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Commit 0229dc93 authored by tjc's avatar tjc
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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
parent fea24403
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......@@ -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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