diff --git a/uk/ac/sanger/artemis/io/ValidateFeature.java b/uk/ac/sanger/artemis/io/ValidateFeature.java
index 333860d2057df76b841523142894fcfd7b1359b8..027893ec348e498eccce0715235d7c5b99ac3d71 100644
--- a/uk/ac/sanger/artemis/io/ValidateFeature.java
+++ b/uk/ac/sanger/artemis/io/ValidateFeature.java
@@ -31,12 +31,12 @@ import java.io.StringReader;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
+import java.util.Set;
import java.util.Vector;
import java.util.regex.Pattern;
import javax.swing.JOptionPane;
-
import org.apache.log4j.Level;
import uk.ac.sanger.artemis.EntryGroup;
@@ -66,7 +66,6 @@ import uk.ac.sanger.artemis.util.StringVector;
public class ValidateFeature
{
-
private static String[] geneModelParts;
//##sequence-region seqid start end
@@ -162,6 +161,7 @@ public class ValidateFeature
* - check boundaries are valid
* - check all features are on the same strand
* - check CDS features have a phase
+ * - check partial attributes consistent
* - check attribute column
* - qualifiers have a value (not empty)
* - only reserved tags start with uppercase
@@ -172,7 +172,7 @@ public class ValidateFeature
* @param showOnlyFailures
* @return report
*/
- public LinkedHashMap<String, Level> featureValidate(final uk.ac.sanger.artemis.io.Feature f,
+ private LinkedHashMap<String, Level> featureValidate(final uk.ac.sanger.artemis.io.Feature f,
final boolean showOnlyFailures)
{
boolean pass = true;
@@ -211,6 +211,17 @@ public class ValidateFeature
pass = false;
report.put("Gene features found on different strand", Level.FATAL);
}
+
+ if(!isPartialConsistent(gffFeature, "Start_range"))
+ {
+ pass = false;
+ report.put("Partial attribute 'Start_range' not consistent", Level.FATAL);
+ }
+ if(!isPartialConsistent(gffFeature, "End_range"))
+ {
+ pass = false;
+ report.put("Partial attribute 'End_range' not consistent", Level.FATAL);
+ }
}
if( (entryGrp == null || !GeneUtils.isDatabaseEntry(entryGrp)) && !isCDSPhaseOK(gffFeature))
@@ -313,9 +324,8 @@ public class ValidateFeature
{
final QualifierInfo qI = eInfo.getQualifierInfo("GO");
final StringVector qualifierStrs = StreamQualifier.toStringVector(qI,q);
- for (int i = 0; i < qualifierStrs.size(); ++i)
+ for (String qualifierStr: qualifierStrs)
{
- final String qualifierStr = qualifierStrs.elementAt(i);
final String code = getEvidenceCodeAbbreviation(qualifierStr);
final String goid = getField("GOid=", qualifierStr);
final String with = getField("with=", qualifierStr);
@@ -412,7 +422,7 @@ public class ValidateFeature
* 1 - no gene found
* 2 - missing transcript
*/
- public static int isCompleteGeneModelOK(final GFFStreamFeature gffFeature)
+ private static int isCompleteGeneModelOK(final GFFStreamFeature gffFeature)
{
final ChadoCanonicalGene gene = gffFeature.getChadoGene();
if(gene == null)
@@ -425,7 +435,7 @@ public class ValidateFeature
return 0;
}
- public static int isBoundaryOK(final GFFStreamFeature gffFeature)
+ private static int isBoundaryOK(final GFFStreamFeature gffFeature)
{
final ChadoCanonicalGene gene = gffFeature.getChadoGene();
int gb = 0;
@@ -434,7 +444,7 @@ public class ValidateFeature
return gb;
}
- public static boolean isStrandOK(final GFFStreamFeature gffFeature)
+ private static boolean isStrandOK(final GFFStreamFeature gffFeature)
{
final ChadoCanonicalGene gene = gffFeature.getChadoGene();
if(gene != null && isGene(gffFeature) && !GeneUtils.isStrandOK(gene))
@@ -442,6 +452,101 @@ public class ValidateFeature
return true;
}
+ /**
+ * Test if the partial qualifiers are consistent within a gene model
+ * @param gffFeature
+ * @param partialKeyStr - either Start_range or End_range qualifier keys
+ * @return
+ */
+ private static boolean isPartialConsistent(final GFFStreamFeature gffFeature,
+ final String partialKeyStr)
+ {
+ final ChadoCanonicalGene gene = gffFeature.getChadoGene();
+ if(gene == null)
+ return true;
+ try
+ {
+ // is the gene marked as partial
+ boolean partial =
+ (gene.getGene().getQualifierByName(partialKeyStr) == null ? false : true);
+
+ if(partial)
+ {
+ if(!isPartialChildren(partial, gene, gene.getGene(), partialKeyStr))
+ return false;
+ }
+ else
+ {
+ final List<uk.ac.sanger.artemis.io.Feature> transcripts = gene.getTranscripts();
+ for(uk.ac.sanger.artemis.io.Feature f: transcripts)
+ {
+ // is the transcript marked as partial
+ partial = (f.getQualifierByName(partialKeyStr) == null ? false : true);
+ if(!isPartialChildren(partial, gene, f, partialKeyStr))
+ return false;
+ }
+ }
+ }
+ catch (Exception e){ e.printStackTrace(); }
+ return true;
+ }
+
+ /**
+ * Return true if the child features agree with the parent
+ * feature for a given key
+ * @param parentIsPartial
+ * @param gene
+ * @param f
+ * @param partialKeyStr
+ * @return
+ * @throws InvalidRelationException
+ */
+ private static boolean isPartialChildren(
+ final boolean parentIsPartial,
+ final ChadoCanonicalGene gene,
+ final uk.ac.sanger.artemis.io.Feature f,
+ final String partialKeyStr) throws InvalidRelationException
+ {
+ final Set<uk.ac.sanger.artemis.io.Feature> children = gene.getChildren(f);
+ for(uk.ac.sanger.artemis.io.Feature child: children)
+ {
+ String keyStr = child.getKey().getKeyString();
+ boolean isComplement = f.getLocation().isComplement();
+ if(keyStr.equals("three_prime_UTR"))
+ {
+ if(isComplement)
+ {
+ if(partialKeyStr.equals("End_range"))
+ continue;
+ }
+ else
+ {
+ if(partialKeyStr.equals("Start_range"))
+ continue;
+ }
+ }
+ else if(keyStr.equals("five_prime_UTR"))
+ {
+ if(isComplement)
+ {
+ if(partialKeyStr.equals("Start_range"))
+ continue;
+ }
+ else
+ {
+ if(partialKeyStr.equals("End_range"))
+ continue;
+ }
+ }
+
+ boolean partial = (child.getQualifierByName(partialKeyStr) == null ? false : true);
+ if( ( partial && !parentIsPartial ) ||
+ ( !partial && parentIsPartial ) )
+ return false;
+ }
+ return true;
+ }
+
/**
* The phase is REQUIRED for all CDS features.
* @param gffFeature