diff --git a/uk/ac/sanger/artemis/util/DatabaseDocument.java b/uk/ac/sanger/artemis/util/DatabaseDocument.java index 82cefdfd3e085dfe0935dcabbc0228f0f5c37e86..a76b1e6543f20509451155e9a752af29560bf8d8 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);