From 5ac0eaa199d12d6d5e0ce4ddca6724867231a94b Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Wed, 26 Jun 2013 09:53:27 +0100
Subject: [PATCH] validation function fixes
---
.../components/database/DatabaseJPanel.java | 19 +++++++++++++------
1 file changed, 13 insertions(+), 6 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/database/DatabaseJPanel.java b/uk/ac/sanger/artemis/components/database/DatabaseJPanel.java
index 28e00d3cb..6988eb0a1 100644
--- a/uk/ac/sanger/artemis/components/database/DatabaseJPanel.java
+++ b/uk/ac/sanger/artemis/components/database/DatabaseJPanel.java
@@ -224,7 +224,8 @@ public class DatabaseJPanel extends JPanel
(DatabaseTreeNode)path.getLastPathComponent();
final String userName = doc.getUserName();
String id = node.getFeatureId();
- final FileViewer fv = new FileViewer((String) node.getUserObject(), false, false, true);
+ final FileViewer fv = new FileViewer(
+ (String) node.getUserObject(), false, false, true);
int nfail = 0;
if(id != null)
@@ -236,8 +237,8 @@ public class DatabaseJPanel extends JPanel
for(int i=0; i<node.getChildCount(); i++)
{
DatabaseTreeNode child = (DatabaseTreeNode)node.getChildAt(i);
- id = node.getFeatureId();
-
+ id = child.getFeatureId();
+
if(id == null)
{
for(int j=0; j<child.getChildCount(); j++)
@@ -249,7 +250,7 @@ public class DatabaseJPanel extends JPanel
}
}
else
- nfail = openValidatePanel(fv, entrySrc, id, userName, node, nfail);
+ nfail = openValidatePanel(fv, entrySrc, id, userName, child, nfail);
}
}
@@ -281,6 +282,13 @@ public class DatabaseJPanel extends JPanel
{
try
{
+ stream_progress_listener.progressMade("Validating... "+(String)node.getUserObject());
+ boolean isMitochondrial = false;
+ if(((String)node.getPreviousNode().getUserObject()).startsWith("mitochondrial_"))
+ isMitochondrial = true;
+ DatabaseTreeNode.setOrganismProps(
+ node.getOrganism().getOrganismProps(), isMitochondrial);
+
final Entry entry = entrySrc.getEntry(srcFeatureId, userName,
stream_progress_listener, null);
((DatabaseDocumentEntry)entry.getEMBLEntry()).setReadOnly(true);
@@ -289,8 +297,7 @@ public class DatabaseJPanel extends JPanel
final ValidateFeature gffTest = new ValidateFeature(entryGrp);
uk.ac.sanger.artemis.io.FeatureVector features = entry.getEMBLEntry().getAllFeatures();
-
-
+
for(int i=0; i<features.size(); i++)
{
if(!gffTest.featureValidate(features.featureAt(i),
--
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