From eeefdb6d9ceb1046f64c3ea2396343d1b2164343 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Mon, 3 Nov 2008 13:40:15 +0000
Subject: [PATCH] split entries
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@9168 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
uk/ac/sanger/artemis/util/DatabaseDocument.java | 16 +++++++++++-----
1 file changed, 11 insertions(+), 5 deletions(-)
diff --git a/uk/ac/sanger/artemis/util/DatabaseDocument.java b/uk/ac/sanger/artemis/util/DatabaseDocument.java
index d26871381..9be4e5a1b 100644
--- a/uk/ac/sanger/artemis/util/DatabaseDocument.java
+++ b/uk/ac/sanger/artemis/util/DatabaseDocument.java
@@ -107,8 +107,13 @@ public class DatabaseDocument extends Document
private ByteBuffer gff_buff;
- /** entries to split into */
- private String[] types = { "repeat_region", "transcript" };
+ /** entries to split into - each is given a name and the features within the entry */
+ private String[][][] types =
+ {
+ { {"repeats"} , {"repeat_region", "direct_repeat"} },
+ { {"EST"} , {"EST_match", "match_part"} },
+ { {"contig+gap"}, {"contig", "gap"}}
+ };
/** true if splitting the GFF into entries */
private boolean splitGFFEntry;
@@ -592,7 +597,7 @@ public class DatabaseDocument extends Document
if(gff_buffer[i].size() == 0)
continue;
- String name = types[i-1];
+ String name = types[i-1][0][0];
new_docs[nentries] = new DatabaseDocument(location, pfield, id, schema,
gff_buffer[i], name);
@@ -705,8 +710,9 @@ public class DatabaseDocument extends Document
this_buff = buffers[0];
for(int j = 0; j < types.length; j++)
{
- if(types[j].equals(typeName))
- this_buff = buffers[j+1];
+ for(int k=0; k<types[j][1].length; k++)
+ if(types[j][1][k].equals(typeName))
+ this_buff = buffers[j+1];
}
chadoToGFF(feat, srcFeature.getUniqueName(),
--
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