From cc6ef18268abcc2aa4b8f42ae9ccf861350a4480 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Tue, 24 Nov 2009 12:14:37 +0000
Subject: [PATCH] show the CDS phase information
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@12422 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../genebuilder/gff/BasicPropertiesPanel.java | 24 ++++++++++++++++---
1 file changed, 21 insertions(+), 3 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/genebuilder/gff/BasicPropertiesPanel.java b/uk/ac/sanger/artemis/components/genebuilder/gff/BasicPropertiesPanel.java
index b600ebc29..c1eca86b3 100644
--- a/uk/ac/sanger/artemis/components/genebuilder/gff/BasicPropertiesPanel.java
+++ b/uk/ac/sanger/artemis/components/genebuilder/gff/BasicPropertiesPanel.java
@@ -23,6 +23,7 @@
package uk.ac.sanger.artemis.components.genebuilder.gff;
import java.awt.FlowLayout;
+import java.util.List;
import javax.swing.Box;
import javax.swing.JPanel;
@@ -34,12 +35,14 @@ import uk.ac.sanger.artemis.components.genebuilder.GeneUtils;
import uk.ac.sanger.artemis.io.ChadoCanonicalGene;
import uk.ac.sanger.artemis.io.GFFStreamFeature;
import uk.ac.sanger.artemis.io.QualifierVector;
+import uk.ac.sanger.artemis.util.DatabaseDocument;
public class BasicPropertiesPanel extends JPanel
{
private static final long serialVersionUID = 1L;
private PropertiesPanel genePropPanel;
private PropertiesPanel transcriptPropPanel;
+ private PropertiesPanel exonPropPanel;
private PropertiesPanel pepPropPanel;
private Feature gene;
@@ -50,21 +53,31 @@ public class BasicPropertiesPanel extends JPanel
Box yBox = Box.createVerticalBox();
gene = (Feature) chadoGene.getGene().getUserData();
- genePropPanel = new PropertiesPanel(gene, false, true, false);
+ genePropPanel = new PropertiesPanel(gene, true, false, true, false);
yBox.add(genePropPanel);
Feature transcript = gbFrame.getSelectedTranscriptFeature();
- transcriptPropPanel = new PropertiesPanel(transcript, false, false, false);
+ transcriptPropPanel = new PropertiesPanel(transcript, true, false, false, false);
yBox.add(transcriptPropPanel);
String transcriptName = GeneUtils.getUniqueName(transcript.getEmblFeature());
+
+ List<uk.ac.sanger.artemis.io.Feature> exons =
+ chadoGene.getSpliceSitesOfTranscript(transcriptName, DatabaseDocument.EXONMODEL);
+ if(exons != null)
+ {
+ Feature exon = (Feature) exons.get(0).getUserData();
+ exonPropPanel = new PropertiesPanel(exon, false, false, false, false);
+ yBox.add(exonPropPanel);
+ }
+
uk.ac.sanger.artemis.io.Feature pep =
chadoGene.getProteinOfTranscript(transcriptName);
if(pep != null)
{
Feature protein = (Feature) pep.getUserData();
- pepPropPanel = new PropertiesPanel(protein, false, false, false);
+ pepPropPanel = new PropertiesPanel(protein, true, false, false, false);
yBox.add(pepPropPanel);
}
@@ -86,6 +99,11 @@ public class BasicPropertiesPanel extends JPanel
return transcriptPropPanel.getGffQualifiers(feature);
}
+ public QualifierVector getExonProperties(Feature feature)
+ {
+ return exonPropPanel.getGffQualifiers(feature);
+ }
+
public void updateObsoleteSettings()
{
if(!genePropPanel.obsoleteChanged)
--
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