From fae6a4a731abee27ece85ab8d112060d672f0e43 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Mon, 21 Jan 2008 16:16:45 +0000
Subject: [PATCH] add range to input option
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@6963 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../sanger/artemis/util/DatabaseDocument.java | 27 ++++++++++++++-----
1 file changed, 20 insertions(+), 7 deletions(-)
diff --git a/uk/ac/sanger/artemis/util/DatabaseDocument.java b/uk/ac/sanger/artemis/util/DatabaseDocument.java
index ae348ec56..940ae4b4b 100644
--- a/uk/ac/sanger/artemis/util/DatabaseDocument.java
+++ b/uk/ac/sanger/artemis/util/DatabaseDocument.java
@@ -127,6 +127,7 @@ public class DatabaseDocument extends Document
// include children in reading from the database
private boolean readChildren = true;
+ // range to retrieve features for
private Range range;
private Feature geneFeature;
@@ -480,14 +481,21 @@ public class DatabaseDocument extends Document
// Retrieve all features within a range
// List schemaList = new Vector();
// schemaList.add(schema);
-
- Collection featureLocs = geneFeature.getFeatureLocsForFeatureId();
- Iterator it = featureLocs.iterator();
- final FeatureLoc featureLoc = (FeatureLoc)it.next();
+ final Feature srcFeature;
+ if(geneFeature != null)
+ {
+ Collection featureLocs = geneFeature.getFeatureLocsForFeatureId();
+ Iterator it = featureLocs.iterator();
+ final FeatureLoc featureLoc = (FeatureLoc)it.next();
- final Feature srcFeature = featureLoc.getFeatureBySrcFeatureId();
- setName(srcFeature.getUniqueName());
- this.srcFeatureId = Integer.toString(srcFeature.getFeatureId());
+ srcFeature = featureLoc.getFeatureBySrcFeatureId();
+ setName(srcFeature.getUniqueName());
+ this.srcFeatureId = Integer.toString(srcFeature.getFeatureId());
+ }
+ else
+ {
+ srcFeature = dao.getFeatureById(Integer.parseInt(srcFeatureId));
+ }
ByteBuffer entryBuffer = getFeaturesInRange(srcFeature, range, dao);
getChadoSequence(srcFeature, entryBuffer);
@@ -2966,4 +2974,9 @@ public class DatabaseDocument extends Document
getCvterms(dao);
}
}
+
+ public void setRange(Range range)
+ {
+ this.range = range;
+ }
}
--
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