From 0229dc93fdfb1162b41e394858dd7880a5a57b5d Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Wed, 5 Jul 2006 12:29:42 +0000
Subject: [PATCH] chadoToGFF takes a featureloc
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@4515 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
uk/ac/sanger/artemis/util/DatabaseDocument.java | 13 ++++++++-----
1 file changed, 8 insertions(+), 5 deletions(-)
diff --git a/uk/ac/sanger/artemis/util/DatabaseDocument.java b/uk/ac/sanger/artemis/util/DatabaseDocument.java
index 82cefdfd3..a76b1e654 100644
--- a/uk/ac/sanger/artemis/util/DatabaseDocument.java
+++ b/uk/ac/sanger/artemis/util/DatabaseDocument.java
@@ -396,7 +396,8 @@ public class DatabaseDocument extends Document
chadoToGFF(feat, parentFeature,
dbxrefs, synonym,
- id_store, dao, this_buff);
+ id_store, dao,
+ feat.getFeatureloc(), this_buff);
progress_listener.progressMade("Read from database: " +
feat.getUniquename());
@@ -413,6 +414,7 @@ public class DatabaseDocument extends Document
* @param synonym hashtable containing synonynms
* @param id_store id store for looking up parent names
* @param dao chado data access
+ * @param featureloc feature location for this chado feature
* @param this_buff byte buffer of GFF line
*/
public static void chadoToGFF(final ChadoFeature feat,
@@ -421,15 +423,16 @@ public class DatabaseDocument extends Document
final Hashtable synonym,
final Hashtable id_store,
final ChadoDAO dao,
+ final ChadoFeatureLoc featureloc,
final ByteBuffer this_buff)
{
String gff_source = null;
- int fmin = feat.getFeatureloc().getFmin() + 1;
- int fmax = feat.getFeatureloc().getFmax();
+ int fmin = featureloc.getFmin() + 1;
+ int fmax = featureloc.getFmax();
long type_id = feat.getCvterm().getCvtermId();
- int strand = feat.getFeatureloc().getStrand();
- int phase = feat.getFeatureloc().getPhase();
+ int strand = featureloc.getStrand();
+ int phase = featureloc.getPhase();
String name = feat.getUniquename();
String typeName = getCvtermName(type_id, dao);
--
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