X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2FfeaturesFormat.html;h=4d13dcdaa32499ba471eee15868e84b87c097ade;hb=77bcd1f60d9c26328d8859445f4225cd0ef571a9;hp=84bc5d43bea31aaa0b8c130de546ad6ab154a3a5;hpb=c17661b22323a66090ea91e04751aa17461b17c5;p=jalview.git diff --git a/help/html/features/featuresFormat.html b/help/html/features/featuresFormat.html index 84bc5d4..4d13dcd 100755 --- a/help/html/features/featuresFormat.html +++ b/help/html/features/featuresFormat.html @@ -60,7 +60,10 @@ contains tab separated text fields. No comments are allowed.

-

The first set of lines contain type definitions: +

+ Feature Colours +

+

The first set of lines contain feature type definitions and their colours: 

 Feature label	Feature Colour
 
@@ -72,21 +75,37 @@
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. + 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.

@@ -161,14 +220,14 @@ 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
+ href="../menus/popupMenu.html#sqid.popup">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. @@ -203,6 +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 @@ -210,10 +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 . .