From 85ce6800fa4f9779dc5a173fb43fcef09760768c Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Thu, 3 Sep 2009 13:49:21 +0000
Subject: [PATCH] add GFF header to stream
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11710 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
uk/ac/sanger/artemis/util/DatabaseDocument.java | 6 ++++++
1 file changed, 6 insertions(+)
diff --git a/uk/ac/sanger/artemis/util/DatabaseDocument.java b/uk/ac/sanger/artemis/util/DatabaseDocument.java
index 7751d4a73..a3ca37793 100644
--- a/uk/ac/sanger/artemis/util/DatabaseDocument.java
+++ b/uk/ac/sanger/artemis/util/DatabaseDocument.java
@@ -549,12 +549,17 @@ public class DatabaseDocument extends Document
ByteBuffer entryBuffer = new ByteBuffer();
try
{
+ entryBuffer.append("##gff-version 3\n");
+
ByteBuffer sequenceBuffer = new ByteBuffer();
if(dao instanceof IBatisDAO)
((IBatisDAO) dao).startTransaction();
logger4j.debug("RETRIEVE SOURCE FEATURE FROM: "+getLocation());
Feature srcFeature = getChadoSequence(dao, sequenceBuffer);
+
+ entryBuffer.append("#sequence-region " + srcFeature.getUniqueName() +
+ " 1 " + srcFeature.getResidues().length + "\n");
gff_buffer = getGff(dao, srcFeature);
if(splitGFFEntry)
@@ -740,6 +745,7 @@ public class DatabaseDocument extends Document
int type_id = feat.getCvTerm().getCvTermId();
String typeName = getCvtermName(type_id, dao, gene_builder);
this_buff = buffers[0];
+
for(int j = 0; j < TYPES.length; j++)
{
for(int k=0; k<TYPES[j][1].length; k++)
--
GitLab