styles.html

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>







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