From 8880fbfee8b65b09488520287cc072d817dea89f Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Fri, 6 Sep 2013 10:29:12 +0100
Subject: [PATCH] change visibility of functions and fix for non coding
transcripts in GFF files
---
uk/ac/sanger/artemis/io/ValidateFeature.java | 41 +++++++++++---------
1 file changed, 23 insertions(+), 18 deletions(-)
diff --git a/uk/ac/sanger/artemis/io/ValidateFeature.java b/uk/ac/sanger/artemis/io/ValidateFeature.java
index 83994ce31..d1dc8836d 100644
--- a/uk/ac/sanger/artemis/io/ValidateFeature.java
+++ b/uk/ac/sanger/artemis/io/ValidateFeature.java
@@ -158,6 +158,14 @@ public class ValidateFeature
new FeatureListFrame (title, sel, gotoSrc, fltrGrp, plotGrp);
featureList.setVisible(true);
}
+
+ protected static boolean isGFF(final uk.ac.sanger.artemis.io.Feature f, final EntryGroup entryGrp)
+ {
+ final boolean isGFF = entryGrp == null || GeneUtils.isGFFEntry( entryGrp );
+ if(isGFF && f instanceof GFFStreamFeature)
+ return true;
+ return false;
+ }
/**
* Check a single feature
@@ -183,8 +191,7 @@ public class ValidateFeature
final LinkedHashMap<String, Level> report = new LinkedHashMap<String, Level>();
final String fTxt = featureTxt(f);
- final boolean isGFF = entryGrp == null || GeneUtils.isGFFEntry( entryGrp );
- if(isGFF && f instanceof GFFStreamFeature)
+ if(isGFF(f, entryGrp))
{
final GFFStreamFeature gffFeature = (GFFStreamFeature)f;
report.put("\n"+GeneUtils.getUniqueName(gffFeature)+" ("+fTxt+"):", Level.INFO);
@@ -229,7 +236,7 @@ public class ValidateFeature
report.put("Prefix of ID attribute not consistent within gene model", Level.FATAL);
}
}
-
+
if( (entryGrp == null || !GeneUtils.isDatabaseEntry(entryGrp)) && !isCDSPhaseOK(gffFeature))
{
pass = false;
@@ -432,7 +439,7 @@ public class ValidateFeature
* 1 - no gene found
* 2 - missing transcript
*/
- private static int isCompleteGeneModelOK(final GFFStreamFeature gffFeature)
+ protected static int isCompleteGeneModelOK(final GFFStreamFeature gffFeature)
{
final ChadoCanonicalGene gene = gffFeature.getChadoGene();
if(gene == null)
@@ -445,7 +452,7 @@ public class ValidateFeature
return 0;
}
- private static int isBoundaryOK(final GFFStreamFeature gffFeature)
+ protected static int isBoundaryOK(final GFFStreamFeature gffFeature)
{
final ChadoCanonicalGene gene = gffFeature.getChadoGene();
int gb = 0;
@@ -454,7 +461,7 @@ public class ValidateFeature
return gb;
}
- private static boolean isStrandOK(final GFFStreamFeature gffFeature)
+ protected static boolean isStrandOK(final GFFStreamFeature gffFeature)
{
final ChadoCanonicalGene gene = gffFeature.getChadoGene();
if(gene != null && isGene(gffFeature) && !GeneUtils.isStrandOK(gene))
@@ -468,7 +475,7 @@ public class ValidateFeature
* @param partialKeyStr - either Start_range or End_range qualifier keys
* @return
*/
- private static boolean isPartialConsistent(final GFFStreamFeature gffFeature,
+ protected static boolean isPartialConsistent(final GFFStreamFeature gffFeature,
final String partialKeyStr)
{
final ChadoCanonicalGene gene = gffFeature.getChadoGene();
@@ -562,7 +569,7 @@ public class ValidateFeature
* @param gffFeature
* @return true if the prefix is the same within the gene model features
*/
- private static boolean isIdPrefixConsistent(final GFFStreamFeature gffFeature)
+ protected static boolean isIdPrefixConsistent(final GFFStreamFeature gffFeature)
{
final ChadoCanonicalGene gene = gffFeature.getChadoGene();
if(gene == null)
@@ -613,7 +620,7 @@ public class ValidateFeature
* Check attribute column
* @param gffFeature
*/
- public static String isAttributesOK(final GFFStreamFeature gffFeature)
+ protected static String isAttributesOK(final GFFStreamFeature gffFeature)
{
final StringBuilder str = new StringBuilder();
final QualifierVector qualifiers = gffFeature.getQualifiers();
@@ -661,7 +668,7 @@ public class ValidateFeature
return str.toString();
}
- public boolean isInternalStops(final uk.ac.sanger.artemis.io.Feature feature)
+ protected boolean isInternalStops(final uk.ac.sanger.artemis.io.Feature feature)
{
if(feature.getUserData() == null)
return false;
@@ -691,7 +698,7 @@ public class ValidateFeature
if(cds_predicate != null)
return cds_predicate;
- if(entryGrp != null && GeneUtils.isDatabaseEntry( entryGrp ))
+ if(entryGrp != null && GeneUtils.isGFFEntry( entryGrp ))
{
final FeaturePredicate codingPredicate = new FeaturePredicate(){
@@ -752,7 +759,7 @@ public class ValidateFeature
return msg;
}
- private static boolean isPartOfGene(final GFFStreamFeature gffFeature)
+ protected static boolean isPartOfGene(final GFFStreamFeature gffFeature)
{
final String keyStr = gffFeature.getKey().getKeyString();
for(String part: getGeneModelParts())
@@ -1052,10 +1059,10 @@ public class ValidateFeature
System.out.println("VALIDATING... "+seq);
uk.ac.sanger.artemis.Entry entry = ReadAndWriteEntry.readEntryFromDatabase(seq, entrySrc);
entrySrc = ReadAndWriteEntry.getEntrySource();
- final EntryGroup egroup = new SimpleEntryGroup();
- egroup.add(entry);
+ final EntryGroup egrp = new SimpleEntryGroup();
+ egrp.add(entry);
- ValidateFeature validate = new ValidateFeature(egroup);
+ ValidateFeature validate = new ValidateFeature(egrp);
if(outfile == null)
validate.showReport(entry.getEMBLEntry(), seq);
else
@@ -1074,10 +1081,8 @@ public class ValidateFeature
{
System.out.println("VALIDATING... "+seq);
final Document doc = DocumentFactory.makeDocument(seq);
- final EntryInformation artemis_entry_information =
- Options.getArtemisEntryInformation();
final uk.ac.sanger.artemis.io.Entry entry = EntryFileDialog.getEntryFromFile(
- null, doc, artemis_entry_information, false);
+ null, doc, Options.getArtemisEntryInformation(), false);
ValidateFeature validate = new ValidateFeature(null);
if(outfile == null)
--
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