X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2FfeaturesFormat.html;h=9d354dca95da55cd41c6afe5e2e8367f183002e9;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=8665e66d6125683e05b329c311017765e72838c8;hpb=e5cbd35e13f46ae1d59a08b0af1086677418141d;p=jalview.git diff --git a/help/html/features/featuresFormat.html b/help/html/features/featuresFormat.html index 8665e66..9d354dc 100755 --- a/help/html/features/featuresFormat.html +++ b/help/html/features/featuresFormat.html @@ -1,7 +1,7 @@ -A feature type has a text label, and a colour specification. This -can be either: + A feature type has a text label, and a colour specification. This can + be either: - +

+ +

The remaining lines in the file are the sequence annotation + definitions, where the now defined features are attached to regions + on particular sequences. Each feature can optionally include some + descriptive text which is displayed in a tooltip when the mouse is + near the feature on that sequence (and can also be used to generate + a colour the feature).

+ +

+ If your sequence annotation is already available in GFF Format (see + http://www.sanger.ac.uk/resources/software/gff/spec.html), + then you can leave it as is, after first adding a line containing + only 'GFF' after any Jalview feature colour definitions (this + mixed format capability was added in Jalview 2.6). Alternately, + you can use Jalview's own sequence feature annotation format, which + additionally allows HTML and URLs to be directly attached to each + piece of annotation. +

+ +

+ Jalview's sequence feature annotation format +

+

Each feature is specified as a tab-separated series of columns + as defined below: + 

 description	sequenceId	sequenceIndex	start	end	featureType	score (optional)
-This format allows two alternate ways of referring to a sequence, either by -its text ID, or its index in an associated alignment. Normally, sequence features are associated with sequences rather -than alignments, and the sequenceIndex field is given as "-1". In -order to specify a sequence by its index in a particular alignment, -the sequenceId should be given as "ID_NOT_SPECIFIED", otherwise the -sequenceId field will be used in preference to the sequenceIndex -field. -

- - -

The description may contain simple HTML document body tags if -enclosed by "<html></html>" and these will be rendered -as formatted tooltips in the Jalview Application (the Jalview -applet is not capable of rendering HTML tooltips, so all formatting -tags will be removed).
-Attaching Links to Sequence Features
-Any anchor tags in an html formatted description line will be -translated into URL links. A link symbol will be displayed adjacent -to any feature which includes links, and these are made available -from the links -submenu of the popup menu which is obtained by right-clicking -when a link symbol is displayed in the tooltip.
-Non-positional features
-Specify the start and end for a feature to be -0 in order to attach it to the whole sequence. -Non-positional features are shown in a tooltip when the mouse -hovers over the sequence ID panel, and any embedded links can be -accessed from the popup menu. Scores
-Scores can be associated with sequence features, and used to sort -sequences or shade the alignment (this was added in jalview 2.5). -The score field is optional, and malformed scores will be -ignored.

- -

Feature annotations can be collected into named groups by -prefixing definitions with lines of the form: - -

+  This format allows two alternate ways of referring to a sequence,
+  either by its text ID, or its index in an associated alignment.
+  Normally, sequence features are associated with sequences rather than
+  alignments, and the sequenceIndex field is given as "-1". In
+  order to specify a sequence by its index in a particular alignment,
+  the sequenceId should be given as "ID_NOT_SPECIFIED",
+  otherwise the sequenceId field will be used in preference to the
+  sequenceIndex field.
+  

+
+
+  

+    The description may contain simple HTML document body tags if
+    enclosed by "<html></html>" and these will be
+    rendered as formatted tooltips in the Jalview Application (the
+    Jalview applet is not capable of rendering HTML tooltips, so all
+    formatting tags will be removed).
 Attaching Links
+      to Sequence Features
 Any anchor tags in an html formatted
+    description line will be translated into URL links. A link symbol
+    will be displayed adjacent to any feature which includes links, and
+    these are made available from the links submenu of the popup menu which is obtained by
+    right-clicking when a link symbol is displayed in the tooltip.

+    Non-positional features
 Specify the start
+    and end for a feature to be 0 in order to
+    attach it to the whole sequence. Non-positional features are shown
+    in a tooltip when the mouse hovers over the sequence ID panel, and
+    any embedded links can be accessed from the popup menu.
 Scores

+    Scores can be associated with sequence features, and used to sort
+    sequences or shade the alignment (this was added in Jalview 2.5).
+    The score field is optional, and malformed scores will be ignored.
+  

+
+  
Feature annotations can be collected into named groups by
+    prefixing definitions with lines of the form:
+  
 startgroup	groupname
 

 
-.. and subsequently post-fixing the group with:
+  .. and subsequently post-fixing the group with:
 
-
+  
 endgroup	groupname
 

 
-Feature grouping was introduced in version 2.08, and used to
-control whether a set of features are either hidden or shown
-together in the sequence Feature
-settings dialog box.

- 
+  Feature grouping was introduced in version 2.08, and used to control
+  whether a set of features are either hidden or shown together in the
+  sequence Feature settings dialog box.
+  

+
 
-
A complete example is shown below :
-
+  
A complete example is shown below :
+  
 domain	red
 metal ion-binding site	00ff00
 transit peptide	0,105,215