From 5ae209ae8cdb7fb2a7342e48d0de10eb86cd56be Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Thu, 30 Oct 2008 15:27:40 +0000
Subject: [PATCH] change types
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@9126 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
uk/ac/sanger/artemis/util/DatabaseDocument.java | 14 +++++---------
1 file changed, 5 insertions(+), 9 deletions(-)
diff --git a/uk/ac/sanger/artemis/util/DatabaseDocument.java b/uk/ac/sanger/artemis/util/DatabaseDocument.java
index 4499a16a9..f639fafa3 100644
--- a/uk/ac/sanger/artemis/util/DatabaseDocument.java
+++ b/uk/ac/sanger/artemis/util/DatabaseDocument.java
@@ -108,7 +108,7 @@ public class DatabaseDocument extends Document
private ByteBuffer gff_buff;
/** entries to split into */
- private String[] types = { "exon", "gene", "CDS", "transcript" };
+ private String[] types = { "repeat_region", "transcript" };
/** true if splitting the GFF into entries */
private boolean splitGFFEntry;
@@ -592,11 +592,7 @@ public class DatabaseDocument extends Document
if(gff_buffer[i].size() == 0)
continue;
- String name;
- if(i >= types.length)
- name = "other";
- else
- name = types[i];
+ String name = types[i-1];
new_docs[nentries] = new DatabaseDocument(location, pfield, id, schema,
gff_buffer[i], name);
@@ -706,11 +702,11 @@ public class DatabaseDocument extends Document
Feature feat = (Feature)featList.get(i);
int type_id = feat.getCvTerm().getCvTermId();
String typeName = getCvtermName(type_id, dao, gene_builder);
- this_buff = buffers[types.length];
+ this_buff = buffers[0];
for(int j = 0; j < types.length; j++)
{
if(types[j].equals(typeName))
- this_buff = buffers[j];
+ this_buff = buffers[j+1];
}
chadoToGFF(feat, srcFeature.getUniqueName(),
@@ -2086,7 +2082,7 @@ public class DatabaseDocument extends Document
*/
public PartialSequence getChadoSequence(final String uniqueName)
{
- Feature feature = getDAOOnly().getResiduesByUniqueName(uniqueName);
+ Feature feature = (Feature) getDAOOnly().getResiduesByUniqueName(uniqueName).get(0);
char[] c = getChars(feature.getResidues());
PartialSequence ps = new PartialSequence(c, feature.getSeqLen(),
--
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