From a1bcf7f851215cffde8164af8b699ea3b383ddd2 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Fri, 14 Dec 2007 11:10:33 +0000
Subject: [PATCH] add option to read children of a feature from the database
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@6772 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../sanger/artemis/util/DatabaseDocument.java | 39 +++++++++++++------
1 file changed, 27 insertions(+), 12 deletions(-)
diff --git a/uk/ac/sanger/artemis/util/DatabaseDocument.java b/uk/ac/sanger/artemis/util/DatabaseDocument.java
index 1d9ddfaaa..09b943075 100644
--- a/uk/ac/sanger/artemis/util/DatabaseDocument.java
+++ b/uk/ac/sanger/artemis/util/DatabaseDocument.java
@@ -122,6 +122,9 @@ public class DatabaseDocument extends Document
private boolean gene_builder;
+ // include children in reading from the database
+ private boolean readChildren = true;
+
private Range range;
private Feature geneFeature;
@@ -323,20 +326,25 @@ public class DatabaseDocument extends Document
{
// add username & host to MDC data for logging
try
- {
+ {
org.apache.log4j.MDC.put("username",doc.getUserName());
}
- catch(NullPointerException npe)
- {
- org.apache.log4j.MDC.put("username",System.getProperty("user.name"));
- }
+ catch(NullPointerException npe)
+ {
+ org.apache.log4j.MDC.put("username",System.getProperty("user.name"));
+ }
- try
- {
- org.apache.log4j.MDC.put("host",
+ try
+ {
+ org.apache.log4j.MDC.put("host",
InetAddress.getLocalHost().getHostAddress());
- }
- catch(Exception e) {}
+ }
+ catch(Exception e) {}
+ }
+
+ public void setReadChildren(final boolean readChildren)
+ {
+ this.readChildren = readChildren;
}
/**
@@ -459,7 +467,7 @@ public class DatabaseDocument extends Document
schemaList.add(schema);
ByteBuffer bb = getGeneFeature(srcFeatureId,
- schemaList, dao);
+ schemaList, dao, readChildren);
return new ByteArrayInputStream(bb.getBytes());
}
else if(range != null)
@@ -902,7 +910,8 @@ public class DatabaseDocument extends Document
*/
private ByteBuffer getGeneFeature(final String search_gene,
final List schema_search,
- GmodDAO dao)
+ GmodDAO dao,
+ final boolean readChildren)
throws SQLException, ReadFormatException, ConnectException
{
if(DatabaseDocument.cvterms == null)
@@ -954,6 +963,12 @@ public class DatabaseDocument extends Document
id_store, parent.getUniqueName(), src_id, buff, chadoFeature);
+ if(!readChildren)
+ {
+ logger4j.debug( new String(buff.getBytes()) );
+ return buff;
+ }
+
// get children of gene
List relations = new Vector(chadoFeature.getFeatureRelationshipsForObjectId());
--
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