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Commit 188e3044 authored by edgrif's avatar edgrif
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update styles stuff for bump modes and further styles description.

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......@@ -15,7 +15,7 @@ display detais or perhaps dumping them to files.
<h3>Mandatory tags</h3>
<p>The policy in ZMap Styles is that a subset of tags must be specified if a feature is to
<p>The policy for ZMap Styles is that a subset of tags must be specified if a feature is to
be displayed. This policy was implemented because past experience has shown that the alternative
is that the code must have embedded in it a large number of defaults that are often "best guesses"
about how features should be displayed. This leads to confusion and uncertainty about how
......@@ -59,13 +59,54 @@ displayed:
<h3>Inheritance</h3>
<p>ZMap_style implement one level of inheritance, this allows you to specify a common base style for
a number of styles that differ perhaps only in colour or some other small detail.
<p>ZMap_styles implement inheritance, this allows any number of styles inheriting settings
from parent styles. This facility can be used to give common colours to sets of features
that are common in some way (e.g. all wublast hits).
<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:
<pre><code>
ZMap_style : "Basic_Feature_Parent"
Remark "The base style for all box like features."
Colours Normal Border "black"
ZMap_style : "BLASTN_Parent"
Alignment
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"
Parent "BLASTN_Parent"
Strand_sensitive
GFF Source "BLASTN_EST_briggsae"
ZMap_style : "BLASTN_EST_elegans"
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 in another strain of C. elegans against the N2 genome sequence."
Parent "BLASTN_Parent"
GFF Source "BLASTN_TC1"
</code></pre>
<h3>Column_group styles</h3>
<p>ZMap allows multiple sets of features within a single column, each set with its own style for
colouring, bumping and so on.
<p>Where several different types of features all perhaps having their own styles are displayed in a
single column specified via the "Column_group" tag, then there must be a style with name given by
that tag. This is partly to make processing within zmap uniform (i.e. everything has a style) and
......@@ -74,27 +115,47 @@ bumping all features in the column or hiding the whole column etc.
<h3>Meta or implicit styles</h3>
<h3>Predefined Styles</h3>
<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.
<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 the 3 frame translation columns are displayed
but the individual column display is controlled by the style for each column.
<p>There are a number of "implicit" or "meta" styles which have predefined (i.e. fixed) names within
zmap. Styles with these names (case insensitive) _MUST_ be available from the server, if they are
not then various types of display (dna, 3 frame) will not be possible.
<p>Other predefined styles are used in the normal way, e.g. the "DNA" style simply controls the
colour of the dna text (normal and selected).
<p>ZMap will fill in the style with some reasonable defaults but users can override these by
specifying their own values in these styles. Users must avoid using these names for any other
styles.
<p>Although these styles are predefined, they must be available from the data source supplied to
zmap if that particular type of data is to be displayed. The style does not have to be completely
filled out as ZMap will fill in the style with some reasonable defaults. Any values from the data
source will override the default values.
<p>The current list of these styles is:
<ul>
<li><b>"3 Frame"</b> controls 3 frame display
<li><b>"3 Frame Translation"</b> controls 3 frame protein translation display
<li><b>"DNA"</b> controls dna sequence display
<li><b>"Locus"</b> controls display of a column of locus names
<li><b>"3 Frame"</b> Meta style controlling 3 frame display
<li><b>"Show Translation"</b> Meta style controlling if translation is shown at all
<li><b>"3 Frame Translation"</b> Predefined style for 3 frame protein translation display
<li><b>"DNA"</b> dna sequence display
<li><b>"Locus"</b> display of a column of locus names
<li><b>"GeneFinderFeatures"</b> splice sites from the Gene Finder program
<li><b>"scale"</b> dna base scale
</ul>
<p><hr>
<h2 id="style_struct">ZMap Styles Struct Details</h3>
<p>Refer to the ZMap code documentation for ZMap Styles. (need an href here...how to refer to it ?)
<h3>Field setting</h3>
<p>stuff needed....
<p><hr>
......@@ -104,18 +165,27 @@ styles.
<h3>Acedb Methods vs. ZMap styles</h3>
<p>The two exist along side each other and have the following relationship/uses:
<p>When ZMap accesses an acedb database as one of its data sources then if styles are to be
specified via acedb classes then there must be a very precise relationship between the
styles and acedbs Method class objects:
<p>For every zmap feature set there must be a ZMap_style object in the acedb database AND also an
acedb Method, they MUST have the same name.
<ul>
<li>ZMap must be instructed to look for ZMap style objects rather than acedb Method objects
by specifying the "use_zmap_styles" tag in the configuration file "source" stanza:
<p>use_zmap_styles = true
<li>All Styles referenced by any feature must be represented by a ZMap_style object in the acedb database AND
also an acedb Method, they MUST have the same name.
<ul>
<li>ZMap feature display is completely controlled by the ZMap_style object.
<li>Retrieval of features from the acedb database is completely controlled by the acedb Method because
we use the acedb GFF dumper which makes heavy use of acedb Methods.
</ul>
<p>ZMap feature display is completely controlled by the ZMap_style object.
<p>It is vital that acedb Methods continue to exist unaltered alongside the new
ZMap_style objects.
</ul>
<p>Retrieval of features from the acedb database is completely controlled by the acedb Method because
we use the acedb GFF dumper which makes heavy use of acedb Methods.
<p>In other words its vital that acedb Methods continue to exist unaltered alongside the new
ZMap_style objects.
......@@ -205,6 +275,10 @@ be copied and pasted direct into a models.wrm file.
//
?Zmap_mode_sequence dummy Text
// Specifies properties unique to a peptide feature.
//
?Zmap_mode_peptide dummy Text
// Specifies properties unique to a text feature.
//
?Zmap_mode_text dummy Text
......@@ -222,6 +296,26 @@ be copied and pasted direct into a models.wrm file.
Mode UNIQUE Splice
// Specifies how columns should be displayed when bumped.
?Zmap_overlap Remark Text
Overlap_mode UNIQUE Complete // Draw on top - default
Compact_cluster // All features with same name in a single column, several names in one
// column but no 2 features overlap.
Compact_cluster_range // All features with same name in a single column if they overlap the
// focus range, all other features in a single column.
Cluster // All features with same name in a single column, several names in one
// column but no interleaving of sets of features.
Ends_range // Sort by 5' and 3' best/biggest matches, one match per column, very
// fmap like but better...
Compact_limit // Constrain matches to be colinear within range or are truncated.
Oscillate // Oscillate between one column and another, useful for displaying tile paths.
Overlap // Bump if match coords overlap.
Position // Bump if match start at same coord.
Name // One column per match target
Item_overlap // Bump if item coords overlap in canvas space
Simple // One column per match, good for testing
//-----------------------------------------------------------------------------------------
......@@ -241,6 +335,7 @@ be copied and pasted direct into a models.wrm file.
Transcript #Zmap_mode_transcript
Alignment #Zmap_mode_alignment
Sequence #Zmap_mode_sequence
Peptide #Zmap_mode_peptide
Plain_Text #Zmap_mode_text
Graph #ZMap_mode_graph
Glyph #ZMap_mode_glyph
......@@ -270,10 +365,9 @@ be copied and pasted direct into a models.wrm file.
// Should boxes have pointy ends to show features direction ? (default = FALSE)
Directional_ends
//
// includes new bump modes directly + bump gap.
Bump_mode UNIQUE Unbumped
Cluster // Packed but not interleaved.
Compact_cluster // Packed and interleaved.
// Bumping controls display of features when there are so many in a column that they overlap.
Bump_mode #Zmap_overlap // sets current mode.
Bump_default #ZMap_overlap // sets normal bumping mode for column.
Bump_spacing UNIQUE Float // default is 0.0, i.e. no gap between bumped features.
//
Strand_sensitive Show_up_strand
......
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