Skip to content
Snippets Groups Projects
Commit 604d7644 authored by edgrif's avatar edgrif
Browse files

files renamed for consistency.

parent eca3f00e
No related branches found
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
web/user_doc/config_file.shtml deleted 100755 → 0
+ 0
− 97
View file @ eca3f00e
<!--#set var="banner" value="ZMap Feature Sets and Styles"-->
<!--#include virtual="/perl/header"-->
<!--#set var="author" value="edgrif@sanger.ac.uk" -->
<style>
pre{ width: 95%; background-color: #DDDDDD; border-style: solid; border-width: 1px; padding: 10px }
.example{ border-color: #000000 }
</style>
<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>
<!--#include virtual="/perl/footer"-->
web/user_doc/resource_files.shtml deleted 100755 → 0
+ 0
− 393
View file @ eca3f00e
<!--#set var="banner" value="Resource Files for ZMap"-->
<!--#include virtual="/perl/header"-->
<!--#set var="author" value="edgrif@sanger.ac.uk" -->
<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>
<fieldset>
<legend>Overview</legend>
<p>ZMap reads resource files to control various aspects of its
configuration. Currently this only occurs at start up, but in the
future will be dynamic and hopefully complete with an editor. The
following is a description of the various files that ZMap reads and
how configuration is specified in those files.</p>
</fieldset><br />
<fieldset>
<legend>File Format</legend>
<p>The format of the <a href="#sectionfiles">files</a> follows a stanza based layout.</p>
<pre class="example">
StanzaName
{
property = "value"
numeric = 1.0
number = 32000
truth = true
list = "one two three four"
}
NamedStanza
{
foreground_colour = "blue"
background_colour = "white"
}
</pre>
</fieldset><br />
<fieldset>
<legend id="sectionfiles">Directories and Files</legend>
<p>The main configuration files are held in the <a
href="#sectionfiles1">.ZMap</a> directory which must be a subdirectory of
the users home directory. Within this directory are a series of files
that control how zmap works.</p>
<h5 id="sectionfiles1">~/.ZMap - The configuration directory</h5>
<p>This is the default directory, in which, ZMap searches for the
configuration files. The user may change this by passing ZMap an
alternate directory on the command line when starting ZMap using the
--conf_dir option (<a href="#commandline">command line options</a>).</p>
<h5 id="sectionfiles2">Main configuration file</h5>
<p>ZMap looks in <a href="#sectionfiles1">the configuration
directory</a> for a file named ZMap. Without this file ZMap will
exit.</p>
<p>Stanzas:</p>
<div class="stanza">
<div class="opt"><a href="#stanza_source">source</a></div>
<div class="desc"> - controls where zmap looks for data sources</div>
</div>
<div class="stanza">
<div class="opt"><a href="#stanza_zmapwindow">ZMapWindow</a></div>
<div class="desc"> - controls some general zmap window styles</div>
</div>
<div class="stanza">
<div class="opt"><a href="#stanza_align">align</a></div>
<div class="desc"> - aligns sequence...</div>
</div>
<div class="spacer">&nbsp;</div>
<h5 id="sectionfiles3">Style configuration file</h5>
<p>This file should be located in the <a href="#sectionfiles1">the
configuration directory</a> and named according to the value of the
stylesfile option in the <a href="#stanza_source">source</a> stanza of
the <a href="#sectionfiles2">main configuration file</a>.</p>
<p>Stanzas:</p>
<div class="stanza">
<div class="opt"><a href="#stanza_type">Type</a></div>
<div class="desc">- defines a named Type</div>
</div>
<div class="spacer">&nbsp;</div>
</fieldset><br />
<fieldset>
<legend id="sectionstanzas">Stanzas</legend>
<h5 id="stanza_source">source</h5>
<p>Describes a data source to ZMap. Multiple source stanzas allowed.</p>
<p>Members:</p>
<div class="stanza">
<div class="opt">url</div>
<div class="desc">- The url where the data source is accessible. This follows usual url standards. Possible protocols are acedb, file and http. Username and passwords maybe specified for sources as with basic http authentication. e.g. acedb://username:password@host. Ports may also be appended to the hostname separated by a colon e.g. host:8080.</div>
</div>
<div class="stanza">
<div class="opt">sequence</div>
<div class="desc">- A boolean to specify whether the data source can supply dna.</div>
</div>
<div class="stanza">
<div class="opt">writeback</div>
<div class="desc">- A boolean to specify whether the data source can accept data to store.</div>
</div>
<div class="stanza">
<div class="opt">stylesfile</div>
<div class="desc">- A filename for the <a href="#sectionfiles3">styles file</a></div>
</div>
<div class="stanza">
<div class="opt">featuresets</div>
<div class="desc">- A list of types for ZMap to display. This acts as a filter and orders the columns. See section on column ordering <a href="#column_ordering">below</a>.</div>
</div>
<div class="stanza">
<div class="opt">timeout </div>
</div>
<div class="stanza">
<div class="opt">version </div>
</div>
<div class="stanza">
<div class="opt">format </div>
</div>
<div class="spacer">&nbsp;</div>
<h5 id="stanza_zmapwindow">ZMapWindow</h5>
<p>Members:</p>
<div class="stanza">
<div class="opt">keep_empty_columns</div>
<div class="desc">a boolean to tell ZMap whether to display empty columns</div>
</div>
<div class="stanza">
<div class="opt">canvas_maxsize</div>
</div>
<div class="stanza">
<div class="opt">colour_root</div>
</div>
<div class="stanza">
<div class="opt">colour_alignment</div>
</div>
<div class="stanza">
<div class="opt">colour_block</div>
</div>
<div class="stanza">
<div class="opt">colour_m_forward</div>
</div>
<div class="stanza">
<div class="opt">colour_m_reverse</div>
</div>
<div class="stanza">
<div class="opt">colour_q_forward</div>
</div>
<div class="stanza">
<div class="opt">colour_q_reverse</div>
</div>
<div class="stanza">
<div class="opt">colour_m_forwardcol</div>
</div>
<div class="stanza">
<div class="opt">colour_m_reversecol</div>
</div>
<div class="stanza">
<div class="opt">colour_q_forwardcol</div>
</div>
<div class="stanza">
<div class="opt">colour_q_reversecol</div>
</div>
<div class="spacer">&nbsp;</div>
<h5 id="stanza_align">align</h5>
<p>A stop gap to specify alignments...</p>
<div class="stanza">
<div class="opt">reference_strand</div>
</div>
<div class="stanza">
<div class="opt">reference_seq</div>
</div>
<div class="stanza">
<div class="opt">non_reference_seq</div>
</div>
<div class="stanza">
<div class="opt">reference_end</div>
</div>
<div class="stanza">
<div class="opt">non_reference_strand</div>
</div>
<div class="stanza">
<div class="opt">non_reference_end</div>
</div>
<div class="stanza">
<div class="opt">non_reference_start</div>
</div>
<div class="stanza">
<div class="opt">reference_start</div>
</div>
<div class="spacer">&nbsp;</div>
</fieldset>
<br />
<fieldset>
<legend id="commandline">Command Line Options</legend>
<p>
ZMap recognises command line options starting with double dashes, as per the usage info here.
</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>The Styles File</legend>
<h5 id="stanza_type">Type</h5>
<p>Describes a style type. Multiple Type stanzas allowed.</p>
<div class="stanza">
<div class="opt">name </div>
<div class="desc">The name of the type</div>
</div>
<div class="stanza">
<div class="opt">outline </div>
<div class="desc">The colour ZMap should use for the outline of features with this type [black]</div>
</div>
<div class="stanza">
<div class="opt">background </div>
<div class="desc">The colour ZMap should use for the background of features with this type [black]</div>
</div>
<div class="stanza">
<div class="opt">foreground </div>
<div class="desc">The colour ZMap should use for the foreground of features with this type [white]</div>
</div>
<div class="stanza">
<div class="opt">width </div>
<div class="desc">The width of the features.</div>
</div>
<div class="stanza">
<div class="opt">show_reverse </div>
<div class="desc">boolean to tell ZMap to display reverse as well as forward stranded features</div>
</div>
<div class="stanza">
<div class="opt">strand_specific </div>
<div class="desc">boolean to control strand ...</div>
</div>
<div class="stanza">
<div class="opt">frame_specific </div>
<div class="desc">boolean to control frame ...</div>
</div>
<div class="stanza">
<div class="opt">minmag </div>
<div class="desc">int to control the minimum magnification at which features of this type are visible</div>
</div>
<div class="stanza">
<div class="opt">bump </div>
<div class="desc">boolean to tell ZMap features with this type are bumpable.</div>
</div>
<div class="stanza">
<div class="opt">gapped_align </div>
<div class="desc">boolean to tell ZMap to display the indels of alignments</div>
</div>
<div class="stanza">
<div class="opt">read_gaps </div>
<div class="desc">boolean to control parsing of gap arrays (Currently forced true)</div>
</div>
<div class="spacer">&nbsp;</div>
</fieldset>
<br />
-->
<fieldset>
<legend id="column_ordering">Column Ordering</legend>
<p>
There are two column orderings required for zmap, the columns in the main zmap window and the
column orderings in the navigator window. These are specified in the ZMap configuration file in
the "source" stanza:
</p>
<pre class="example">
source
{
featuresets = "Locus \"3 Frame\" \"3 Frame Translation\" vertebrate_mRNA Assembly_Tags etc."
navigator = "Genomic_canonical Locus Scale"
}
</pre>
<p>
(Note that feature set names can have embedded blanks)
</p>
<p>
These lists not only specify the order of columns but also control which feature sets will be
displayed, if the feature set (or its Column_group) is not in this list then the feature will not
be displayed.
</p>
</fieldset>
<br />
<fieldset>
<legend>Other Column Settings</legend>
<p>
acedb did not allow configuration of attributes such as "between column" spacing, we could
add this to the acedb database in the form of some kind of "meta style" but probably its
better to simply specify this in the configuration file.
</p>
<pre class="example">
Currently we have:
"canvas_maxsize" maximum size in pixels of canvas window
"canvas_maxbases" &lt;not used&gt;
"keep_empty_columns" maintain empty columns to keep even spacing on screen between blocks
"display_forward_coords" when specified means coords for reverse complement view are -ve of forward coords
"show_3_frame_reverse" when specified means 3 frame cols are displayed on reverse strand as well
spacing:
"align_spacing" these all control the horizontal space between various parts of zmap,
"block_spacing" probably column spacing is the most relevant.
"strand_spacing"
"column_spacing"
"feature_spacing"
"feature_line_width" controls default thickness of lines used for feature display.
</pre>
</fieldset>
<br />
<!--#include virtual="/perl/footer"-->
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment