String)cvterm.get(new Long(feature.getType_id()));
rowData[i][3] = Integer.toString(feature.getId());
rowData[i][4] = fmin + "..." + fmax;
- rowData[i][5] = Integer.toString(feature.getFeatureloc().getStrand());
+ rowData[i][5] = Integer.toString(loc.getStrand());
rowData[i][6] = feature.getTimelastmodified().toString();
}
return rowData;
diff --git a/uk/ac/sanger/artemis/chado/ChadoFeature.java b/uk/ac/sanger/artemis/chado/ChadoFeature.java
index dbd304096..eb24f47ed 100644
--- a/uk/ac/sanger/artemis/chado/ChadoFeature.java
+++ b/uk/ac/sanger/artemis/chado/ChadoFeature.java
@@ -26,7 +26,9 @@
package uk.ac.sanger.artemis.chado;
import java.sql.Timestamp;
+import java.util.HashSet;
import java.util.Hashtable;
+import java.util.Set;
import java.util.Vector;
import java.util.List;
@@ -56,7 +58,7 @@ public class ChadoFeature
private ChadoCvterm cvterm;
/** feature property */
private ChadoFeatureProp featureprop;
- /** feature location */
+ /** feature location (for a given srcfeature) */
private ChadoFeatureLoc featureloc;
/** feature relationship */
private ChadoFeatureRelationship feature_relationship;
@@ -72,9 +74,13 @@ public class ChadoFeature
private List featureRelationshipsForObjectId;
/** list of ChadoFeatureRelationship parent */
private List featureRelationshipsForSubjectId;
-
+ /** list of feature dbxrefs (ChadoFeatureDbxref) */
+ private List featureDbxrefs;
+ /** list of feature locations for a feature_id */
+ private List featurelocsForFeatureId;
private List featureCvterms = new Vector();
+
/**
* Get the feature_id.
* @return the feature_id
@@ -361,28 +367,80 @@ public class ChadoFeature
}
}
+ /**
+ * Get a list of <code>ChadoFeatureRelationship</code> children
+ * @return
+ */
public List getFeatureRelationshipsForObjectId()
{
return featureRelationshipsForObjectId;
}
+ /**
+ * Set a list of <code>ChadoFeatureRelationship</code> children
+ * @param featureRelationshipsForObjectId
+ */
public void setFeatureRelationshipsForObjectId(
List featureRelationshipsForObjectId)
{
this.featureRelationshipsForObjectId = featureRelationshipsForObjectId;
}
+ /**
+ * Get a list of <code>ChadoFeatureRelationship</code> parent
+ * @return
+ */
public List getFeatureRelationshipsForSubjectId()
{
return featureRelationshipsForSubjectId;
}
+ /**
+ * Set a list of <code>ChadoFeatureRelationship</code> parent
+ * @param featureRelationshipsForSubjectId
+ */
public void setFeatureRelationshipsForSubjectId(
List featureRelationshipsForSubjectId)
{
this.featureRelationshipsForSubjectId = featureRelationshipsForSubjectId;
}
+ /**
+ * Get a list of feature dbxrefs (<code>ChadoFeatureDbxref</code>)
+ * @return
+ */
+ public List getFeatureDbxrefs()
+ {
+ return featureDbxrefs;
+ }
+
+ /**
+ * Set a list of feature dbxrefs (<code>ChadoFeatureDbxref</code>)
+ * @param featureDbxrefs
+ */
+ public void setFeatureDbxrefs(List featureDbxrefs)
+ {
+ this.featureDbxrefs = featureDbxrefs;
+ }
+
+ /**
+ * Get list of feature locations for a feature_id
+ * @return
+ */
+ public List getFeaturelocsForFeatureId()
+ {
+ return featurelocsForFeatureId;
+ }
+
+ /**
+ * Set a list of feature locations for a feature_id
+ * @param featurelocsForFeatureId
+ */
+ public void setFeaturelocsForFeatureId(List featurelocsForFeatureId)
+ {
+ this.featurelocsForFeatureId = featurelocsForFeatureId;
+ }
+
/**
* Used in merging the qualifiers to store them as a <code>Hashtable</code> of
* the cvterm type_id (of the property name) and the property values as a
@@ -419,5 +477,23 @@ public class ChadoFeature
{
return qualifiers;
}
+
+ /**
+ * Utility for finding a feature location from a List that corresponds
+ * to a particular srcfeature.
+ * @param locs List of ChadoFeatureLoc
+ * @param srcfeature_id srcfeature id
+ * @return
+ */
+ public static ChadoFeatureLoc getFeatureLoc(List locs, int srcfeature_id)
+ {
+ for(int i=0; i<locs.size(); i++)
+ {
+ ChadoFeatureLoc loc = (ChadoFeatureLoc)locs.get(i);
+ if(loc.getSrcfeature_id() == srcfeature_id)
+ return loc;
+ }
+ return null;
+ }
}
diff --git a/uk/ac/sanger/artemis/chado/IBatisDAO.java b/uk/ac/sanger/artemis/chado/IBatisDAO.java
index 7276ff54b..ad615761c 100644
--- a/uk/ac/sanger/artemis/chado/IBatisDAO.java
+++ b/uk/ac/sanger/artemis/chado/IBatisDAO.java
@@ -181,7 +181,7 @@ public class IBatisDAO implements ChadoDAO
feature.setSchema(schema);
feature.setFeatureCvterms(cvterm_ids);
- return sqlMap.queryForList("getSchemaResidueFeatures",
+ return sqlMap.queryForList("getResidueFeatures",
feature);
}
--
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