From 3a907ff7336b1816dfa2367a8b57f0e842b4e807 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Thu, 18 Sep 2008 08:16:42 +0000
Subject: [PATCH] load CvTerms in a separate thread when opening standalone
gene editor
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8857 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../sanger/artemis/util/DatabaseDocument.java | 38 +++++++++++++++++--
1 file changed, 34 insertions(+), 4 deletions(-)
diff --git a/uk/ac/sanger/artemis/util/DatabaseDocument.java b/uk/ac/sanger/artemis/util/DatabaseDocument.java
index f9dfc1044..4d2bfe969 100644
--- a/uk/ac/sanger/artemis/util/DatabaseDocument.java
+++ b/uk/ac/sanger/artemis/util/DatabaseDocument.java
@@ -50,6 +50,7 @@ import org.gmod.schema.sequence.FeatureCvTerm;
import org.gmod.schema.sequence.FeatureCvTermProp;
import org.gmod.schema.sequence.FeatureCvTermDbXRef;
import org.gmod.schema.sequence.FeatureCvTermPub;
+import org.gmod.schema.cv.Cv;
import org.gmod.schema.cv.CvTerm;
import org.gmod.schema.general.Db;
import org.gmod.schema.general.DbXRef;
@@ -949,8 +950,12 @@ public class DatabaseDocument extends Document
final boolean readChildren)
throws SQLException, ReadFormatException, ConnectException
{
+ CvTermThread cvThread = null;
if(DatabaseDocument.cvterms == null)
- getCvterms(dao);
+ {
+ cvThread = new CvTermThread(dao);
+ cvThread.start();
+ }
final Hashtable id_store = new Hashtable();
@@ -1030,8 +1035,21 @@ public class DatabaseDocument extends Document
}
logger4j.debug( new String(buff.getBytes()) );
-
+ // now wait for cvterm to be loaded
+ if(cvThread != null)
+ {
+ while(cvThread.isAlive())
+ try
+ {
+ Thread.sleep(10);
+ }
+ catch(InterruptedException e)
+ {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ }
return buff;
}
@@ -1243,7 +1261,9 @@ public class DatabaseDocument extends Document
this_buff.append("ID=" + name + ";");
this_buff.append("feature_id=" + featureId.toString() + ";");
-
+
+ if(feat.getName() != null)
+ this_buff.append("Name=" + feat.getName() + ";");
if(parent_id != null && !parent_id.equals("0"))
{
@@ -1799,7 +1819,10 @@ public class DatabaseDocument extends Document
public Vector getCvTermsByCvName(final String cvName)
{
if(cvterms == null)
+ {
+ logger4j.debug("getCvTermsByCvName LOADING CVTERMS");
getCvterms(getDAOOnly());
+ }
return getCvterms("", cvName);
}
@@ -1890,7 +1913,14 @@ public class DatabaseDocument extends Document
DatabaseDocument doc = (DatabaseDocument)feature.getDocumentEntry().getDocument();
try
{
- cvterms = getCvterms(doc.getDAO());
+ Cv cv = new Cv();
+ cv.setName(cv_name);
+ List synonymCvTerms = doc.getDAO().getCvTermByNameInCv(null, cv);
+ String synonymNames[] = new String[synonymCvTerms.size()];
+ for(int i=0; i<synonymCvTerms.size(); i++)
+ synonymNames[i] = ((CvTerm) synonymCvTerms.get(i)).getName();
+
+ return synonymNames;
}
catch(ConnectException e){}
catch(SQLException e){}
--
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