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Commit 9a7ca78c authored by rds's avatar rds
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update, still missing information though :(

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......@@ -6,9 +6,10 @@
<style>
pre{ width: 95%; background-color: #DDDDDD; border-style: solid; border-width: 1px; padding: 10px }
.example{ border-color: #000000 }
li.stanza { width: 95% }
li.stanza span.opt { float: left; width: 100px; text-align: right; }
li.stanza span.desc { float: right; width: 235px; text-align: left; }
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>
......@@ -68,22 +69,24 @@ alternate directory on the command line when starting ZMap using the
directory</a> for a file named ZMap. Without this file ZMap will
exit.</p>
<p>Stanzas:
<p>Stanzas:</p>
<div class="stanza">
<span class="opt"><a href="#stanza_source">source</a></span>
<span class="desc"> - controls where zmap looks for data sources</span>
<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">
<span class="opt"><a href="#stanza_zmapwindow">ZMapWindow</a></span>
<span class="desc"> - controls some general zmap window styles</span>
<div class="opt"><a href="#stanza_zmapwindow">ZMapWindow</a></div>
<div class="desc"> - controls some general zmap window styles</div>
</div>
<div class="stanza">
<span class="opt"><a href="#stanza_align">align</a></span>
<span class="desc"> - aligns sequence...</span>
<div class="opt"><a href="#stanza_align">align</a></div>
<div class="desc"> - aligns sequence...</div>
</div>
</p>
<div class="spacer">&nbsp;</div>
<h5 id="sectionfiles3">Style configuration file</h5>
......@@ -92,12 +95,13 @@ 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:
<ul>
<li><a href="#stanza_type">Type</a> - defines a named Type</li>
<li><a href="#stanza...">...</a></li>
<li><a href="#stanza...">...</a></li>
</ul></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 />
......@@ -108,53 +112,123 @@ the <a href="#sectionfiles2">main configuration file</a>.</p>
<p>Describes a data source to ZMap. Multiple source stanzas allowed.</p>
<p>Members:
<ul>
<li>url<p>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.</p></li>
<li>sequence<p>a boolean to specify whether the data source can supply dna.</p></li>
<li>writeback<p>a boolean to specify whether the data source can accept data to store.</p></li>
<li>stylesfile<p>a filename for the <a href="#sectionfiles3">styles file</a></p></li>
<li>featuresets<p>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>.</p></li>
<li>timeout </li>
<li>version </li>
<li>format </li>
</ul></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></p>
<p>Members:
<ul>
<li>keep_empty_columns<p>a boolean to tell ZMap whether to display empty columns</p></li>
<li>canvas_maxsize</li>
<li>colour_root</li>
<li>colour_alignment</li>
<li>colour_block</li>
<li>colour_m_forward</li>
<li>colour_m_reverse</li>
<li>colour_q_forward</li>
<li>colour_q_reverse</li>
<li>colour_m_forwardcol</li>
<li>colour_m_reversecol</li>
<li>colour_q_forwardcol</li>
<li>colour_q_reversecol</li>
</ul>
<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>
<ul>
<li>reference_strand</li>
<li>reference_seq</li>
<li>non_reference_seq</li>
<li>reference_end</li>
<li>non_reference_strand</li>
<li>non_reference_end</li>
<li>non_reference_start</li>
<li>reference_start</li>
</ul>
<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 />
......@@ -197,20 +271,56 @@ Application Options:
<p>Describes a style type. Multiple Type stanzas allowed.</p>
<ul>
<li>name <p>The name of the type</p></li>
<li>outline <p>The colour ZMap should use for the outline of features with this type [black]</p></li>
<li>background <p>The colour ZMap should use for the background of features with this type [black]</p></li>
<li>foreground <p>The colour ZMap should use for the foreground of features with this type [white]</p></li>
<li>width <p>The width of the features.</p></li>
<li>show_reverse <p>boolean to tell ZMap to display reverse as well as forward stranded features</p></li>
<li>strand_specific <p>boolean to control strand ...</p></li>
<li>frame_specific <p>boolean to control frame ...</p></li>
<li>minmag <p>int to control the minimum magnification at which features of this type are visible</p></li>
<li>bump <p>boolean to tell ZMap features with this type are bumpable.</p></li>
<li>gapped_align <p>boolean to tell ZMap to display the indels of alignments</p></li>
<li>read_gaps <p>boolean to control parsing of gap arrays (Currently forced true)</p></li>
</ul>
<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 />
......
web/user_doc/xremote_overview.shtml
+ 25
− 14
View file @ 9a7ca78c
<!--#set var="banner" value="ZMap External Control Interface Guide"-->
<!--#set var="banner" value="Controlling ZMap from another program"-->
<!--#include virtual="/perl/header"-->
<!--#set var="author" value="rds@sanger.ac.uk" -->
......@@ -14,7 +14,9 @@ table.zmap_actions tr{ vertical-align: top; }
table.zmap_actions th{ border-width: 0px 0px 1px 0px; border-style: solid; }
</style>
<h2>Controlling zmap from another program.</h2>
<fieldset>
<legend>Overview</legend>
<p>
It is relatively easy to control zmap from another program using a
......@@ -32,9 +34,11 @@ the requests but there has been some reorganisation in the way zmap
accepts requests so that requests can be simplier than was otherwise
possible.
</p>
</fieldset>
<br />
<h2>Otterlace chain of events</h2>
<fieldset>
<legend>Otterlace chain of events</legend>
<p>
Firstly running zmap with a --win_id option makes zmap register a
......@@ -96,7 +100,7 @@ understands.
&lt;action&gt;close&lt;/action&gt;
&lt;/client&gt;
&lt;/response&gt;
&lt;meta display="localhost:10.0" windowid="0x2c00004" application="" version="$Revision: 1.1 $" /&gt;
&lt;meta display="localhost:10.0" windowid="0x2c00004" application="" version="$Revision: 1.2 $" /&gt;
&lt;/zmap&gt;
</pre>
......@@ -105,7 +109,11 @@ From the above examples I hope it's easy to see how the following
tables fit in.
</p>
<h2>Table of Windows and valid Actions</h2>
</fieldset>
<br />
<fieldset>
<legend>Table of Windows and valid Actions</legend>
<table class="zmap_actions">
<tr>
......@@ -146,10 +154,10 @@ tables fit in.
<td>zoom_to<br />register_client</td>
</tr>
</table>
</fieldset>
<br />
<h2>Table of Actions</h2>
<fieldset>
<legend>Table of Actions</legend>
<table class="zmap_actions">
<tr>
......@@ -190,7 +198,7 @@ tables fit in.
&lt;meta display="localhost:10.0"
windowid="0x2c00004"
application=""
version="$Revision: 1.1 $" /&gt;
version="$Revision: 1.2 $" /&gt;
&lt;/zmap&gt;</pre></td>
</tr>
......@@ -352,7 +360,7 @@ featuresets = "Coding Repeats BLASTX"
&lt;meta display="localhost:10.0"
windowid="0x2c00084"
application=""
version="$Revision: 1.1 $" /&gt;
version="$Revision: 1.2 $" /&gt;
&lt;/zmap&gt;</pre></td>
</tr>
......@@ -364,9 +372,11 @@ featuresets = "Coding Repeats BLASTX"
</table>
<p>(*) initial = the first window zmap displays. view = the zmap
window which displays the sequence/features.</p>
</fieldset>
<br />
<h2>Table of Actions zmap might Generate</h2>
<fieldset>
<legend>Table of Actions zmap might Generate</legend>
<p>ZMap will generate the actions (register_client, single_select, multiple_select) from the above table, plus those from the following table.</p>
......@@ -486,5 +496,6 @@ repeated as often as required but must be nested as shown.</li>
</tr>
</table>
</fieldset>
<br />
<!--#include virtual="/perl/footer"-->
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