From 8b81877c7a66ad0cef59bee4be6ef1331e6ac8b5 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Mon, 23 Mar 2009 09:24:50 +0000
Subject: [PATCH] change predicate to fix multiple transcripts
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10225 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../components/TransferAnnotationTool.java | 35 +++++++++++++------
1 file changed, 24 insertions(+), 11 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/TransferAnnotationTool.java b/uk/ac/sanger/artemis/components/TransferAnnotationTool.java
index ca7efb230..83923de1c 100644
--- a/uk/ac/sanger/artemis/components/TransferAnnotationTool.java
+++ b/uk/ac/sanger/artemis/components/TransferAnnotationTool.java
@@ -45,7 +45,6 @@ import java.util.Vector;
import javax.swing.Box;
import javax.swing.JButton;
import javax.swing.JCheckBox;
-import javax.swing.JComponent;
import javax.swing.JFrame;
import javax.swing.JLabel;
import javax.swing.JOptionPane;
@@ -63,6 +62,7 @@ import uk.ac.sanger.artemis.SimpleEntryGroup;
import uk.ac.sanger.artemis.chado.ChadoTransactionManager;
import uk.ac.sanger.artemis.components.genebuilder.GeneEdit;
import uk.ac.sanger.artemis.components.genebuilder.GeneUtils;
+import uk.ac.sanger.artemis.io.ChadoCanonicalGene;
import uk.ac.sanger.artemis.io.DatabaseDocumentEntry;
import uk.ac.sanger.artemis.io.GFFStreamFeature;
import uk.ac.sanger.artemis.io.InvalidRelationException;
@@ -222,7 +222,6 @@ class TransferAnnotationTool extends JFrame
final Box geneNameBox = Box.createVerticalBox();
pane.add(geneNameBox, c);
-
if(geneNames != null)
{
for(int i = 0; i < geneNames.size(); i++)
@@ -277,7 +276,7 @@ class TransferAnnotationTool extends JFrame
JScrollPane jsp = new JScrollPane(geneNameTextArea);
int res = JOptionPane.showConfirmDialog(TransferAnnotationTool.this,
- jsp, "Paste Features to Add",
+ jsp, "Paste Feature Names to Add",
JOptionPane.OK_CANCEL_OPTION);
if(res == JOptionPane.CANCEL_OPTION)
return;
@@ -697,7 +696,8 @@ class TransferAnnotationTool extends JFrame
/**
* Test if the feature is nominated to have annotation transferred
- * to it.
+ * to it. For genes in a chado database it looks at the gene name
+ * and transcript name.
*/
class TransferFeaturePredicate implements FeaturePredicate
{
@@ -707,8 +707,10 @@ class TransferAnnotationTool extends JFrame
private boolean isDatabaseEntry;
private String[] geneNames;
- public TransferFeaturePredicate(final String key, final boolean sameKey,
- final boolean isDatabaseEntry, final String[] geneNames)
+ public TransferFeaturePredicate(final String key,
+ final boolean sameKey,
+ final boolean isDatabaseEntry,
+ final String[] geneNames)
{
this.key = key;
this.sameKey = sameKey;
@@ -722,21 +724,32 @@ class TransferAnnotationTool extends JFrame
if (!sameKey || !targetKey.equals(key))
return false;
- String chadoGeneName = null;
+ Vector chadoNames = null;
if (isDatabaseEntry)
{
GFFStreamFeature gffFeature =
((GFFStreamFeature) targetFeature.getEmblFeature());
if (gffFeature.getChadoGene() != null)
- chadoGeneName = gffFeature.getChadoGene().getGeneUniqueName();
+ {
+ chadoNames = new Vector();
+
+ ChadoCanonicalGene chadoGene = gffFeature.getChadoGene();
+ chadoNames.add(chadoGene.getGeneUniqueName());
+ List transcripts = chadoGene.getTranscripts();
+ for(int i=0;i<transcripts.size();i++)
+ {
+ GFFStreamFeature feature = (GFFStreamFeature) transcripts.get(i);
+ chadoNames.add(GeneUtils.getUniqueName(feature));
+ }
+ }
}
String thisFeatureSystematicName = targetFeature.getSystematicName();
for (int i = 0; i < geneNames.length; i++)
{
- if (geneNames[i].equals(thisFeatureSystematicName)
- || (chadoGeneName != null && geneNames[i].equals(chadoGeneName)))
+ if(geneNames[i].equals(thisFeatureSystematicName) ||
+ (chadoNames != null && chadoNames.contains(geneNames[i])))
{
geneName = geneNames[i];
return true;
@@ -745,7 +758,7 @@ class TransferAnnotationTool extends JFrame
return false;
}
- public String getGeneName()
+ protected String getGeneName()
{
return geneName;
}
--
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