From e2d440ca1f1c8b8ccdcb81e265a3cdb47d0d1720 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Tue, 10 Feb 2009 11:28:49 +0000
Subject: [PATCH] include database options
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@9775 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
docs/options.sgml | 33 +++++++++++++++++++++++++++++++++
1 file changed, 33 insertions(+)
diff --git a/docs/options.sgml b/docs/options.sgml
index 19934f807..5543bf500 100644
--- a/docs/options.sgml
+++ b/docs/options.sgml
@@ -400,6 +400,39 @@ gc_content_default_window_size = 150
See also <XREF LINKEND="GRAPHS">.
</PARA>
</SECT2>
+
+ <SECT2 ID="OPTIONS-CHADO">
+ <TITLE>Options For A Chado Database</TITLE>
+
+ <SECT3 ID="OPTIONS-CHADO-EXON-MODEL">
+ <TITLE><LITERAL>chado_exon_model</LITERAL></TITLE>
+ <PARA>
+ This is the feature key used when chado exons are joined and displayed in &prog;.
+ For example: <SYNOPSIS>chado_exon_model=CDS</SYNOPSIS>
+ [default: "exon-model"]
+ </PARA>
+ </SECT3>
+
+ <SECT3 ID="OPTIONS-CHADO-TRANSCRIPT">
+ <TITLE><LITERAL>chado_transcript</LITERAL></TITLE>
+ <PARA>
+ This is the feature key used when chado transcripts are created in a gene
+ model. [default: "mRNA"]
+ </PARA>
+ </SECT3>
+
+ <SECT3 ID="OPTIONS-CHADO-SERVERS">
+ <TITLE><LITERAL>chado_servers</LITERAL></TITLE>
+ <PARA>
+ This can be used to provide a list of available databases. For example:
+ <SYNOPSIS>chado_servers = \
+ test localhost:5432/test?userName \
+ genedb_ro db.genedb.org:5432/snapshot?genedb_ro
+ </SYNOPSIS>
+ </PARA>
+ </SECT3>
+
+ </SECT2>
</SECT1>
<SECT1 ID="OPTIONS-FILE">
--
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