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 (specified as a
-red,green,blue 24 bit triplet either in hexadecimal (eg. 00ff00) or as comma
-separated numbers (ranging from 0 to 255)).
-
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 featureTypeNormally, -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.
-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 -chain 225,105,0 -modified residue 105,225,35 -signal peptide 0,155,165 -helix ff0000 -strand 00ff00 -coil cccccc -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 -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 -PDB secondary structure annotation FER1_SPIOL -1 52 59 strand -PDB secondary structure annotation FER1_SPIOL -1 74 80 helix -endgroup secondarystructure -- - - - + + + +
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 (specified as a red,green,blue 24
+bit triplet either in hexadecimal (eg. 00ff00) or as comma separated
+numbers (ranging from 0 to 255)). The text label may contain simple HTML
+document body tags if enclosed by "<html></html>"
+and 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.
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+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. + +
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 +chain 225,105,0 +modified residue 105,225,35 +signal peptide 0,155,165 +helix ff0000 +strand 00ff00 +coil cccccc +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 +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 +PDB secondary structure annotation FER1_SPIOL -1 52 59 strand +PDB secondary structure annotation FER1_SPIOL -1 74 80 helix +endgroup secondarystructure ++ + + +