From f20232461caa4ebc36f00bdae6601718f355b2b1 Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Fri, 15 Jun 2012 09:41:20 +0100
Subject: [PATCH] use mitochondrialTranslationTable in chado organismprop
---
.../components/database/DatabaseJPanel.java | 13 ++++++-
.../components/database/DatabaseTreeNode.java | 38 ++++++++++++-------
2 files changed, 36 insertions(+), 15 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/database/DatabaseJPanel.java b/uk/ac/sanger/artemis/components/database/DatabaseJPanel.java
index 278ffee91..fa3de918c 100644
--- a/uk/ac/sanger/artemis/components/database/DatabaseJPanel.java
+++ b/uk/ac/sanger/artemis/components/database/DatabaseJPanel.java
@@ -183,7 +183,12 @@ public class DatabaseJPanel extends JPanel
final String id = seq_node.getFeatureId();
if(id != null)
{
- boolean readOnly = DatabaseTreeNode.setOrganismProps(seq_node.getOrganism().getOrganismProps());
+ boolean isMitochondrial = false;
+ if(seq_node.getFeatureType() != null &&
+ seq_node.getFeatureType().startsWith("mitochondrial_"))
+ isMitochondrial = true;
+ boolean readOnly = DatabaseTreeNode.setOrganismProps(
+ seq_node.getOrganism().getOrganismProps(), isMitochondrial);
getEntryEditFromDatabase(id, entry_source, tree,
status_line, stream_progress_listener,
splitGFFEntry, splash_main,
@@ -276,7 +281,11 @@ public class DatabaseJPanel extends JPanel
f = it.next().getFeatureBySrcFeatureId();
}
- boolean readOnly = DatabaseTreeNode.setOrganismProps(f.getOrganism().getOrganismProps());
+ boolean isMitochondrial = false;
+ if(f.getCvTerm().getName().startsWith("mitochondrial_"))
+ isMitochondrial = true;
+ boolean readOnly = DatabaseTreeNode.setOrganismProps(
+ f.getOrganism().getOrganismProps(), isMitochondrial);
// warn when opening duplicate entries at the same time
if(opening.contains(f.getUniqueName()))
{
diff --git a/uk/ac/sanger/artemis/components/database/DatabaseTreeNode.java b/uk/ac/sanger/artemis/components/database/DatabaseTreeNode.java
index 567bc4f73..5a576b544 100644
--- a/uk/ac/sanger/artemis/components/database/DatabaseTreeNode.java
+++ b/uk/ac/sanger/artemis/components/database/DatabaseTreeNode.java
@@ -52,9 +52,7 @@ import java.util.List;
import java.util.Set;
/**
-*
* File node for local file tree manager
-*
*/
public class DatabaseTreeNode extends DefaultMutableTreeNode
implements Transferable, Serializable
@@ -68,6 +66,7 @@ public class DatabaseTreeNode extends DefaultMutableTreeNode
{ DATABASETREENODE, DataFlavor.stringFlavor };
private String featureId;
+ private String featureType; // e.g. chromosome, mitochondrial_chromosome
private transient Organism organism;
private String organismCommonName;
private boolean isLeaf = false;
@@ -75,12 +74,12 @@ public class DatabaseTreeNode extends DefaultMutableTreeNode
private static transient DatabaseDocument dbDoc;
private boolean explored = false;
- public DatabaseTreeNode(final String name)
+ protected DatabaseTreeNode(final String name)
{
super(name);
}
- public DatabaseTreeNode(final String name,
+ private DatabaseTreeNode(final String name,
final boolean isLeaf)
{
super(name);
@@ -95,7 +94,7 @@ public class DatabaseTreeNode extends DefaultMutableTreeNode
* @param userName
* @param dbDoc
*/
- public DatabaseTreeNode(final String name,
+ protected DatabaseTreeNode(final String name,
final boolean isLeaf,
final Organism organism,
final String userName,
@@ -116,14 +115,16 @@ public class DatabaseTreeNode extends DefaultMutableTreeNode
* @param featureId
* @param userName
*/
- public DatabaseTreeNode(final String name,
+ private DatabaseTreeNode(final String name,
final Organism organism,
final String featureId,
+ final String featureType,
final String userName)
{
super(name);
this.organism = organism;
this.featureId = featureId;
+ this.featureType = featureType;
this.userName = userName;
if(getOrganism() != null)
setOrganismCommonName();
@@ -147,7 +148,7 @@ public class DatabaseTreeNode extends DefaultMutableTreeNode
* @param op
* @return
*/
- public static boolean setOrganismProps(Set<OrganismProp> op)
+ public static boolean setOrganismProps(Set<OrganismProp> op, final boolean isMitochondrial)
{
Splash splash = getSplash();
boolean readOnly = false;
@@ -155,9 +156,14 @@ public class DatabaseTreeNode extends DefaultMutableTreeNode
while (it.hasNext())
{
OrganismProp organismProp = it.next();
- if(splash != null &&
- organismProp.getCvTerm().getName().equals("translationTable"))
- splash.setTranslationTable(organismProp.getValue());
+ if(splash != null)
+ {
+ if( (isMitochondrial &&
+ organismProp.getCvTerm().getName().equals("mitochondrialTranslationTable")) ||
+ (!isMitochondrial &&
+ organismProp.getCvTerm().getName().equals("translationTable")))
+ splash.setTranslationTable(organismProp.getValue());
+ }
if(organismProp.getCvTerm().getName().equals("frozen") &&
organismProp.getValue().equals("yes"))
@@ -211,7 +217,9 @@ public class DatabaseTreeNode extends DefaultMutableTreeNode
typeNode = (DatabaseTreeNode) sequenceNode.get(f.getCvTerm().getName());
DatabaseTreeNode seqNode = new DatabaseTreeNode(
- f.getUniqueName(), getOrganism(), Integer.toString(f.getFeatureId()), getUserName());
+ f.getUniqueName(), getOrganism(),
+ Integer.toString(f.getFeatureId()),
+ f.getCvTerm().getName(), getUserName());
seqNode.isLeaf = true;
typeNode.add(seqNode);
@@ -266,7 +274,7 @@ public class DatabaseTreeNode extends DefaultMutableTreeNode
if(d.equals(DATABASETREENODE))
return new DatabaseTreeNode((String)getUserObject(),
organism,
- getFeatureId(), getUserName());
+ getFeatureId(), getFeatureType(), getUserName());
else if(d.equals(DataFlavor.stringFlavor))
{
String name = getOrganism().getCommonName();
@@ -277,11 +285,15 @@ public class DatabaseTreeNode extends DefaultMutableTreeNode
else throw new UnsupportedFlavorException(d);
}
-
public String getFeatureId()
{
return featureId;
}
+
+ public String getFeatureType()
+ {
+ return featureType;
+ }
protected void setDbDoc(DatabaseDocument dbDoc)
{
--
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