From 7edab300ca99091689b3aae05374ab9b409254b4 Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Wed, 17 Aug 2011 12:46:25 +0100
Subject: [PATCH] fix for partials and UTR ordering
---
.../artemis/io/PublicDBDocumentEntry.java | 44 +++++++++++++++++++
1 file changed, 44 insertions(+)
diff --git a/uk/ac/sanger/artemis/io/PublicDBDocumentEntry.java b/uk/ac/sanger/artemis/io/PublicDBDocumentEntry.java
index a6f00db82..b8ab91767 100644
--- a/uk/ac/sanger/artemis/io/PublicDBDocumentEntry.java
+++ b/uk/ac/sanger/artemis/io/PublicDBDocumentEntry.java
@@ -250,6 +250,13 @@ public class PublicDBDocumentEntry extends SimpleDocumentEntry
addNewQualifier(qualifiers, newIDQualifier);
geneQualifiers.removeQualifierByName("ID");
}
+ else if(ntranscripts == 1)
+ {
+ if(qualifiers.getQualifierByName("isFminPartial") != null)
+ addNewQualifier(qualifiers, qualifiers.getQualifierByName("isFminPartial"));
+ if(qualifiers.getQualifierByName("isFmaxPartial") != null)
+ addNewQualifier(qualifiers, qualifiers.getQualifierByName("isFmaxPartial"));
+ }
combineQualifiers(qualifiers, geneQualifiers, true);
}
else if(GeneUtils.isNonCodingTranscripts(key))
@@ -266,6 +273,7 @@ public class PublicDBDocumentEntry extends SimpleDocumentEntry
try
{
+ location = handlePartials(qualifiers, location);
for(int i=0; i<DATABASE_QUALIFIERS_TO_MAP.length; i++)
{
if(!getEntryInformation().isValidQualifier(DATABASE_QUALIFIERS_TO_MAP[i][0]))
@@ -355,6 +363,8 @@ public class PublicDBDocumentEntry extends SimpleDocumentEntry
if(start != feature.getLocation().getTotalRange().getStart())
return null;
+ if(feature.getLocation().isComplement())
+ ranges.reverse();
location =
new Location(ranges, feature.getLocation().isComplement());
}
@@ -743,6 +753,40 @@ public class PublicDBDocumentEntry extends SimpleDocumentEntry
}
}
+ /**
+ * Use '<' and '>' signs in the location descriptors to
+ * indicate that the sequence is partial.
+ * @param qualifiers
+ * @param location
+ * @return
+ */
+ private Location handlePartials(QualifierVector qualifiers, Location location)
+ {
+ if(qualifiers.getQualifierByName("isFminPartial") != null)
+ {
+ try
+ {
+ location = new Location(location.toString().replaceFirst("(\\d)", "<$1"));
+ }
+ catch (LocationParseException e)
+ {
+ e.printStackTrace();
+ }
+ }
+ else if(qualifiers.getQualifierByName("isFmaxPartial") != null)
+ {
+ try
+ {
+ location = new Location(location.toString().replaceAll("^(.*)(\\.)(.*)$","$1$2>$3"));
+ }
+ catch (LocationParseException e)
+ {
+ e.printStackTrace();
+ }
+ }
+ return location;
+ }
+
/**
* Change the stop_codon_redefined_as_selenocysteine SO qualifier
* to the transl_except EMBL qualifier.
--
GitLab