From 0b7e5aee8a2f159e260ae29dbda67b4ce17dbdf3 Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Tue, 23 Aug 2011 10:11:30 +0100
Subject: [PATCH] use isStrandOK() to check strand is consistent within the
gene model
---
.../genebuilder/GeneBuilderFrame.java | 20 ++++++++--
.../components/genebuilder/GeneUtils.java | 37 ++++++++++++++++++-
2 files changed, 51 insertions(+), 6 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/genebuilder/GeneBuilderFrame.java b/uk/ac/sanger/artemis/components/genebuilder/GeneBuilderFrame.java
index 847710b30..ad4232479 100644
--- a/uk/ac/sanger/artemis/components/genebuilder/GeneBuilderFrame.java
+++ b/uk/ac/sanger/artemis/components/genebuilder/GeneBuilderFrame.java
@@ -343,13 +343,25 @@ public class GeneBuilderFrame extends JFrame
geneBuilderHash.put(chado_gene.getGeneUniqueName(), gbFrame);
}
}
- else if(!GeneUtils.isBoundaryOK(chado_gene))
+ else
{
- int result = JOptionPane.showConfirmDialog(this,
+ if(!GeneUtils.isBoundaryOK(chado_gene))
+ {
+ int result = JOptionPane.showConfirmDialog(this,
"Gene model boundary needs fixing.\nFix this now?",
"Gene Boundary", JOptionPane.YES_NO_OPTION);
- if(result == JOptionPane.YES_OPTION)
- GeneUtils.checkGeneBoundary(chado_gene);
+ if(result == JOptionPane.YES_OPTION)
+ GeneUtils.checkGeneBoundary(chado_gene);
+ }
+
+ if(!GeneUtils.isStrandOK(chado_gene))
+ {
+ JOptionPane.showMessageDialog(this,
+ "All gene features should be on the same strand.\n"+
+ "Check the strand of each of the features (gene,\n"+
+ "transcript, CDS, polypeptide).",
+ "Check Strand", JOptionPane.WARNING_MESSAGE);
+ }
}
super.dispose();
diff --git a/uk/ac/sanger/artemis/components/genebuilder/GeneUtils.java b/uk/ac/sanger/artemis/components/genebuilder/GeneUtils.java
index c771f0b9c..e14ddb2f1 100644
--- a/uk/ac/sanger/artemis/components/genebuilder/GeneUtils.java
+++ b/uk/ac/sanger/artemis/components/genebuilder/GeneUtils.java
@@ -90,8 +90,7 @@ import uk.ac.sanger.artemis.Selection;
public class GeneUtils
{
- private static final long serialVersionUID = 1L;
- private static Vector hideFeatures = new Vector();
+ private static Vector<String> hideFeatures = new Vector<String>();
private static JCheckBox showObsolete = new JCheckBox("Show Obsolete Features",false);
private static String nonCodingTranscripts[] =
{ "tRNA", "rRNA", "snRNA", "snoRNA", "ncRNA", "scRNA" };
@@ -1003,6 +1002,40 @@ public class GeneUtils
chado_gene.deleteFeature(embl_feature);
}
}
+
+ /**
+ * Check gene model strands for any inconsistencies
+ * @param chado_gene
+ * @return true is gene model ranges are correct
+ */
+ protected static boolean isStrandOK(final ChadoCanonicalGene chado_gene)
+ {
+ boolean isRev = chado_gene.getGene().getLocation().isComplement();
+ final List<Feature> transcripts = chado_gene.getTranscripts();
+
+ for(int i=0; i<transcripts.size(); i++)
+ {
+ final Feature transcript = (Feature)transcripts.get(i);
+
+ if(isRev ^ transcript.getLocation().isComplement())
+ return false;
+
+ final Feature protein =
+ chado_gene.getProteinOfTranscript(GeneUtils.getUniqueName(transcript));
+ if(protein != null && (isRev ^ protein.getLocation().isComplement()))
+ return false;
+
+ final Set<Feature> children = chado_gene.getChildren(transcript);
+ final Iterator<Feature> it = children.iterator();
+ while(it.hasNext())
+ {
+ final Feature feature = it.next();
+ if(isRev ^ feature.getLocation().isComplement())
+ return false;
+ }
+ }
+ return true;
+ }
/**
* Check gene model boundaries for any inconsistencies
--
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