X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2FfeaturesFormat.html;h=4d13dcdaa32499ba471eee15868e84b87c097ade;hb=06beaa2f6eb56b94f4dd6408078a14e572cf0eb3;hp=27f9b17d1370eb7f3fadbc7cb888e0cd1d3df039;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git
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+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see
Sequence Features File
-The Sequence features file (which used to be known as the -"Groups file" prior to version 2.08) is a simple way of -getting your own sequence annotations into Jalview. It was introduced to -allow sequence features to be rendered in the Jalview applet, and so is -intentionally lightweight and minimal because the applet is often used -in situations where data file size must be kept to a minimum, and no XML -parser is available.
-Features files are imported into Jalview in the following ways:
-
- -features <Features filename>
Sequence Features File Format
-A features file is a simple ASCII text file, where each line -contains tab separated text fields. No comments are -allowed.
-The first set of lines contain type definitions:
-Feature label Feature Colour
A feature
-type has a text label, and a colour specification. This can be either:
-
-<mincolor>|<maxcolor>|[absolute|]<minvalue>|<maxvalue>[|<thresholdtype>|[<threshold value>]] -The fields are as follows -
The remaining lines in the file are the sequence annotation -definitions, where the now defined features are attached to regions on -particular sequences, optionally with some descriptive text (displayed -in a tooltip when the mouse is near the feature on that sequence). There -are two alternate ways of referring to a sequence, either by its text -ID, or its index in an associated alignment. -
-description sequenceId sequenceIndex start end featureType score (optional)-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 2.4.X). 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: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.
A complete example is shown below : -
++ Sequence Features File +
+
The Sequence features file (which used to be known as the + "Groups file" prior to version 2.08) is a simple way of getting your + own sequence annotations into Jalview. It was introduced to allow + sequence features to be rendered in the Jalview applet, and so is + intentionally lightweight and minimal because the applet is often + used in situations where data file size must be kept to a minimum, + and no XML parser is available.
+ ++ Features files are imported into Jalview in the following ways:
+
+ -features <Features filename> ++
+ Sequence Features File Format +
++ A features file is a simple ASCII text file, where each line + contains tab separated text fields. No comments are + allowed. +
++ Feature Colours +
+The first set of lines contain feature type definitions and their colours: +
+Feature label Feature Colour + ++ + A feature type has a text label, and a colour specification. This can + be either: + +
+[label or score or attribute|attName|]<mincolor>|<maxcolor>|[absolute|]<minvalue>|<maxvalue>[|<novalue>][|<thresholdtype>|[<threshold value>]] +The fields are as follows: + +
+ Feature Filters +
+This section is optional, and allows one or more filters to be defined for each feature type.
+
Only features that satisfy the filter conditions will be displayed.
+
Begin with a line which is just STARTFILTERS, and end with a line which is just ENDFILTERS.
+
Each line has the format:
+
featureType <tab> (filtercondition1) [and|or] (filtercondition2) [and|or]...+ The parentheses are not needed if there is only one condition. + Combine multiple conditions with either and or or (but not a mixture). +
Label or Score or AttributeName condition [value]+ where either the label (description), (numeric) score, or (text or numeric) attribute is tested against the condition. +
+ Feature Instances +
+ +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 may also be used to generate + a colour for the feature).
+ ++ If your sequence annotation is already available in GFF2 (http://gmod.org/wiki/GFF2) or + GFF3 + (http://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md) format, + 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 (base 0) 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: + +
+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. + + + +
A complete example is shown below : +
domain red metal ion-binding site 00ff00 transit peptide 0,105,215 @@ -124,6 +262,13 @@ signal peptide 0,155,165 helix ff0000 strand 00ff00 coil cccccc +kdHydrophobicity ccffcc|333300|-3.9|4.5|above|-2.0 + +STARTFILTERS +metal ion-binding site Label Contains sulfur +kdHydrophobicity (Score LT 1.5) OR (Score GE 2.8) +ENDFILTERS + Your Own description here FER_CAPAA -1 3 93 domain Your Own description here FER_CAPAN -1 48 144 chain Your Own description here FER_CAPAN -1 50 140 domain @@ -131,12 +276,19 @@ Your Own description here FER_CAPAN -1 136 136 modified residue Your Own description here FER1_LYCES -1 1 47 transit peptide Your Own description here Q93XJ9_SOLTU -1 1 48 signal peptide Your Own description here Q93XJ9_SOLTU -1 49 144 chain -startgroup secondarystucture + +STARTGROUP secondarystucture PDB secondary structure annotation FER1_SPIOL -1 52 59 strand PDB secondary structure annotation FER1_SPIOL -1 74 80 helix -endgroup secondarystructure +ENDGROUP secondarystructure + +STARTGROUP kd +Hydrophobicity score by kD Q93XJ9_SOLTU -1 48 48 kdHydrophobicity 1.8 +ENDGROUP kd + +GFF +FER_CAPAA GffGroup domain 3 93 . .- - +