From c3811093adb3becc9f0f6f2ea18491d8f0db8f4f Mon Sep 17 00:00:00 2001
From: mh17 <mh17>
Date: Fri, 19 Mar 2010 11:07:35 +0000
Subject: [PATCH] copied files over from web/user-doc, need to update
---
doc/user_doc/config_file_examples.html | 99 +++++++++++++
doc/user_doc/configuration.html | 198 +++++++++++++++++++++++++
2 files changed, 297 insertions(+)
create mode 100644 doc/user_doc/config_file_examples.html
create mode 100644 doc/user_doc/configuration.html
diff --git a/doc/user_doc/config_file_examples.html b/doc/user_doc/config_file_examples.html
new file mode 100644
index 000000000..48aa96a0e
--- /dev/null
+++ b/doc/user_doc/config_file_examples.html
@@ -0,0 +1,99 @@
+<!--#set var="banner" value="ZMap Feature Sets and Styles"-->
+<!--#include virtual="/perl/header"-->
+
+<!--#set var="author" value="edgrif@sanger.ac.uk" -->
+<!-- $Id: config_file_examples.html,v 1.1 2010-03-19 11:07:35 mh17 Exp $ -->
+<style>
+pre{ width: 95%; background-color: #DDDDDD; border-style: solid; border-width: 1px; padding: 10px }
+.example{ border-color: #000000 }
+</style>
+<h2>ZMap Config File Example</h2>
+<p>NB: this documentation may be quite old and need updating</p>
+<fieldset>
+<pre class="example">
+
+# -----------------------------------------------------------------------------
+# ZMap config file format for views.
+#
+#
+
+
+
+# -----------------------------------------------------------------------------
+# "ZMap" stanza:
+# Specifies general properties.
+#
+[ZMap]
+
+# replaced by views keyword and 'mapping' in the view stanza
+# default_sequence = b0250
+
+default_printer = n318bw
+
+
+# names of view stanzas.
+views = b0250
+
+# new keyword, display listed views, single means all in one window,
+# multiple means all in their own windows, default is multiple.
+view_windows = < single | multiple >
+
+
+
+# -----------------------------------------------------------------------------
+# "View" stanza:
+# Specifies properties for fetching a feature context to display to the
+# the user.
+#
+# Currently we support one of these but in the future there can be multiple
+# views, all of which get displayed. Each view stanza must have a unique name
+# and it must in turn name the source stanzas which will specify servers
+# to fetch the view data.
+#
+[b0250]
+
+# List of featuresets to be displayed, the order is the column order on the screen,
+# reverse strand is displayed in reverse order.
+featuresets_display_order = GeneFinderFeatures ; eds_column ; 3 Frame ; 3 Frame Translation ; and many more...
+
+
+# features to be displayed in the navigator window.
+navigator_sets = Locus ; scale ; genomic_canonical
+
+# The _default_ mapping for the view (in the end this should specify blocks etc....)
+mapping = <assembly [start [end] ] >
+
+# list specifying all sources for this view.
+sources = b0250_acedb_server
+
+
+
+# -----------------------------------------------------------------------------
+# source stanzas specify the servers that fetch the data for sequence
+# display. Each stanza must have a unique name.
+#
+[b0250_acedb_server]
+
+url = acedb://any:any@cbi4c:20000
+
+# list of feature sets for this source
+# (optional, default list is featuresets_display_order from parent view stanza)
+featuresets = GeneFinderFeatures ; eds_column ; pseudogene ; curated
+
+# fetch styles ? (optional, default is true)
+styles = false
+
+# mapping for this source only (optional, default taken from parent view stanza)
+mapping = <sub-assembly [start [end] ] >
+
+# fetch sequence for mapping from this source (optional, default is true)
+sequence = false
+
+</pre>
+</fieldset>
+
+
+
+
+<!--#include virtual="/perl/footer"-->
+
diff --git a/doc/user_doc/configuration.html b/doc/user_doc/configuration.html
new file mode 100644
index 000000000..ce6acde16
--- /dev/null
+++ b/doc/user_doc/configuration.html
@@ -0,0 +1,198 @@
+<!--#set var="banner" value="Configuration Files for ZMap"-->
+<!--#include virtual="/perl/header"-->
+
+<!--#set var="author" value="edgrif@sanger.ac.uk" -->
+<!-- $Id: configuration.html,v 1.1 2010-03-19 11:07:35 mh17 Exp $ -->
+<style>
+pre{ width: 95%; background-color: #DDDDDD; border-style: solid; border-width: 1px; padding: 10px }
+.example{ border-color: #000000 }
+div.spacer { clear: both; }
+div.stanza { clear: both; padding-top: 5px; }
+div.stanza div.opt { float: left; width: 15%; text-align: left; font-weight: bold; }
+div.stanza div.desc { float: right; width: 85%; text-align: left; }
+</style>
+
+
+<h2>ZMap Configuration</h2>
+
+
+
+<fieldset> <legend>Overview</legend>
+
+<p>
+ZMap configuration is via command line options and a number of resource files
+read during intitialisation and during subsequent processing.
+This section describes the various ways ZMap can be configured.
+</p>
+
+</fieldset><br />
+
+
+<fieldset>
+<legend id="commandline">Command Line Options</legend>
+
+<p>
+ZMap recognises command line options starting with double dashes:
+</p>
+
+<pre id="usage" class="example">
+Usage:
+ zmap [OPTION...] <sequence name>
+
+A multi-threaded genome browser and annotation tool.
+
+Help Options:
+ -?, --help Show help options
+
+Application Options:
+ --version=<none> Program version.
+ --start=coord Start coord in sequence, must be in range 1 -> seq_length.
+ --end=coord End coord in sequence, must be in range start -> seq_length, but end == 0 means show to end of sequence.
+ --conf_file=file path Relative or full path to configuration file.
+ --conf_dir=directory Relative or full path to configuration directory.
+ --win_id=0x0000000 Window ID of the controlling application.
+</pre>
+
+</fieldset><br />
+
+
+
+
+
+
+
+<fieldset>
+<legend>Configuration Files - Format</legend>
+
+<p>
+The format of the configuration files follows a stanza-based key-value format
+defined in the <a href="http://library.gnome.org/devel/glib/stable/glib-Key-value-file-parser.html">
+GLib Key-value parser</a> package, e.g.
+</p>
+
+<pre class="example">
+# this is a comment.
+
+[StanzaName]
+# another comment.
+property = value # string
+numeric = 1.0 # float
+number = 32000 # int
+truth = true # boolean
+list = one ; two ; three ; four # multiple strings
+
+[Next Stanza]
+
+<i>etc.</i>
+
+</pre>
+
+<p>
+A longer annotated example can see seen <a href="config_file_examples.shtml">here</a>.
+</p>
+
+
+</fieldset><br />
+
+
+<fieldset>
+<legend id="sectionfiles">Directories and Files</legend>
+
+<p>
+ZMap uses configuration files to find its servers, files and
+to configure aspects of its interface.
+By default ZMap looks for these files in the users <code><b>$HOME/.ZMap</b></code> directory.
+The user can specify an alternative directory using the
+<a href="#commandline">--conf_dir</a> option.
+</p>
+
+<p>
+If the configuration directory does not exist then ZMap will not run.
+</p>
+
+
+<h4 id="stylefile">ZMap configuration file</h4>
+
+<p>
+By default the <code><b>ZMap</b></code> configuration file is searched for
+in the configuration directory but an alternative file can be specified with
+the <a href="#commandline">--conf_file</a> option.
+If this file does not exist ZMap will not run.
+</p>
+
+
+<h4 id="stylefile">Styles configuration file</h4>
+
+<p>This file should be located in the
+configuration directory and named according to the value of the
+stylesfile option in the <a href="#stanzas">ZMap</a> stanza of
+the <code><b>ZMap</b></code> configuration file.</p>
+
+</fieldset><br />
+
+
+<fieldset>
+<legend id="stanzas">ZMap Configuration File Stanzas</legend>
+
+
+<!-- Notes about connecting to doxygen generated html files.
+
+Our doxygen documentation generator creates html files from the C source
+header files which document the configuration information.
+
+The resulting html files are named in the following way:
+
+In the source file we have:
+
+/*! @addtogroup config_stanzas
+ *
+etc....
+
+from this doxygen generates an html file called:
+
+group__config__stanzas.shtml
+
+I can't see a way to tell doxygen what name to call the file so it's just hard
+coded here.....
+
+These files are all in an "html" subdirectory at the same level as the directory
+containing these files.
+
+-->
+
+<p>
+The following stanzas are supported by ZMap:
+</p>
+
+<ul>
+ <li><b><a href="../html/group__config__stanzas.shtml#app">ZMap</a> -</b>
+ main configuration stanza controlling the zmap application.
+ <li><b><a href="../html/group__config__stanzas.shtml#view">View</a> -</b>
+ stanza(s) controlling display of a named set of features.
+ <li><b><a href="../html/group__config__stanzas.shtml#source">Source</a> -</b>
+ stanza(s) specifying data sources from which to load a feature view.
+ <li><b><a href="../html/group__config__stanzas.shtml#style">Style</a> -</b>
+ stanza(s) specifying styles for displaying feature sets.
+ <li><b><a href="../html/group__config__stanzas.shtml#window">Window</a> -</b>
+ stanza controlling the ZMap feature display window.
+ <li><b><a href="../html/group__config__stanzas.shtml#blixem">Blixem</a> -</b>
+ stanza specifying parameters for running the blixem sequence viewer.
+ <li><b><a href="../html/group__config__stanzas.shtml#logging">Logging</a> -</b>
+ stanza controlling zmap logging facility.
+ <li><b><a href="../html/group__config__stanzas.shtml#debug">Debug</a> -</b>
+ stanza controlling zmap debugging output.
+</ul>
+
+
+<p>
+ZMap will work with single or multiple data sources. If there is only one data source it can be named 'source' and will be used automatically. If there are multiple data sources each one must be named uniquely and listed in the sources key in the ZMap stanza.
+<br />
+Styles should be defined a separate configuration file, referred to in the ZMap stanza wiht the 'stylesfile' key.
+</p>
+
+</fieldset><br />
+
+
+
+
+<!--#include virtual="/perl/footer"-->
--
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