update

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11153 ee4ac58c-ac51-4696-9907-e4b3aa274f04

docs/chado/admin.shtml

@@ -17,6 +17,10 @@ using and setting up an Artemis and ACT connection with a Chado database.
 
 <h3><a name="DATABASEMANAGER">Opening the Database Manager</a></h3>
 <p>
+The Artemis Database Manager is cached between sessions in the directory
+'.artemis/cache' in the users home directory. There is an option under the File menu
+to clear this cache.
+<p>
 To open the Artemis Database Manager panel (from which the browser is launched), 
 Artemis looks initially for the existence of the cvterm.name = 'top_level_seq' which 
 belongs to cv.name = 'genedb_misc'. If these exist it follows method A:
@@ -101,32 +105,68 @@ Feature. The joined exons become an Artemis CDS feature (GFFStreamFeature), whic
 the uniquenames of the original exons in the database.
 
 <p>
-<h3><a name="CONFIG">Option File Configuration</a></h3>
-<p>
-Artemis combines the exons stored in chado and describes it as an 'exon-model' 
-feature by default (defined by uk.ac.sanger.artemis.util.DatabaseDocument.EXONMODEL).
-The chado_exon_model flag in the options file allows this to be changed. 
-<p>
-When a gene model is created in Artemis it creates the transcript as a 'mRNA' 
-feature by default (defined by uk.ac.sanger.artemis.util.DatabaseDocument.TRANSCRIPT).
-The chado_transcript flag in the options file allows this to be changed.
-<p>
-A list of available databases can be configured in the options file (chado_servers flag).
-For each an alias is given followed by its location (host:port/database?user), each alias
-is displayed in a drop down menu in the login box.
+<h3><a name="CONFIG">Artemis Chado Configuration</a></h3>
+
+This is an example extract from the Artemis options file for the chado related options:
+
 <p>
-Below is an example configuration option:
-<pre>
+<pre style="color: #0000FF;">
+#
+# CHADO DATABASE OPTIONS 
+#
 # chado gene model features default types
 chado_exon_model=CDS
 #chado_transcript=transcript
 
+# infer CDS and UTR features from gene model
+chado_infer_CDS_UTR=no
+
 # provide a list of available servers
 chado_servers = \
-   test localhost:5432/test?userName \
-   genedb_ro db.genedb.org:5432/snapshot?genedb_ro
+  workshop localhost:10101/workshop?user \
+  GeneDB db.genedb.org:5432/snapshot?genedb_ro
+
+# define how product qualifiers are stored (as a cv or as a featureprop)
+product_cv=yes
+product_cvname = genedb_products
+# cv containing synonym names
+synonym_cvname = genedb_synonym_type
+
+# set default delete behaviour to make things obsolete, if
+# this is not provided the default is to permanently delete
+set_obsolete_on_delete=yes
+
+# list of features to record residues for in the database
+# - these are included when inserting or updating their featurelocs
+sequence_update_features = polypeptide mRNA rRNA tRNA snRNA snoRNA
 </pre>
 
+<p>
+Artemis combines the exons stored in chado and describes it as a 'CDS' 
+feature by default. The <b>chado_exon_model</b> flag in the options file 
+allows this to be changed. 
+<p>
+When a gene model is created in Artemis it creates the transcript as a 'mRNA' 
+feature by default. The <b>chado_transcript</b> flag in the options file allows this 
+to be changed.
+<p>
+For Artemis the default gene model representation is described in the <a href="overview.shtml#GENE">
+overview</a>. In this representation the UTRs are explicitly created in the database.
+However the gmod loader (gmod_bulk_load_gff3.pl) does not create the UTRs and they can 
+be inferred from the exon and protein features. If the gmod loader is used then Artemis
+can infer the CDS and UTR features by setting <b>chado_infer_CDS_UTR=yes</b> in the 
+options file.
+<p>
+A list of available databases can be configured in the options file with the <b>chado_servers</b> flag.
+For each database an alias is given followed by its location (host:port/database?user), each alias
+is displayed in a drop down menu in the login box.
+<p>
+If product qualifiers are stored as an ontology (in cvterm) then set <b>product_cv=yes</b>
+and set <b>product_cvname</b> is set to the name of the controlled vocabulary (cv) used in chado.
+<p>
+When features are deleted in Artemis the default behaviour can be set to make these
+features obsolete rather than permanently delete them from the database.
+
 <a name="GENEBUILDER"></a><h3>Opening the Standalone Gene Builder</h3>
 <p>
 The Gene Builder can be launched on its own without opening up Artemis. The following

docs/chado/overview.shtml

@@ -25,7 +25,9 @@
 				The address of the database (hostname, port and name) can be conveniently
 				included as follows:
 				<br><pre>-Dchado="hostname:port/test?username"</pre>
-				So that these details are already completed in the popup login pane.
+				these details are then the default database address in the popup login window. A
+                                list of available databases can be provided in the Artemis <a href="admin.shtml#CONFIG">options file</a>
+				these are presented in a drop down list in the login window.
 				<br><br>
 				<img src="login.gif" align="middle" alt="login"/>
 				<br>
@@ -53,7 +55,9 @@ For a read only connection -Dread_only is specified on the command line:
 		On a successful login a database and file manager window will open up. 
         The database manager will display "Database Loading...". The organisms
 		in the database with residues are shown in a expandable tree. Double
-		clicking on the sequence names opens them up in Artemis.
+		clicking on the sequence names opens them up in Artemis. Alternatively
+		a gene name or chromosome name came be typed into the text field at the
+		top and the Open button used to launch Artemis.
 		<br><br>
 		<img src="databasemanager.gif"/>
 		<p>
@@ -103,6 +107,10 @@ For a read only connection -Dread_only is specified on the command line:
 		automatically generated by the gene builder from an ID provided by the
 		user. <i>N.B.</i> in our data model UTRs are represented as distinct from 
         exons.
+		<p>
+		For the scenario where both the CDS and UTRs are not stored and their positions can be 
+		inferred from the exon and polypeptide features set <i>chado_infer_CDS_UTR=yes</i> in the 
+		Artemis <a href="admin.shtml#CONFIG">options file</a>.
 		<a NAME="GENEBUILDING"></a><h3>Gene Building</h3>
 		A gene can be created in Artemis (or ACT) by highlighting a base range and selecting
         from the '<i>Create</i>' menu the '<i>Gene Model From Base Range</i>' option. 
@@ -302,7 +310,7 @@ For a read only connection -Dread_only is specified on the command line:
        These mappings are stored in the 'etc/key_mapping' and 'etc/qualifier_mapping'
        files.
        <p>
-       A script (etc/write_db_entry) is also provided as a means of writing out multiple
+       A script (etc/writedb_entry) is also provided as a means of writing out multiple
        sequences from the database. The script takes the following options:
        <pre>
 -h      show help
@@ -310,5 +318,6 @@ For a read only connection -Dread_only is specified on the command line:
 -i      [y|n] ignore obsolete features, default is y
 -s      space separated list of sequences to read and write out
 -o      [EMBL|GFF] output format, default is EMBL
+-a      [y|n] for EMBL submission format change to n, default is y
        </pre>