From f5aaa2c6f00261dbd144d4c5476109ef582c44bd Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Wed, 18 Sep 2013 15:23:32 +0100
Subject: [PATCH] add options to show obsolete features
---
.../artemis/components/ValidateViewer.java | 30 +++++++++++++++----
1 file changed, 24 insertions(+), 6 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/ValidateViewer.java b/uk/ac/sanger/artemis/components/ValidateViewer.java
index 96906e1e8..adc685952 100644
--- a/uk/ac/sanger/artemis/components/ValidateViewer.java
+++ b/uk/ac/sanger/artemis/components/ValidateViewer.java
@@ -55,7 +55,8 @@ public class ValidateViewer extends FileViewer implements EntryGroupChangeListen
private static final long serialVersionUID = 1L;
private EntryGroup entryGrp;
private FeatureVector selectedFeatures;
- private JCheckBox showFailedFeatures = new JCheckBox("Show only failed features", true);
+ private JCheckBox showFailedFeatures = new JCheckBox("failed features only", true);
+ private JCheckBox showObsoleteFeatures = new JCheckBox("obsolete features", false);
private boolean inAutoFix = false;
/**
@@ -154,7 +155,6 @@ public class ValidateViewer extends FileViewer implements EntryGroupChangeListen
fixButton.setEnabled(false);
button_panel.add(fixButton);
-
button_panel.add(showFailedFeatures);
showFailedFeatures.addItemListener(new ItemListener(){
public void itemStateChanged(ItemEvent arg0)
@@ -163,6 +163,15 @@ public class ValidateViewer extends FileViewer implements EntryGroupChangeListen
}
});
+ if(GeneUtils.isGFFEntry(entryGrp))
+ button_panel.add(showObsoleteFeatures);
+ showObsoleteFeatures.addItemListener(new ItemListener(){
+ public void itemStateChanged(ItemEvent arg0)
+ {
+ update();
+ }
+ });
+
entryGrp.addEntryGroupChangeListener(new EntryGroupChangeListener(){
public void entryGroupChanged(EntryGroupChangeEvent event)
{
@@ -203,13 +212,22 @@ public class ValidateViewer extends FileViewer implements EntryGroupChangeListen
super.setText("");
final ValidateFeature gffTest = new ValidateFeature(entryGrp);
int nfail = 0;
+ int total = 0;
for(int i=0; i<features.size(); i++)
- if(!gffTest.featureValidate(features.elementAt(i).getEmblFeature(),
+ {
+ uk.ac.sanger.artemis.io.Feature f = features.elementAt(i).getEmblFeature();
+ if(!showObsoleteFeatures.isSelected() &&
+ f instanceof GFFStreamFeature && GeneUtils.isObsolete((GFFStreamFeature)f))
+ continue;
+
+ if(!gffTest.featureValidate(f,
this, showFailedFeatures.isSelected()))
nfail++;
-
- setTitle("Validation Report :: "+ features.size()+
- " feature(s) Pass: "+(features.size()-nfail)+" Failed: "+nfail);
+ total++;
+ }
+
+ setTitle("Validation Report :: "+ total+
+ " feature(s) Pass: "+(total-nfail)+" Failed: "+nfail);
}
private FeatureVector getFeatures()
--
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