// 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>
<h3 id="acedb_minimum_style">The Minimum Style specification for feature display</h3>
<h4>Using ?Method objects for styles</h4>
<p>Rules for using ?Method objects:</p>
<ul>
<li>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:
<pre class="example">
source
{
use_methods = true
}
</pre>
<li>ZMap will only read a subset of the ?Method object display and processing tags (see below)
to create styles for feature display.
</ul>
<p>ZMap Styles require that certain tags and values must be specified if features are to
be displayed, the following give examples of minimum specifications:
<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">
ZMap_style : "Allele"
Remark "Alleles in WormBase represent small sequence mutations (substitutions or indels) with the differences usually being between the sequenced (N2) strain of C. elegans and some other strain. The Allele track on the WormBase web site also includes SNPs and transposon mediated insertions"
Basic
Colours Normal Fill "orange"
Width 1.100000
Unbumped
// 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
ZMap_style : "BLASTN_EST_briggsae"
Alignment
Colours Normal Fill "brown"
Width 15.000000
Unbumped
Score_by_width
</pre>
ZMap_style : "curated"
Remark "Predicted protein-coding genes are flagged with this method. All of these genes have been looked at by a human curator at some point and have usually been modified with respect to the initial computer prediction."
Transcript CDS_colour Normal Fill "darkblue"
Colours Normal Border "darkblue"
Width 15.000000
Compact_cluster
</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,
