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<!--#set var="banner" value="ZMap Feature Sets and Styles"-->
<!--#include virtual="/perl/header"-->
<!--#set var="author" value="edgrif@sanger.ac.uk" -->
<!-- Start of page. -->
<!-- CVS info: $Id: styles.html,v 1.1 2010-03-09 10:27:12 mh17 Exp $ -->
<h2>ZMap Feature Sets and Styles</h2>
<br/>
<fieldset>
<legend>Preface</legend>
<p>Configuration examples for Styles and other components of ZMap are given in
GLib keyword value file format, if you are unfamiliar with this then read the
<a href="#keyword_value_format">Keyword Value Format</a> section.</p>
<p>Note that ZMap can also support Styles in other formats as shown in the section on
<a href="#acedb_styles">acedb</a>.
</p>
<p>NB: This file has beed copied frorm the web old web directory and may need updating. (mh17 09 Mar 2010)</p>
</fieldset>
<br/>
<fieldset>
<legend>Overview</legend>
<p>ZMap displays features using "<b>Feature Sets</b>" and "<b>Styles</b>", the distinction
between these two is:</p>
<p>"<b>Feature Sets</b>":</p>
<p>Are the fundamental groups of features that ZMap displays. Each feature
set has a unique name which can be used to query, find and retrieve the features within that set.
</p>
<p>Which feature sets are displayed is controlled by the "featuresets" keyword in the "source" stanza
in the ZMap config file:
</p>
<pre class="example">
[source]
url = acedb://localhost:12345?use_methods=true
featuresets = Genomic_canonical;ORF;CDS;Locus;Restriction map;External_transcript;etc...
</pre>
<p>Normally the names given are the names of individual feature sets but ZMap also allows grouping of feature sets
into column groups (<a href="#featureset_method">see Column tags</a>),
in this case you only need to put the "column" names in this list,
you do not need to include all the column children, ZMap will sort all that out for you.
</p>
<p>"<b>Styles</b>":</p>
Control the appearance and processing of features within ZMap.
They control aspects such as colour, width, style of feature display but also how
those features are processed during user interaction, e.g. by clicking on them to
display details or perhaps dumping them to files. These properties are specified
in keyword value format in configuration files. The following example defines
a Style called "Allele" with a column width of 2 and coloured red with a black border:</p>
<pre class="example">
[Allele]
mode = basic
width = 2
colours = normal fill red ; normal border black
</pre>
<p>The following sections describe the data types used in specifying the properties and
the properties themselves.
</fieldset>
<br/>
<fieldset>
<legend>Data Types used in Style Properties</legend>
<table class="zebra" id="data_types" border="2" cellpadding="10" valign="top">
<caption align=top>Special Value Types</caption>
<thead>
<tr>
<th>Type</th>
<th>Value range</th>
<th>Description</th>
</tr>
</thead>
<tbody>
<tr>
<td>boolean</td>
<td>true | false</td>
<td>be sure to use lower case ! </td>
</tr>
<tr>
<td>int</td>
<td nowrap>min_int <= value <= max_int</td>
<td>Min and Max values for int are system dependent and usually
much more than required by ZMap.</td>
</tr>
<tr>
<td>double</td>
<td nowrap>min_double <= value <= max_double</td>
<td>Min and Max values for double are system dependent and usually
much more than required by ZMap.</td>
</tr>
<tr>
<td>one-of</td>
<td>&lt; value | value | value &gt;</td>
<td>Several properties can take only one of several values, these are explained
in the property table that follows.
</tr>
<tr>
<td>colour_type</td>
<td>"Type Target Colour" triplet(s)</td>
<td>The triplet specifies colours for "normal" or "selected" feature display with "fill", "draw"
and "border" colours:
<ul>
<li>Type = &lt; normal | selected &gt;
<li>Target = &lt; fill | draw | border &gt;
<li>Colour = a colour from the X11 rgb.txt list or in hex format:
'#rgb', '#rrggbb', '#rrrgggbbb' or '#rrrrggggbbbb'.
</ul>
e.g. "normal fill light blue".</td>
</tr>
</tbody>
</table>
</fieldset>
<br/>
<fieldset>
<legend>Style Properties</legend>
<p>The following table gives a definitive list of Styles properties:
</p>
<table class="zebra" id="properties" border="2" cellpadding="10">
<caption align=top>Styles Properties</caption>
<thead>
<tr>
<th width="25%">Keyword</th>
<th width="25%">Value Type</th>
<th>Description</th>
</tr>
</thead>
<tbody>
<tr>
<td>parent</td>
<td>string</td>
<td>Name of a style from which to inherit properties.</td>
</tr>
<tr>
<td>description</td>
<td>string</td>
<td>Text describing the style perhaps with comments about inheritance etc.</td>
</tr>
<tr>
<td>mode</td>
<td>&lt; basic | alignment | transcript | dna | peptide | text | graph | glyph
| assembly-path &gt; </td>
<td>Identifies how a feature should be displayed and processed, e.g. a transcript will be displayed
using the accepted block/angle line style.</td>
</tr>
<tr>
<td>colours</td>
<td>colour_type</td>
<td>Feature colours for normal display.</td>
</tr>
<tr>
<td>frame0-colours</td>
<td>colour_type</td>
<td>Feature colours for frame zero in 3 frame display.</td>
</tr>
<tr>
<td>frame1-colours</td>
<td>colour_type</td>
<td>Feature colours for frame one in 3 frame display.</td>
</tr>
<tr>
<td>frame2-colours</td>
<td>colour_type</td>
<td>Feature colours for frame two in 3 frame display.</td>
</tr>
<tr>
<td>rev-colours</td>
<td>colour_type</td>
<td>Feature colours for display on reverse strand.</td>
</tr>
<tr>
<td>display-mode</td>
<td>&lt; hide | show_hide | show &gt;</td>
<td>Controls when features are displayed:
<ul>
<li><b>hide:</b> never show the features.
<li><b>show_hide:</b> show/hide according to zoom, min/max mag.
<li><b>show:</b> always show features.
</ul>
</td>
</tr>
<tr>
<td>bump-mode</td>
<td>&lt; unbump | overlap | start-position | alternating | all
| name | name-interleave | name-no-interleave | name-colinear | name-best-ends &gt;</td>
<td>Controls how features are arranged within their column:
<ul>
<li><b>unbump:</b> No bumping (default)
<li><b>overlap:</b> Bump any features overlapping each other.
<li><b>start-position:</b> Bump if features have same start coord.
<li><b>alternating:</b> Alternate features between two sub_columns, e.g. to display assemblies.
<li><b>all:</b> A sub-column for every feature.
<li><b>name:</b> A sub-column for features with the same name.
<li><b>name-interleave:</b> All features with same name in a single sub-column
but several names interleaved in each sub-column, the most compact display.
<li><b>name-no-interleave:</b> Display as for Interleave but no interleaving of different names.
<li><b>name-colinear:</b> As for No Interleave but for alignments only colinear shown.
<li><b>name-best-ends:</b> As for No Interleave but for alignments sorted by 5' and 3' best/biggest matches, one sub_column per match.
</ul>
</td>
</tr>
<tr>
<td>default-bump-mode</td>
<td>(as for bump-mode)</td>
<td>(as for bump-mode)</td>
</tr>
<tr>
<td>bump-spacing</td>
<td>double</td>
<td>Specifies space to leave between sub-columns of features.</td>
</tr>
<tr>
<td>frame-mode</td>
<td>&lt; never | always | only-3 | only-1 &gt;</td>
<td>Controls how a column is processed for 3 Frame display:
<ul>
<li><b>never:</b> column is not 3 frame sensitive, display as normal.
<li><b>always:</b> in 3 frame mode, display column features in their 3 columns, as single column
otherwise.
<li><b>only-3:</b> display as 3 frame columns only in 3 frame mode.
<li><b>only-1:</b> display as single column only in 3 frame mode.
</ul>
</td>
</tr>
<tr>
<td>min-mag</td>
<td>double</td>
<td>Do not display features when zoom is below this magnification.</td>
</tr>
<tr>
<td>max-mag</td>
<td>double</td>
<td>Do not display features when zoom is above this magnification.</td>
</tr>
<tr>
<td>width</td>
<td>double</td>
<td>Gives a default width to the feature, some features will have different
widths, e.g. if they are scaled by score.</td>
</tr>
<tr>
<td>score-mode</td>
<td>&lt; width | offset | histogram | percent &gt;</td>
<td>For features with scores, controls how they are displayed:
<ul>
<li><b>width:</b> features displayed as blocks, higher the score, wider the block.
<li><b>offset:</b> features displayed as blocks, higher the score, bigger the offset.
<li><b>histogram:</b> features displayed as a graph/histogram.
<li><b>percent:</b> features displayed as graph within certain percentage range.
</ul>
</td>
</tr>
<tr>
<td>min-score</td>
<td>double</td>
<td>features with a score below this are not displayed.</td>
</tr>
<tr>
<td>max-score</td>
<td>double</td>
<td>features with a score above this are not displayed.</td>
</tr>
<tr>
<td>gff-source</td>
<td>string</td>
<td>Alternative GFF "source" name to output in GFF dump, default is style name.</td>
</tr>
<tr>
<td>gff-feature</td>
<td>string</td>
<td>Alternative GFF "feature" type to output in GFF dump, default is taken from features type.</td>
</tr>
<tr>
<td>displayable</td>
<td>boolean</td>
<td>if false, never display column.</td>
</tr>
<tr>
<td>show-when-empty</td>
<td>boolean</td>
<td>If true, show column even if it has no features.</td>
</tr>
<tr>
<td>show-text</td>
<td>boolean</td>
<td>If true, display any remarks/text relating to the feature.</td>
</tr>
<tr>
<td>strand-specific</td>
<td>boolean</td>
<td>If true, feature is strand specific meaning that in normal display only forward strand
features get displayed (see show-reverse-strand for reverse strand features).</td>
</tr>
<tr>
<td>show-reverse-strand</td>
<td>boolean</td>
<td>If true, for strand specific features, features on reverse strand are displayed in the reverse strand
area.</td>
</tr>
<tr>
<td>show-only-in-separator</td>
<td>boolean</td>
<td>If true, features are displayed in the strand separator bar.</td>
</tr>
<tr>
<td>directional-ends</td>
<td>boolean</td>
<td>If true, features which are directional (transcripts, matches etc)
are drawn with arrow ends to show direction.</td>
</tr>
<tr>
<td>deferred</td>
<td>boolean</td>
<td>If true, features are not loaded at start up but later by user request.</td>
</tr>
<tr>
<td>loaded</td>
<td>boolean</td>
<td>If true, indicates that a set of features has been loaded.</td>
</tr>
<tr>
<td>graph-mode</td>
<td>&lt; line | histogram &gt;</td>
<td>Controls drawing style for a graph column:
<ul>
<li><b>line:</b> a line graph.
<li><b>histogram:</b> a histogram.
</ul>
</td>
</tr>
<tr>
<td>graph-baseline</td>
<td>double</td>
<td>Set's a baseline for drawing, graphs are drawn up and downwards from this value.</td>
</tr>
<tr>
<td>glyph-mode</td>
<td>&lt; splice &gt;</td>
<td>Controls how which glyph is used to draw a column:
<li><b>splice:</b> walking stick shapes indicate splice sites.
</td>
</tr>
<tr>
<td>alignment-parse-gaps</td>
<td>boolean</td>
<td>If true, gapped alignment data is parsed out of the incoming data stream.</td>
</tr>
<tr>
<td>alignment-align-gaps</td>
<td>boolean</td>
<td>If true, gapped alignment data is drawn.</td>
</tr>
<tr>
<td>alignment-within-error</td>
<td>int</td>
<td>Specifies allowable alignment error in bases between sub-blocks <b>within</b> a single gapped alignment.</td>
</tr>
<tr>
<td>alignment-between-error</td>
<td>int</td>
<td>Specifies allowable alignment error in bases between separate alignments.</td>
</tr>
<tr>
<td>alignment-allow-misalign</td>
<td>boolean</td>
<td>If true then match and reference do not have to be exactly the same length, reference
coords will be used for display.</td>
</tr>
<tr>
<td>alignment-blixem</td>
<td>&lt; blixem-n | blixem-x &gt;</td>
<td>If specified then the sequences of the features will be passed to blixem for:
<ul>
<li><b>blixem-n:</b> nucleotide alignment.
<li><b>blixem-x:</b> peptide alignment.
</ul>
</td>
</tr>
<tr>
<td>alignment-pfetchable</td>
<td>boolean</td>
<td>If true, the sequence for an alignment feature can be retrieved using the pfetch server.</td>
</tr>
<tr>
<td>alignment-perfect-colours</td>
<td>colour type</td>
<td>Specifies the colour for the bar joining perfectly colinear alignments.</td>
</tr>
<tr>
<td>alignment-colinear-colours</td>
<td>colour type</td>
<td>Specifies the colour for the bar joining colinear alignments.</td>
</tr>
<tr>
<td>alignment-noncolinear-colours</td>
<td>colour type</td>
<td>Specifies the colour for the bar joining non-colinear alignments.</td>
</tr>
<tr>
<td>transcript-cds-colours</td>
<td>colour type</td>
<td>Specifies the colour for the CDS part of a transcript.</td>
</tr>
<tr>
<td>non-assembly-colours</td>
<td>colour_type</td>
<td>Colours for the non-assembly section of a clone.</td>
</tr>
</tbody>
</table>
</fieldset>
<br/>
<fieldset>
<legend>Inheritance</legend>
<p>There is only one mandatory property for a style and that is it's name, the name is used
to make a unique id for the style. This very flexible policy is what allows inheritance to
work but has the disadvantage that the user must set certain properties explicitly for there
to be enough information for ZMap to display the set of features referencing that style.</p>
<p>The implementation allows any number of styles inheriting settings
from parent styles to any number of levels. This facility can be used to give common
properties to sets of features
that are common in some way (e.g. all wublast hits).
</p>
<p>If you have several styles that are similar you can specify all the common properties in
one parent style and then in the child styles just specify those properties that are
different. You can have any level of inheritance you like BUT the inheritance must be
a DAG, no circularities or multiple inheritance are allowed:</p>
<pre class="example">
# parent-style gives the name of a style from which to inherit properties
# which can be overridden in this style.
parent-style = &lt; name of parent style &gt;
</pre>
<p>Here's an example in keyword-value format showing a base parent for all box like features, a subparent
for all BLASTN data sets and then some styles for different BLASTN columns:
</p>
<pre class="example">
[Basic_Feature_Parent]
description = The base style for all box like features.
Colours = Normal Border black
[BLASTN_Parent]
mode = alignment
parent-style = basic_feature_parent
colours = normal fill brown
width = 15.000000
bump-mode = complete
score-mode = width
min-score = 100.000000
max-score = 400.000000
gff-feature = transcription
[blastn_est_briggsae]
style-parent = blastn_parent
strand-sensitive = true
gff-source = blastn_est_briggsae
[blastn_est_elegans]
style-parent = blastn_parent
strand-sensitive = true
gff-source = blastn_est_elegans
[blastn_tc1]
description = this method was used to map flanking sequences of tc1 insertions etc etc
style-parent = blastn_parent
gff-source = blastn_tc1
</pre>
</fieldset>
<br/>
<fieldset>
<legend>Minimum Drawable Style</legend>
<p>In order to support inheritance (see later) there are _no_ defaults in styles, this means that
the user needs to specify a minimum subset of properties in order for a style to be "drawable".
<b>Note</b> that ZMap does not have display defaults embedded in the code because past experience has shown that
this requires a large number of defaults that are at best "guesses" as to what the user wants to
see. This leads to confusion and uncertainty about how feature display is controlled. </p>
<p>The following properties <b>must</b> be specified if the features referencing the style are to be
displayed:
</p>
<table class="zebra" id="min_displayable" border="2" cellpadding="10" valign="top">
<caption align=top>Minimum Displayable Style</caption>
<thead>
<tr>
<th>Property</th>
<th>Description</th>
</tr>
</thead>
<tbody>
<tr>
<td>"mode"</td>
<td>How the feature should be displayed/processed.</td>
</tr>
<tr>
<td>"bump-mode"</td>
<td>How the feature should be bumped.</td>
</tr>
<tr>
<td>"width"</td>
<td>Basic display width of feature.</td>
</tr>
<tr>
<td>"border" and/or "fill" and/or "draw" colour</td>
<td>Basic, Transcript and Alignment features require fill and/or border colours,
all text (e.g. dna) requires fill and/or draw colours.</td>
</tr>
</tbody>
</table>
<p>Thus the minimum specification of a style is:
<pre class="example">
# Min drawable class.
[min_drawable_style]
mode = xxxxx
width = nnn.nnn
colours = normal border some colour
bump-mode = xxxx
</pre>
<p>
Here are some examples:
</p>
<pre class="example">
[allele]
mode = basic
colours = normal fill orange
width = 1.100000
bump-mode = complete
[blastn_est_briggsae]
mode = alignment
colours = normal fill brown
width = 15.000000
bump-mode = complete
[curated]
mode = transcript
colours = normal border darkblue
width = 15.000000
bump-mode = compact_cluster
</pre>
<h4>Colours</h4>
<p>There is no automatic border colour so it needs to be specified for most
features, e.g.</p>
<pre class="example">
colours = normal fill blue
colours = normal border black
</pre>
<p>The following colours are used by Otterlace but do not exist in the X11 rgb.txt file
and so produce errors in the colour conversion call in the style code:</p>
<pre class="example">
paleviolet
paleorange
palegray
cerise
</pre>
<h4>Strand stuff</h4>
<p>In acedb "frame_sensitive" had more than one meaning:</p>
<ul>
<li>show this column but when 3 frame is turned on redisplay the column
split into the three frames
<li>only show this column when 3 frame is turned on split into the three frames.
<li>only show this column when 3 frame is turned on but as a single column.
</ul>
<p>which of these happened with methods is hard coded in acedb. With styles you must specify which behaviour
you want:</p>
<pre class="example">
frame-mode = always gives the first behaviour
frame-mode = only-3 gives the second behaviour
frame-mode = only-1 gives the third behaviour
</pre>
<h4>Bump stuff</h4>
<p>Bump modes now need to be set explicitly or nothing will happen to the column on bumping.</p>
<pre class="example">
bump-mode = XXXXXXX sets the initial bump mode.
bump-mode-default = XXXXXX sets the mode that the column will be bumped with by default.
</pre>
<p>If you want the column to be initially "unbumped" but bumped with colinear lines etc when
it is bumped you just need to set bump-mode-default, bump-mode will be unbumped by default, e.g.</p>
<pre class="example">
bump-mode-default = range_colinear
</pre>
<h4>Alignments</h4>
<p>All alignments, e.g. EST_human, should be given the mode "Alignment", not "Basic" and also need
the "Internal" and "External" tags setting if internal and external (between HSP) gaps for all matches
for a given sequence should be
joined up with lines:</p>
<pre class="example">
[WABA_parent_all]
description = Inherited method for all WABA hits.
colours = normal fill darkgreen ; normal border black
width = 6.000000
bump-mode = complete
bump-mode-default = range_colinear
score-mode = width
score_min = 40.000000
score_max = 120.000000
alignment-align-gaps = true
</pre>
</fieldset>
<br/>
<fieldset>
<legend>Predefined Styles</legend>
<p>There are a number of predefined styles for common features such as DNA sequence display. These
features have reserved names which should not be used for other sorts of features. The feature set
and the style for these features have the same name.
</p>
<p>Some of these styles are "meta" styles which control the action of a column rather than
specific features, e.g. "3 Frame" controls whether and where the 3 frame translation columns are displayed
but the individual 3 Frame columns display is controlled by the style for each column. Others are normal
styles and some of their settings can be overridden by the user. The following table summarises
the predefined styles:
</p>
<table class="zebra" id="predefined" border="2" cellpadding="10" valign="top">
<caption align=top>Predefined Styles</caption>
<thead>
<tr>
<th>Style</th>
<th>Style Type</th>
<th>User Modifiable</th>
<th>Description</th>
</tr>
</thead>
<tbody>
<tr>
<td>3 Frame</td>
<td>Meta</td>
<td>No</td>
<td>controlling 3 frame display</td>
</tr>
<tr>
<td>3 Frame Translation</td>
<td>Normal</td>
<td>Yes</td>
<td>3 frame protein translation display</td>
</tr>
<tr>
<td>dna</td>
<td>Normal</td>
<td>Yes</td>
<td>dna sequence display</td>
</tr>
<tr>
<td>Locus</td>
<td>Normal</td>
<td>Yes</td>
<td>display of a column of locus names + display of locus names in navigator</td>
</tr>
<tr>
<td>GeneFinderFeatures</td>
<td>Meta</td>
<td>No</td>
<td>splice sites from the Gene Finder program</td>
</tr>
<tr>
<td>Show Translation</td>
<td>Normal</td>
<td>Yes</td>
<td>Show peptide translation column</td>
</tr>
<tr>
<td>Assembly Path</td>
<td>Normal</td>
<td>Yes</td>
<td>Show reference sequence assembly path</td>
</tr>
</table>
<p>The rules for using these predefined styles are:
<ul>
<li>The features for the predefined style must be fetchable from the database,
e.g. no "dna" means no dna display.
<li>To display the data for a predefined style the <b>style name</b> must be specified
in the "feature_sets" list in the "source" stanza of the config file. For predefined
styles the feature set name, method name and style name are all the same.
<li>The style itself does not have to exist in the database, ZMap will create the
style with sensible defaults for display.
<li>"Normal" styles can have relevant fields overriden by specifying them in
a style of the same name in the database, e.g. foreground/background colours
can be overidden for "dna".
</ul>
<p>
</fieldset>
<br/>
<fieldset>
<legend id="acedb_styles">ZMap Styles and Acedb</legend>
<p>
ZMap will read either acedb ?Method or ?ZMap_style objects for style information.
The default is to read ?ZMap_style objects and you should convert to using these instead
of methods as many features are not available with methods.
</p>
<p>
The relationship between features and ?Method objects is different according to
whether you are using ?ZMap_style objects or ?Method objects to specify styles. The
following sections describe how to use each one. Support for ?Method object styles
will be maintained to allow immediate usage of acedb databases without the need to convert
to styles.
</p>
<h4>Using ?ZMap_style objects for Styles</h4>
<ul>
<li>The semantics of the ?Method class are changed: all features must reference a ?Method object
which now <b>only</b> represents the feature set containing those features. Specifically, none of
the display information in the object is referenced. The only tags used are those in
the Feature_set tag set (see below). Feature sets are defined by their Methods,
the name of the set <b>is</b> the Method object name.
<p>The ?Method object name will be the column name for that feature set when displayed unless
the ?Method object contains a Column_parent tag (see below).</p>
<li>A ?Method object can optionally contain a Column_parent tag pointing to a valid
?Method object, the feature set will then be displayed as part of the Column_parent column
along with any other feature sets referencing that Column_parent.
<li><p>Each ?Method object <b>must</b> contain a Style tag pointing to a valid ?ZMap_Style
object unless it is a Column_parent method object in which case no style should be specified..
The style object contains all the display/processing options for that feature set.
A single style can be referenced from multiple method objects.</p>
</ul>
<p> Using ?ZMap_style objects means that all feature display is completely controlled by the
ZMap_style object and all retrieval of features from the acedb database is completely controlled
by the acedb ?Methods. This echoes the separation adopted by DAS and other feature display protocols.
</p>
<p>This is where we always wanted to get to, the style is now completely independent of the feature
set. BUT note the corollary of this: each feature set must now have both a method object AND a
style.
</p>
<p>A number of classes must be added to wspec/models.wrm to fully support ZMap Styles
from an acedb database and several tags must be added to the ?Method class.
The following is a definitive, annotated list of the new classes and tags which can
be copied and pasted direct into a models.wrm file.
</p>
<h4>The ?ZMap_style Class</h4>
<!-- models included here (see zmapsServer/acedb directory)-->
<pre class="example">
<!--#include virtual="models.wrm.shtml"-->
</pre>
<h4>Expressing Inheritance using the ZMap_style class</h4>
<p>The principles of inheritance have already been covered, this section gives details
for the acedb ?ZMap_style class specification.</p>
<p>The inheritance tags in the ?ZMap_style class are:</p>
<pre class="example">
// Parent points to a parent style from which attributes can be inherited,
// there can be an arbitrary depth of parents/children but they must form
// a DAG, cycles and multiple inheritance are _not_ permitted.
Parent Style_parent UNIQUE ?ZMap_Style XREF Style_child
Style_child ?ZMap_Style XREF Style_parent
</pre>
<p>Note that you need only specify the Style_parent in your ace file, the XREFs will take
care of all the Style_child entries. Note also that the tags attempt to enforce a DAB by allowing
only one parent but multiple children.</p>
<p>Here's an example in ace format showing a base parent for all box like features, a subparent
for all BLASTN data sets and then some styles for different BLASTN columns:
</p>
<pre class="example">
ZMap_style : "Basic_Feature_Parent"
Remark "The base style for all box like features."
Colours Normal Border "black"
ZMap_style : "BLASTN_Parent"
Alignment
Style_Parent "Basic_Feature_Parent"
Colours Normal Fill "brown"
Width 15.000000
Unbumped
Score_by_width
Score_bounds 100.000000 400.000000
GFF Feature "transcription"
ZMap_style : "BLASTN_EST_briggsae"
Style_Parent "BLASTN_Parent"
Strand_sensitive
GFF Source "BLASTN_EST_briggsae"
ZMap_style : "BLASTN_EST_elegans"
Style_Parent "BLASTN_Parent"
Strand_sensitive
GFF Source "BLASTN_EST_elegans"
ZMap_style : "BLASTN_TC1"
Remark "This method was used to map flanking sequences of Tc1 insertions etc etc"
Style_Parent "BLASTN_Parent"
GFF Source "BLASTN_TC1"
</pre>
<h4>The ?Method Class</h4>
<p>
The ?Method class has existed in Acedb since the first display code was written but
when using ?ZMap_style objects it's usage changes. ZMap only uses the tags outlined in this section.
</p>
<pre class="example" id="featureset_method">
//=========================================================================================
// Method:
// With styles the method class will have a different meaning, it will be
// be used to represent different sets of features and the Column_group tag
// can be used to clump sets of features into one common set.
//
//
?Method Remark ?Text #Evidence
// ZMap related tags.
//
// ZMap_style points to a style specifying how to display/process this feature set.
//
// Column_parent specifies the parent "feature set" for features that reference
// this method, this is the "column" in zmap.
// Column_child specifies child feature sets that exist within this parent
// feature set or column. Note that this is a one level thing: children do not
// have their own children, parents do not have parents. N.B. the XREF will fill in
// this tag.
//
Feature_set Style UNIQUE ?ZMap_style
Group UNIQUE Column_child ?Method XREF Column_parent
Column_parent UNIQUE ?Method XREF Column_child
//
// All other method tags are as before and will be ignored by ZMap.
//
//=========================================================================================
</pre>
<p>The Style tag _must_ be populated for a feature set to be displayed by zmap.</p>
<p>The Column_group tag is now defunct, instead there are parent/child tags which take advantage of
acedbs UNIQUE and XREF mechanisms to ensure that there is only one level of parent/child i.e. that
methods are either parents or children. When using the Group tags you only need to specify the
Column_parent tag, the XREF will fill in the Column_children tag.</p>
<p>The name of the column is the name of the method unless there is a Column_parent method in which
case it is the name of the Column_parent method.</p>
<p>The trailing Float for the Column_parent tag specifies a priority for ordering the column children
features into "sub_columns". Low to high priorities go left to right on the forward strand, right to
left on the reverse strand.
<p>An example of column group usage:</p>
<pre class="example">
//------------------------------------------------------------------------------------
// A feature set with no parent which will display in the column "Eds_alignments":
Method : "Eds_alignments"
Style "My favourite lovely style"
// A feature set with child feature sets which will all be displayed in the column "Parent column".
Method : "Parent column"
Style "overall column style"
Method : "First Child feature set"
Column_parent "Parent column"
Style "my style"
Method : "Second Child feature set"
Column_parent "Parent column"
Style "my style"
//------------------------------------------------------------------------------------
</pre>
The entry in the "featuresets" stanza in the ZMap config file would be:
<pre class="example">
[source]
featuresets = Eds_alignments ; Parent column
</pre>
<h4>Genefinder and Auto-created Method objects</h4>
<p>The acedb code creates some method objects itself, this is generally for display of features
calculated by the code, e.g. gene finder features. (In fact I think this is the only case we
need to be aware of...famous last words....)
<p>To avoid zmap having to second guess acedbs self generation stuff it is necessary for the database
administrator to add these methods in advance. A simple way to do this is as follows:
<ol>
<li><p> run the genefinder from within fmap and then "Save" the database before exitting, the
auto-created methods will then be saved in the database. </p>
<li><p>Add a "Style" tag to each genefinder:</p>
<pre class="example">
//------------------------------------------------------------------------------------
Method : "ATG"
Style "ATG"
Method : "hexExon"
Style "hexExon"
Method : "hexIntron"
Style "hexIntron"
Method : "GF_coding_seg"
Style "GF_coding_seg"
Method : "GF_ATG"
Style "GF_ATG"
Method : "GF_splice"
Style "GF_splice"
//------------------------------------------------------------------------------------
</pre>
<li><p>Add the Style for each method:</p>
<pre class="example">
//------------------------------------------------------------------------------------
ZMap_Style : "ATG"
Remark "This method is used by acedb to display potential methionine initiation codons"
Basic
Colours Normal Fill "yellow"
Width 15.000000
Bump_mode Complete
Strand_sensitive
Show_only_as_3_frame
GFF Source "ATG"
GFF Feature "translation"
ZMap_Style : "hexExon"
Remark "GeneFinder method"
Basic
Colours Normal Fill "orange"
Colours Normal Border "black"
Width 15.000000
Bump_mode Complete
Strand_sensitive
Show_only_as_3_frame
Score_by_width
Score_bounds 10.000000 100.000000
ZMap_Style : "hexIntron"
Remark "GeneFinder method"
Basic
Colours Normal Fill "orange"
Colours Normal Border "black"
Width 15.000000
Bump_mode Complete
Strand_sensitive
Show_only_as_3_frame
Score_by_width
Score_bounds 10.000000 100.000000
ZMap_Style : "GF_coding_seg"
Remark "GeneFinder method"
Basic
Colours Normal Fill "gray"
Colours Normal Border "black"
Width 15.000000
Bump_mode Complete
Strand_sensitive
Show_only_as_3_frame
Score_by_width
Score_bounds 2.0 8.0
ZMap_Style : "GF_ATG"
Remark "GeneFinder method"
Basic
Colours Normal Fill "orange"
Colours Normal Border "black"
Width 15.000000
Bump_mode Complete
Strand_sensitive
Show_only_as_3_frame
Show_only_as_3_frame
Score_by_width
Score_bounds 0.000000 3.000000
ZMap_Style : "GF_splice"
Remark "GeneFinder method"
Glyph Splice
Frame_0 Normal Fill "red"
Frame_1 Normal Fill "blue"
Frame_2 Normal Fill "green"
Width 10.000000
Bump_mode Complete
Strand_sensitive
Show_only_as_3_frame
Show_only_as_1_column
Score_by_width
Score_bounds -2.000000 4.000000
//------------------------------------------------------------------------------------
</pre>
</ol>
<h4>Using ?Method objects for styles (deprecated)</h4>
<p>Rules for using ?Method objects:</p>
<ul>
<li><p>ZMap must be instructed to look for ?Method objects rather than ?ZMap_style objects
by specifying the "use_methods" tag in the configuration file "source" stanza:</p>
<pre class="example">
[source]
use_methods = true
</pre>
<li><p>ZMap will only read a subset of the ?Method object display and processing tags (see below)
to create styles for feature display.</p>
</ul>
<p> Using ?Method objects means that both feature display and feature retrieval is completely controlled by the
?Method object. There is no separation of these two, the ?Method is both the feature set and
it's display/processing. The ?Method object tags will not be extended so only a subset of ZMap
display features can be used. Use of ?Method objects should be seen as a "quick and easy" way of display
which will duplicate most of the acedb FMap display but that is all. The following extract from the ?Method class
shows which tags ZMap reads.
</p>
<pre class="example">
// Method:
//
// These are the only tags read by ZMap.
//
//
?Method Remark ?Text #Evidence
//
// the Display information controls how the column looks.
Display Control UNIQUE No_display // never display features
Init_hidden // initially hide features
Colour #Colour
CDS_colour #Colour
Frame_sensitive // Is feature read frame dependent ?
Strand_sensitive Show_up_strand #Colour
Score Score_by_offset // has priority over width, for Jean
Score_by_histogram UNIQUE Float // baseline value
Score_bounds UNIQUE Float UNIQUE Float
Overlap_mode UNIQUE Overlap // draw on top - default
Bumpable // bump to avoid overlap
Cluster // one column per homol target
Width UNIQUE Float
Max_mag UNIQUE Float // don't show if more bases per line
Min_mag UNIQUE Float // don't show if fewer bases per line
Gapped // draw sequences or homols with gaps
Join_blocks // link up all blocks of a single feature with lines
GFF GFF_source UNIQUE Text
GFF_feature UNIQUE Text
</pre>
<h4>Converting from ?Method to ?ZMap_style objects</h4>
<p>ZMap includes a small utility script, methods2style.pl, to do a first pass conversion, the result will
require hand editting as some fields cannot be determined from the ?Method object,
e.g. Mode.</p>
<pre class="example">
SYNOPSIS: methods2style.pl -file <methods.ace> -help
e.g. methods2style.pl -file ./my/methods/file > ./my_new/styles/file
</pre>
</fieldset>
<br/>
<fieldset>
<legend id="keyword_value_format">Keyword Value Format</legend>
<p>"<b>Key Files</b>" are derived from MS Windows <b>".ini"</b> files although the standard they follow
(<a href="http://freedesktop.org/wiki/Specifications/desktop-entry-spec?action=show&redirect=Standards%2Fdesktop-entry-spec">
the Desktop Entry Specification</a>)
is different in places. The basic format is:</p>
<pre class="example">
# this is an example copied from the GLib documentation of these files.
[First Group]
Name=Key File Example\tthis value shows\nescaping
Welcome = Hello
[Another Group]
Numbers=2;20;-200;0
Booleans=true;false;true;true
</pre>
<p>"<b>Case Sensitivity</b>:" key files are case sensitive and you should be careful to
sepecify all information in lower case.
</p>
<p>A restriction of Key Files is that because they support merging of groups
within a file you cannot use multiple groups with the same name to produce
separate groups. Each separate group <b>must</b> have a unique name. What this
means for Styles is that the Style name <b>is</b> the group name:
</p>
<pre class="example">
[Curated]
width = 2
[Allele]
width = 1
<i>etc.</i>
</pre>
</fieldset>
<!--#include virtual="/perl/footer"-->
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