+[label or score or attribute|attName|]<mincolor>|<maxcolor>|[absolute|]<minvalue>|<maxvalue>[|<novalue>][|<thresholdtype>|[<threshold value>]] +The fields are as follows: -
-[label|]<mincolor>|<maxcolor>|[absolute|]<minvalue>|<maxvalue>[|<thresholdtype>|[<threshold value>]] -+
+ 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 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. 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: -
+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 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 (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: + .. 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 @@ -199,6 +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 @@ -206,10 +276,16 @@ 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 . .