From 0c4d308e554bdb7acb196a032e3233f8615f9cd0 Mon Sep 17 00:00:00 2001
From: edgrif <edgrif>
Date: Mon, 29 Sep 2008 16:26:09 +0000
Subject: [PATCH] produce some kind of first draft of styles docs for users.
---
web/user_doc/styles.shtml | 467 +++++++++++++++++++++++++-------------
1 file changed, 307 insertions(+), 160 deletions(-)
diff --git a/web/user_doc/styles.shtml b/web/user_doc/styles.shtml
index 2f01a065d..d11828096 100755
--- a/web/user_doc/styles.shtml
+++ b/web/user_doc/styles.shtml
@@ -9,6 +9,8 @@ pre{ width: 95%; background-color: #DDDDDD; border-style: solid; border-width: 1
</style>
+
+<br />
<fieldset>
<legend>Overview</legend>
@@ -18,53 +20,100 @@ those features are processed during user interaction, e.g. by clicking on them t
display detais or perhaps dumping them to files.
</fieldset>
-<br />
+
+
+<br />
<fieldset>
-<legend>Mandatory Tags</legend>
+<legend>Mandatory Properties</legend>
-<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
-feature display is controlled.
-</p>
+<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>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 tags <b>must</b> be specified if the features referencing the style are to be
+
+<p>The following properties <b>must</b> be specified if the features referencing the style are to be
displayed:
</p>
-<ul>
- <li><b>mode:</b> must be set to one of
- <ul>
- <li><b>ZMAPSTYLE_MODE_BASIC</b>
- <li><b>ZMAPSTYLE_MODE_TRANSCRIPT</b>
- <li><b>ZMAPSTYLE_MODE_ALIGNMENT</b>
- <li><b>ZMAPSTYLE_MODE_TEXT</b>
- <li><b>ZMAPSTYLE_MODE_GRAPH</b>
- <li><b>ZMAPSTYLE_MODE_GLYPH</b>
- <p>also requires glyph mode to be set, currrently only ZMAPSTYLE_GLYPH_SPLICE
- is supported.
- </ul>
- <li><b>overlap:</b> must be set to one of
- <ul>
- <li>...</li>
- </ul>
- <li><b>width:</b> must be set.
- <li><b>colours:</b> different modes require different colours to be set:
- <ul>
- <li><b>ZMAPSTYLE_MODE_BASIC</b>, <b>ZMAPSTYLE_MODE_TRANSCRIPT</b>, <b>ZMAPSTYLE_MODE_ALIGNMENT</b>
- need fill and or border to be set.
- <li><b>ZMAPSTYLE_MODE_TEXT</b> needs fill and draw to be set.
- <li><b>ZMAPSTYLE_MODE_GRAPH</b>
- <li><b>ZMAPSTYLE_MODE_GLYPH</b>
- <p>ZMAPSTYLE_GLYPH_SPLICE requires all 3 frame colours to be set.
- </ul>
-</ul>
+
+<table class="zebra" id="timtable">
+ <caption align=top>Displayable Styles</caption>
+ <thead>
+ <tr>
+ <th>Property</th>
+ <th>Type</th>
+ <th>Value Range</th>
+ <th>Description</th>
+ </tr>
+ </thead>
+ <tbody>
+ <tr>
+ <td>"mode"</td>
+ <td>one of</td>
+ <td>"basic", "transcript" etc.</td>
+ <td>Identifies how feature should be processed, e.g. as a transcript, match etc.</td>
+ </tr>
+ <tr>
+ <td>"overlap_mode"</td>
+ <td>one of</td>
+ <td>"complete", "Overlap" etc</td>
+ <td>Controls how features are arranged in within the column, e.g. overlapping, by name etc.</td>
+ </tr>
+ <tr>
+ <td>"width"</td>
+ <td>double</td>
+ <td>0 < width < col_max</td>
+ <td>gives a default width to the feature (in pixels ???), some features will have different
+ widths, e.g. if they are scaled by score.</td>
+ </tr>
+ <tr>
+ <td>"border" and/or "fill" and/or "draw"</td>
+ <td>string</td>
+ <td>standard colour specifier</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>
+</table>
+
+
+<p>
+Here are some examples:
+</p>
+
+<pre class="example">
+
+ZMap_style : "Allele"
+Basic
+Colours Normal Fill "orange"
+Width 1.100000
+Unbumped
+
+
+ZMap_style : "BLASTN_EST_briggsae"
+Alignment
+Colours Normal Fill "brown"
+Width 15.000000
+Unbumped
+
+
+ZMap_style : "curated"
+Transcript
+Colours Normal Border "darkblue"
+Width 15.000000
+Compact_cluster
+
+</pre>
</fieldset>
-<br />
+
+<br />
<fieldset>
<legend>Inheritance</legend>
@@ -114,116 +163,141 @@ GFF Source "BLASTN_TC1"
</pre>
</fieldset>
-<br />
-<fieldset>
-<legend>Column_group styles</legend>
-<p>ZMap allows multiple sets of features within a single column, each set with its own style for
-colouring, bumping and so on.
-</p>
-<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
-partly because we need an overall style for the column to allow column wide operations such as
-bumping all features in the column or hiding the whole column etc.
-</p>
-</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.
+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 the 3 frame translation columns are displayed
-but the individual column display is controlled by the style for each column.
-</p>
-
-<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>
-
-<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.
+specific features, e.g. "3 Frame" controls whether and where the 3 frame translation columns are displayed
+but the individual column 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>
-<p>The current list of these styles is:
+<table class="zebra" id="timtable">
+ <caption align=top>Predefined Styles</caption>
+ <thead>
+ <tr>
+ <th>Style</th>
+ <th>Style Type</th>
+ <th>User Specifiable</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 + navigator bit</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>
+</table>
+
+<p>The rules for using these predefined styles are:
<ul>
- <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
+ <li>The features for the predefined style must be fetchable from the database.
+ <li>To display the data for a predefined style the style name must be specified
+ in the "feature_sets" list in the "ZMap" stanza of the config file.
+ <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 />
-
-<hr>
-
-<fieldset>
-<legend>ZMap Styles Struct Details</legend>
-
-<p>Refer to the ZMap code documentation for ZMap Styles <a href="../html/index.shtml">here</a></p>
-
-
-<h5>Field setting</h5>
-<p>stuff needed....</p>
-</fieldset>
<br />
-
-<hr>
-
<fieldset>
<legend>ZMap Styles and Acedb</legend>
-<h3>Acedb Methods vs. ZMap styles</h3>
-<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>
+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>
-<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>It is vital that acedb Methods continue to exist unaltered alongside the new
- ZMap_style objects.
-</ul>
+<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 each time.
+</p>
-<h3>Acedb Classes required to support ZMap Styles</h3>
+<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).
+ <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><p>Each ?Method object <b>must</b> contain a Style tag pointing to a valid ?ZMap_Style
+ object. The style object contains all the display/processing options for that feature set.</p>
+ <li>Each ?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. Note that the Column_parent
+ column must also reference a valid ?ZMap_Style.
+</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>A number of classes must be added to wspec/models.wrm to fully support ZMap Styles
-from an acedb database. The following is a definitive, annotated list of these classes which can
+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>
@@ -298,6 +372,7 @@ be copied and pasted direct into a models.wrm file.
Match_colours Perfect UNIQUE #ZMap_feature_colour
Colinear UNIQUE #ZMap_feature_colour
Non_colinear UNIQUE #ZMap_feature_colour
+ Pfetchable // If present it means these alignments have pfetch entries.
// Specifies properties unique to a sequence feature.
//
@@ -327,21 +402,21 @@ be copied and pasted direct into a models.wrm file.
// 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.
+ Overlap // Bump by set amount if coords overlap.
+ Item_overlap // Bump so items do not overlap at all if coords overlap.
+ Start // Bump if match start at same coord.
Name // One column per match target
- Item_overlap // Bump if item coords overlap in canvas space
+ Oscillate // Oscillate between one column and another, useful for displaying tile paths.
Simple // One column per match, good for testing
+ Ends_range // Sort by 5' and 3' best/biggest matches, one match per column, very
+ // fmap like but better...
+ Compact // All features with same name in a single column, several names in one
+ // column but no 2 features overlap.
+ Compact_no_interleave // All features with same name in a single column, several names in one
+ // column but no interleaving of sets of features.
+ Range // All features with same name in a single column if they overlap the
+ // mark range.
+ Range_colinear // As for "Range" but constrain matches to be colinear across range.
@@ -356,7 +431,8 @@ be copied and pasted direct into a models.wrm file.
// 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 are _not_ permitted.
- Parent UNIQUE ?ZMap_Style
+ Parent Style_parent UNIQUE ?ZMap_Style XREF Style_child
+ Style_child ?ZMap_Style XREF Style_parent
//
// The mode of the features, i.e. transcript, text or what.....
Mode UNIQUE Basic #Zmap_mode_basic
@@ -368,21 +444,20 @@ be copied and pasted direct into a models.wrm file.
Graph #ZMap_mode_graph
Glyph #ZMap_mode_glyph
//
- // Column_group allows placement of different sets of features within a single column:
- //
- // Column_group "column group name"
+ // Controls all aspects of feature display.
//
- Column_group UNIQUE Text UNIQUE ?ZMap_Style
+ //Display Hide UNIQUE Always // never display features (default FALSE)
+ // Initially // Hide features initially (default FALSE)
+ // Show_when_empty // Show set even if empty (default FALSE)
//
- // Controls all aspects of feature display.
- Display Hide UNIQUE Always // never display features (default FALSE)
- Initially // Hide features initially (default FALSE)
- Show_when_empty // Show set even if empty (default FALSE)
+ Display Col_display UNIQUE Not_displayable // never display this column (for meta columns)
+ Displayable Col_state UNIQUE Hide // hide column always (can be unset by user)
+ Show_hide // hide column according to zoom/mark etc. (can be unset by user)
+ Show // show column always (can be unset by user)
+ Show_when_empty // Show set even if empty (default FALSE)
+ // No_Compress // Always show, even in "compressed" display.
//
Colours UNIQUE #ZMap_feature_colour
- Frame_colours Frame_0 UNIQUE #ZMap_feature_colour
- Frame_1 UNIQUE #ZMap_feature_colour
- Frame_2 UNIQUE #ZMap_feature_colour
//
Width UNIQUE Float // default is 0.0
//
@@ -400,8 +475,12 @@ be copied and pasted direct into a models.wrm file.
//
Strand_sensitive Show_up_strand
//
- // Is feature read frame dependent ? (optionally only ever show as 3 frames)
- Frame_sensitive Show_only_as_3_frame
+ // Read frame sensitive features, in 3 frame mode shown in separate reading frame cols.
+ Frame_sensitive Frame_display Show_only_as_3_frame // show only in 3 frame mode.
+ Show_only_as_1_column // show only in 3 frame mode but as single col.
+ Frame_colours Frame_0 UNIQUE #ZMap_feature_colour
+ Frame_1 UNIQUE #ZMap_feature_colour
+ Frame_2 UNIQUE #ZMap_feature_colour
//
// Score_bounds controls feature width when related to score, specifies min/max.
Score Score_style UNIQUE Score_by_width // only visual display supported for now.
@@ -414,47 +493,115 @@ be copied and pasted direct into a models.wrm file.
//=========================================================================================
+// 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>
-<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,
+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>
-ADD STUFF ABOUT CONVERTING FROM METHODS TO STYLES....
</fieldset>
<br />
--
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